python /media/sf_a01_code/sortmerna/scripts/run.py --name t41 --envn LNX_VBox_Ubuntu_1604
Current dir: /media/sf_a01_code/sortmerna/scripts
[run.py:__main__] Using Environment configuration file: /media/sf_a01_code/sortmerna/scripts/env.jinja.yaml
[run.py:__main__] Using Build configuration template: /media/sf_a01_code/sortmerna/scripts/test.jinja.yaml
[run.py:__main__] using /home/biocodz/sortmerna/dist/bin/sortmerna
[process_smr_opts] '-workdir' option was provided. Using workdir: [/home/biocodz/sortmerna/run]
[process_smr_opts] '-workdir' option was provided. Using workdir: [/home/biocodz/sortmerna/run]
[run.py:__main__] Removing KVDB dir: /home/biocodz/sortmerna/run/kvdb
[run.py:__main__] Removing Aligned Output: /home/biocodz/sortmerna/run/out
[run.py:__main__] Running t41: issue 231 8x1M
[run] Running: /home/biocodz/sortmerna/dist/bin/sortmerna -ref /media/sf_a01_code/sortmerna/data/rRNA_databases/silva-euk-28s-id98.fasta -ref /media/sf_a01_code/sortmerna/data/rRNA_databases/silva-euk-18s-id95.fasta -ref /media/sf_a01_code/sortmerna/data/rRNA_databases/silva-bac-23s-id98.fasta -ref /media/sf_a01_code/sortmerna/data/rRNA_databases/silva-bac-16s-id90.fasta -ref /media/sf_a01_code/sortmerna/data/rRNA_databases/silva-arc-23s-id98.fasta -ref /media/sf_a01_code/sortmerna/data/rRNA_databases/silva-arc-16s-id95.fasta -ref /media/sf_a01_code/sortmerna/data/rRNA_databases/rfam-5s-database-id98.fasta -ref /media/sf_a01_code/sortmerna/data/rRNA_databases/rfam-5.8s-database-id98.fasta -reads /media/sf_a01_data/bio/reads/rna/SRR1635864_1_2M.fq.gz -reads /media/sf_a01_data/bio/reads/rna/SRR1635864_2_2M.fq.gz -fastx -blast 1 cigar qcov -out2 -sout -other -v -threads 8 -index 2 -workdir /home/biocodz/sortmerna/run in /media/sf_a01_code/sortmerna
[process:1372] === Options processing starts ... ===
Found value: /home/biocodz/sortmerna/dist/bin/sortmerna
Found flag: -ref
Found value: /media/sf_a01_code/sortmerna/data/rRNA_databases/silva-euk-28s-id98.fasta of previous flag: -ref
Found flag: -ref
Found value: /media/sf_a01_code/sortmerna/data/rRNA_databases/silva-euk-18s-id95.fasta of previous flag: -ref
Found flag: -ref
Found value: /media/sf_a01_code/sortmerna/data/rRNA_databases/silva-bac-23s-id98.fasta of previous flag: -ref
Found flag: -ref
Found value: /media/sf_a01_code/sortmerna/data/rRNA_databases/silva-bac-16s-id90.fasta of previous flag: -ref
Found flag: -ref
Found value: /media/sf_a01_code/sortmerna/data/rRNA_databases/silva-arc-23s-id98.fasta of previous flag: -ref
Found flag: -ref
Found value: /media/sf_a01_code/sortmerna/data/rRNA_databases/silva-arc-16s-id95.fasta of previous flag: -ref
Found flag: -ref
Found value: /media/sf_a01_code/sortmerna/data/rRNA_databases/rfam-5s-database-id98.fasta of previous flag: -ref
Found flag: -ref
Found value: /media/sf_a01_code/sortmerna/data/rRNA_databases/rfam-5.8s-database-id98.fasta of previous flag: -ref
Found flag: -reads
Found value: /media/sf_a01_data/bio/reads/rna/SRR1635864_1_2M.fq.gz of previous flag: -reads
Found flag: -reads
Found value: /media/sf_a01_data/bio/reads/rna/SRR1635864_2_2M.fq.gz of previous flag: -reads
Found flag: -fastx
Previous flag: -fastx is Boolean. Setting to True
Found flag: -blast
Found value: 1 cigar qcov of previous flag: -blast
Found flag: -out2
Previous flag: -out2 is Boolean. Setting to True
Found flag: -sout
Previous flag: -sout is Boolean. Setting to True
Found flag: -other
Previous flag: -other is Boolean. Setting to True
Found flag: -v
Previous flag: -v is Boolean. Setting to True
Found flag: -threads
Found value: 8 of previous flag: -threads
Found flag: -index
Found value: 2 of previous flag: -index
Found flag: -workdir
Found value: /home/biocodz/sortmerna/run of previous flag: -workdir
[opt_workdir:990] Using WORKDIR: "/home/biocodz/sortmerna/run" as specified
[process:1456] Processing option: blast with value: 1 cigar qcov
[process:1456] Processing option: fastx with value:
[process:1456] Processing option: index with value: 2
[opt_index:1157] using 'index' with specified value 2
[process:1456] Processing option: other with value:
[opt_other:267] other was specified without argument. Will use default Directory and Prefix for the non-aligned output.
[process:1456] Processing option: out2 with value:
[process:1456] Processing option: reads with value: /media/sf_a01_data/bio/reads/rna/SRR1635864_1_2M.fq.gz
[opt_reads:97] Processing reads file [1] out of total [2] files
[process:1456] Processing option: reads with value: /media/sf_a01_data/bio/reads/rna/SRR1635864_2_2M.fq.gz
[opt_reads:97] Processing reads file [2] out of total [2] files
[process:1456] Processing option: ref with value: /media/sf_a01_code/sortmerna/data/rRNA_databases/silva-euk-28s-id98.fasta
[opt_ref:157] Processing reference [1] out of total [8] references
[opt_ref:205] File "/media/sf_a01_code/sortmerna/data/rRNA_databases/silva-euk-28s-id98.fasta" exists and is readable
[process:1456] Processing option: ref with value: /media/sf_a01_code/sortmerna/data/rRNA_databases/silva-euk-18s-id95.fasta
[opt_ref:157] Processing reference [2] out of total [8] references
[opt_ref:205] File "/media/sf_a01_code/sortmerna/data/rRNA_databases/silva-euk-18s-id95.fasta" exists and is readable
[process:1456] Processing option: ref with value: /media/sf_a01_code/sortmerna/data/rRNA_databases/silva-bac-23s-id98.fasta
[opt_ref:157] Processing reference [3] out of total [8] references
[opt_ref:205] File "/media/sf_a01_code/sortmerna/data/rRNA_databases/silva-bac-23s-id98.fasta" exists and is readable
[process:1456] Processing option: ref with value: /media/sf_a01_code/sortmerna/data/rRNA_databases/silva-bac-16s-id90.fasta
[opt_ref:157] Processing reference [4] out of total [8] references
[opt_ref:205] File "/media/sf_a01_code/sortmerna/data/rRNA_databases/silva-bac-16s-id90.fasta" exists and is readable
[process:1456] Processing option: ref with value: /media/sf_a01_code/sortmerna/data/rRNA_databases/silva-arc-23s-id98.fasta
[opt_ref:157] Processing reference [5] out of total [8] references
[opt_ref:205] File "/media/sf_a01_code/sortmerna/data/rRNA_databases/silva-arc-23s-id98.fasta" exists and is readable
[process:1456] Processing option: ref with value: /media/sf_a01_code/sortmerna/data/rRNA_databases/silva-arc-16s-id95.fasta
[opt_ref:157] Processing reference [6] out of total [8] references
[opt_ref:205] File "/media/sf_a01_code/sortmerna/data/rRNA_databases/silva-arc-16s-id95.fasta" exists and is readable
[process:1456] Processing option: ref with value: /media/sf_a01_code/sortmerna/data/rRNA_databases/rfam-5s-database-id98.fasta
[opt_ref:157] Processing reference [7] out of total [8] references
[opt_ref:205] File "/media/sf_a01_code/sortmerna/data/rRNA_databases/rfam-5s-database-id98.fasta" exists and is readable
[process:1456] Processing option: ref with value: /media/sf_a01_code/sortmerna/data/rRNA_databases/rfam-5.8s-database-id98.fasta
[opt_ref:157] Processing reference [8] out of total [8] references
[opt_ref:205] File "/media/sf_a01_code/sortmerna/data/rRNA_databases/rfam-5.8s-database-id98.fasta" exists and is readable
[process:1456] Processing option: sout with value:
[process:1456] Processing option: threads with value: 8
[process:1456] Processing option: v with value:
[process:1476] === Options processing done ===
[process:1477] Alignment type: [best:1 num_alignments:1 min_lis:2 seeds:2]
[validate_kvdbdir:1223] Key-value DB location "/home/biocodz/sortmerna/run/kvdb"
[validate_kvdbdir:1259] Creating KVDB directory: "/home/biocodz/sortmerna/run/kvdb"
[validate_idxdir:1189] Using index directory: "/home/biocodz/sortmerna/run/idx"
[validate_idxdir:1205] IDX directory: "/home/biocodz/sortmerna/run/idx" exists and is not empty
[validate_readb_dir:1281] Using split reads directory : "/home/biocodz/sortmerna/run/readb"
[validate_readb_dir:1297] split reads directory : "/home/biocodz/sortmerna/run/readb" exists and is not empty
[validate_aligned_pfx:1310] Checking output directory: "/home/biocodz/sortmerna/run/out"
[main:62] Running command:
/home/biocodz/sortmerna/dist/bin/sortmerna -ref /media/sf_a01_code/sortmerna/data/rRNA_databases/silva-euk-28s-id98.fasta -ref /media/sf_a01_code/sortmerna/data/rRNA_databases/silva-euk-18s-id95.fasta -ref /media/sf_a01_code/sortmerna/data/rRNA_databases/silva-bac-23s-id98.fasta -ref /media/sf_a01_code/sortmerna/data/rRNA_databases/silva-bac-16s-id90.fasta -ref /media/sf_a01_code/sortmerna/data/rRNA_databases/silva-arc-23s-id98.fasta -ref /media/sf_a01_code/sortmerna/data/rRNA_databases/silva-arc-16s-id95.fasta -ref /media/sf_a01_code/sortmerna/data/rRNA_databases/rfam-5s-database-id98.fasta -ref /media/sf_a01_code/sortmerna/data/rRNA_databases/rfam-5.8s-database-id98.fasta -reads /media/sf_a01_data/bio/reads/rna/SRR1635864_1_2M.fq.gz -reads /media/sf_a01_data/bio/reads/rna/SRR1635864_2_2M.fq.gz -fastx -blast 1 cigar qcov -out2 -sout -other -v -threads 8 -index 2 -workdir /home/biocodz/sortmerna/run
[Index:102] Found 32 non-empty index files. Skipping indexing.
[init:108] Readfeed init started
[define_format:885] file: "/media/sf_a01_data/bio/reads/rna/SRR1635864_1_2M.fq.gz" is FASTQ gzipped
[define_format:885] file: "/media/sf_a01_data/bio/reads/rna/SRR1635864_2_2M.fq.gz" is FASTQ gzipped
[count_reads:919] started count ...
[next:311] EOF FWD reached. Total reads: 500000
[next:311] EOF REV reached. Total reads: 500000
[count_reads:949] done count. Elapsed time: 5.73545 sec. Total reads: 1000000
[init_split_files:971] added file: /home/biocodz/sortmerna/run/readb/fwd_0.fq.gz
[init_split_files:971] added file: /home/biocodz/sortmerna/run/readb/rev_0.fq.gz
[init_split_files:971] added file: /home/biocodz/sortmerna/run/readb/fwd_1.fq.gz
[init_split_files:971] added file: /home/biocodz/sortmerna/run/readb/rev_1.fq.gz
[init_split_files:971] added file: /home/biocodz/sortmerna/run/readb/fwd_2.fq.gz
[init_split_files:971] added file: /home/biocodz/sortmerna/run/readb/rev_2.fq.gz
[init_split_files:971] added file: /home/biocodz/sortmerna/run/readb/fwd_3.fq.gz
[init_split_files:971] added file: /home/biocodz/sortmerna/run/readb/rev_3.fq.gz
[init_split_files:971] added file: /home/biocodz/sortmerna/run/readb/fwd_4.fq.gz
[init_split_files:971] added file: /home/biocodz/sortmerna/run/readb/rev_4.fq.gz
[init_split_files:971] added file: /home/biocodz/sortmerna/run/readb/fwd_5.fq.gz
[init_split_files:971] added file: /home/biocodz/sortmerna/run/readb/rev_5.fq.gz
[init_split_files:971] added file: /home/biocodz/sortmerna/run/readb/fwd_6.fq.gz
[init_split_files:971] added file: /home/biocodz/sortmerna/run/readb/rev_6.fq.gz
[init_split_files:971] added file: /home/biocodz/sortmerna/run/readb/fwd_7.fq.gz
[init_split_files:971] added file: /home/biocodz/sortmerna/run/readb/rev_7.fq.gz
[is_split_ready:723] found existing readfeed descriptor /home/biocodz/sortmerna/run/readb/readfeed
[split:583] start splitting. Using number of splits equals number of processing threads: 8
[clean:1102] found descriptor /home/biocodz/sortmerna/run/readb/readfeed
[clean:1146] removing split file: /home/biocodz/sortmerna/run/readb/fwd_0.fq.gz
[clean:1146] removing split file: /home/biocodz/sortmerna/run/readb/rev_0.fq.gz
[clean:1146] removing split file: /home/biocodz/sortmerna/run/readb/fwd_1.fq.gz
[clean:1146] removing split file: /home/biocodz/sortmerna/run/readb/rev_1.fq.gz
[clean:1146] removing split file: /home/biocodz/sortmerna/run/readb/fwd_2.fq.gz
[clean:1146] removing split file: /home/biocodz/sortmerna/run/readb/rev_2.fq.gz
[clean:1146] removing split file: /home/biocodz/sortmerna/run/readb/fwd_3.fq.gz
[clean:1146] removing split file: /home/biocodz/sortmerna/run/readb/rev_3.fq.gz
[clean:1146] removing split file: /home/biocodz/sortmerna/run/readb/fwd_4.fq.gz
[clean:1146] removing split file: /home/biocodz/sortmerna/run/readb/rev_4.fq.gz
[clean:1146] removing split file: /home/biocodz/sortmerna/run/readb/fwd_5.fq.gz
[clean:1146] removing split file: /home/biocodz/sortmerna/run/readb/rev_5.fq.gz
[clean:1146] removing split file: /home/biocodz/sortmerna/run/readb/fwd_6.fq.gz
[clean:1146] removing split file: /home/biocodz/sortmerna/run/readb/rev_6.fq.gz
[clean:1146] removing split file: /home/biocodz/sortmerna/run/readb/fwd_7.fq.gz
[clean:1146] removing split file: /home/biocodz/sortmerna/run/readb/rev_7.fq.gz
[next:311] EOF FWD reached. Total reads: 500000
[next:311] EOF REV reached. Total reads: 500000
[split:694] Done splitting. Reads count: 1000000 Runtime sec: 55.3599
[init:135] Readfeed init done in sec [61.114]
[store_to_db:292] Stored Reads statistics to DB:
all_reads_count= 1000000 all_reads_len= 99050688 min_read_len= 101 max_read_len= 55 total_aligned= 0 total_aligned_id= 0 total_aligned_cov= 0 total_aligned_id_cov= 0 total_denovo= 0 num_short= 0 reads_matched_per_db= TODO is_stats_calc= 0 is_total_reads_mapped_cov= 0
[align:143] ==== Starting alignment ====
[align:146] Number of cores: 8
[align:163] Using number of Processor threads: 8
[Refstats:60] Index Statistics calculation starts ... done in: 4.26797 sec
[align:185] Loading index: 0 part: 1/1 Memory KB: 9 ...
[align:190] done in [0.937722] sec Memory KB: 407
[align:193] Loading references ...
[align:197] done in [0.70624] sec. Memory KB: 422
[align2:70] Processor 0 thread 140010330240768 started
[align2:70] Processor 1 thread 140010338633472 started
[align2:70] Processor 7 thread 140010147415808 started
[align2:70] Processor 4 thread 140010355418880 started
[align2:70] Processor 5 thread 140010347026176 started
[align2:70] Processor 6 thread 140010155808512 started
[align2:70] Processor 2 thread 140010917435136 started
[align2:70] Processor 3 thread 140010363811584 started
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 5 thread 140010347026176 done. Processed 125000 reads. Skipped already processed: 0 reads Aligned reads (passing E-value): 551 Runtime sec: 21.6408
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 0 thread 140010330240768 done. Processed 125000 reads. Skipped already processed: 0 reads Aligned reads (passing E-value): 659 Runtime sec: 21.6978
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 4 thread 140010355418880 done. Processed 125000 reads. Skipped already processed: 0 reads Aligned reads (passing E-value): 656 Runtime sec: 21.6984
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 2 thread 140010917435136 done. Processed 125000 reads. Skipped already processed: 0 reads Aligned reads (passing E-value): 650 Runtime sec: 21.7438
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 1 thread 140010338633472 done. Processed 125000 reads. Skipped already processed: 0 reads Aligned reads (passing E-value): 559 Runtime sec: 21.9022
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 7 thread 140010147415808 done. Processed 125000 reads. Skipped already processed: 0 reads Aligned reads (passing E-value): 649 Runtime sec: 21.9709
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 3 thread 140010363811584 done. Processed 125000 reads. Skipped already processed: 0 reads Aligned reads (passing E-value): 730 Runtime sec: 22.0211
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 6 thread 140010155808512 done. Processed 125000 reads. Skipped already processed: 0 reads Aligned reads (passing E-value): 667 Runtime sec: 22.0475
[align:220] done index: 0 part: 1 in 22.0595 sec Memory KB: 427
[align:227] Index and References unloaded in 0.197478 sec. Memory KB: 427
[align:185] Loading index: 1 part: 1/1 Memory KB: 427 ...
[align:190] done in [0.92918] sec Memory KB: 427
[align:193] Loading references ...
[align:197] done in [0.692128] sec. Memory KB: 427
[align2:70] Processor 0 thread 140010147415808 started
[align2:70] Processor 1 thread 140010155808512 started
[align2:70] Processor 2 thread 140010347026176 started
[align2:70] Processor 3 thread 140010355418880 started
[align2:70] Processor 4 thread 140010917435136 started
[align2:70] Processor 5 thread 140010363811584 started
[align2:70] Processor 6 thread 140010338633472 started
[align2:70] Processor 7 thread 140010330240768 started
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 1 thread 140010155808512 done. Processed 125000 reads. Skipped already processed: 0 reads Aligned reads (passing E-value): 590 Runtime sec: 21.1139
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 5 thread 140010363811584 done. Processed 125000 reads. Skipped already processed: 0 reads Aligned reads (passing E-value): 576 Runtime sec: 21.6393
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 7 thread 140010330240768 done. Processed 125000 reads. Skipped already processed: 0 reads Aligned reads (passing E-value): 680 Runtime sec: 21.7497
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 2 thread 140010347026176 done. Processed 125000 reads. Skipped already processed: 0 reads Aligned reads (passing E-value): 677 Runtime sec: 21.7859
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 3 thread 140010355418880 done. Processed 125000 reads. Skipped already processed: 0 reads Aligned reads (passing E-value): 769 Runtime sec: 21.9126
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 4 thread 140010917435136 done. Processed 125000 reads. Skipped already processed: 0 reads Aligned reads (passing E-value): 702 Runtime sec: 21.97
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 0 thread 140010147415808 done. Processed 125000 reads. Skipped already processed: 0 reads Aligned reads (passing E-value): 701 Runtime sec: 22.0073
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 6 thread 140010338633472 done. Processed 125000 reads. Skipped already processed: 0 reads Aligned reads (passing E-value): 709 Runtime sec: 23.2707
[align:220] done index: 1 part: 1 in 23.2729 sec Memory KB: 429
[align:227] Index and References unloaded in 0.170446 sec. Memory KB: 429
[align:185] Loading index: 2 part: 1/1 Memory KB: 429 ...
[align:190] done in [0.797775] sec Memory KB: 429
[align:193] Loading references ...
[align:197] done in [0.672418] sec. Memory KB: 429
[align2:70] Processor 0 thread 140010330240768 started
[align2:70] Processor 1 thread 140010338633472 started
[align2:70] Processor 2 thread 140010363811584 started
[align2:70] Processor 3 thread 140010917435136 started
[align2:70] Processor 4 thread 140010355418880 started
[align2:70] Processor 5 thread 140010347026176 started
[align2:70] Processor 6 thread 140010155808512 started
[align2:70] Processor 7 thread 140010147415808 started
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 5 thread 140010347026176 done. Processed 125000 reads. Skipped already processed: 0 reads Aligned reads (passing E-value): 4344 Runtime sec: 23.7947
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 2 thread 140010363811584 done. Processed 125000 reads. Skipped already processed: 0 reads Aligned reads (passing E-value): 4550 Runtime sec: 24.0882
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 1 thread 140010338633472 done. Processed 125000 reads. Skipped already processed: 0 reads Aligned reads (passing E-value): 4313 Runtime sec: 24.5213
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 0 thread 140010330240768 done. Processed 125000 reads. Skipped already processed: 0 reads Aligned reads (passing E-value): 4526 Runtime sec: 24.5237
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 6 thread 140010155808512 done. Processed 125000 reads. Skipped already processed: 0 reads Aligned reads (passing E-value): 4659 Runtime sec: 24.6418
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 7 thread 140010147415808 done. Processed 125000 reads. Skipped already processed: 0 reads Aligned reads (passing E-value): 4527 Runtime sec: 24.6815
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 4 thread 140010355418880 done. Processed 125000 reads. Skipped already processed: 0 reads Aligned reads (passing E-value): 4716 Runtime sec: 24.9354
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 3 thread 140010917435136 done. Processed 125000 reads. Skipped already processed: 0 reads Aligned reads (passing E-value): 4652 Runtime sec: 24.9785
[align:220] done index: 2 part: 1 in 24.9854 sec Memory KB: 453
[align:227] Index and References unloaded in 0.165393 sec. Memory KB: 453
[align:185] Loading index: 3 part: 1/1 Memory KB: 453 ...
[align:190] done in [1.09961] sec Memory KB: 528
[align:193] Loading references ...
[align:197] done in [0.959064] sec. Memory KB: 547
[align2:70] Processor 0 thread 140010147415808 started
[align2:70] Processor 1 thread 140010155808512 started
[align2:70] Processor 2 thread 140010347026176 started
[align2:70] Processor 3 thread 140010355418880 started
[align2:70] Processor 4 thread 140010917435136 started
[align2:70] Processor 5 thread 140010363811584 started
[align2:70] Processor 6 thread 140010338633472 started
[align2:70] Processor 7 thread 140010330240768 started
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 0 thread 140010147415808 done. Processed 124991 reads. Skipped already processed: 5 reads Aligned reads (passing E-value): 6149 Runtime sec: 26.0607
[next:433] EOF REV reached. Total reads: 62500
[next:433] EOF FWD reached. Total reads: 62500
[align2:133] Processor 3 thread 140010355418880 done. Processed 124997 reads. Skipped already processed: 3 reads Aligned reads (passing E-value): 6341 Runtime sec: 27.4329
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 6 thread 140010338633472 done. Processed 124996 reads. Skipped already processed: 4 reads Aligned reads (passing E-value): 6333 Runtime sec: 27.4787
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 1 thread 140010155808512 done. Processed 124996 reads. Skipped already processed: 4 reads Aligned reads (passing E-value): 5921 Runtime sec: 27.7387
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 4 thread 140010917435136 done. Processed 124993 reads. Skipped already processed: 6 reads Aligned reads (passing E-value): 6326 Runtime sec: 27.956
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 7 thread 140010330240768 done. Processed 124996 reads. Skipped already processed: 4 reads Aligned reads (passing E-value): 6202 Runtime sec: 28.2308
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 5 thread 140010363811584 done. Processed 125000 reads. Skipped already processed: 0 reads Aligned reads (passing E-value): 5950 Runtime sec: 28.3352
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 2 thread 140010347026176 done. Processed 124995 reads. Skipped already processed: 4 reads Aligned reads (passing E-value): 6285 Runtime sec: 28.5799
[align:220] done index: 3 part: 1 in 28.5808 sec Memory KB: 573
[align:227] Index and References unloaded in 0.221517 sec. Memory KB: 573
[align:185] Loading index: 4 part: 1/1 Memory KB: 573 ...
[align:190] done in [0.252196] sec Memory KB: 573
[align:193] Loading references ...
[align:197] done in [0.0478474] sec. Memory KB: 573
[align2:70] Processor 0 thread 140010330240768 started
[align2:70] Processor 1 thread 140010338633472 started
[align2:70] Processor 7 thread 140010221201152 started
[align2:70] Processor 6 thread 140010229593856 started
[align2:70] Processor 2 thread 140010363811584 started
[align2:70] Processor 3 thread 140010917435136 started
[align2:70] Processor 4 thread 140010355418880 started
[align2:70] Processor 5 thread 140010347026176 started
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 1 thread 140010338633472 done. Processed 124996 reads. Skipped already processed: 4 reads Aligned reads (passing E-value): 5921 Runtime sec: 10.3744
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 2 thread 140010363811584 done. Processed 124995 reads. Skipped already processed: 4 reads Aligned reads (passing E-value): 6285 Runtime sec: 10.457
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 5 thread 140010347026176 done. Processed 125000 reads. Skipped already processed: 0 reads Aligned reads (passing E-value): 5950 Runtime sec: 10.4737
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 6 thread 140010229593856 done. Processed 124996 reads. Skipped already processed: 4 reads Aligned reads (passing E-value): 6333 Runtime sec: 10.5179
[next:433] EOF REV reached. Total reads: 62500
[next:433] EOF FWD reached. Total reads: 62500
[align2:133] Processor 3 thread 140010917435136 done. Processed 124997 reads. Skipped already processed: 3 reads Aligned reads (passing E-value): 6341 Runtime sec: 10.5141
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 4 thread 140010355418880 done. Processed 124993 reads. Skipped already processed: 6 reads Aligned reads (passing E-value): 6326 Runtime sec: 10.5275
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 7 thread 140010221201152 done. Processed 124996 reads. Skipped already processed: 4 reads Aligned reads (passing E-value): 6202 Runtime sec: 10.5978
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 0 thread 140010330240768 done. Processed 124991 reads. Skipped already processed: 5 reads Aligned reads (passing E-value): 6149 Runtime sec: 10.8378
[align:220] done index: 4 part: 1 in 10.9213 sec Memory KB: 573
[align:227] Index and References unloaded in 0.109545 sec. Memory KB: 573
[align:185] Loading index: 5 part: 1/1 Memory KB: 573 ...
[align:190] done in [0.469406] sec Memory KB: 573
[align:193] Loading references ...
[align:197] done in [0.244222] sec. Memory KB: 573
[align2:70] Processor 0 thread 140010221201152 started
[align2:70] Processor 1 thread 140010229593856 started
[align2:70] Processor 7 thread 140010330240768 started
[align2:70] Processor 2 thread 140010347026176 started
[align2:70] Processor 3 thread 140010355418880 started
[align2:70] Processor 4 thread 140010917435136 started
[align2:70] Processor 5 thread 140010363811584 started
[align2:70] Processor 6 thread 140010338633472 started
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 6 thread 140010338633472 done. Processed 124996 reads. Skipped already processed: 4 reads Aligned reads (passing E-value): 6334 Runtime sec: 11.6236
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 7 thread 140010330240768 done. Processed 124996 reads. Skipped already processed: 4 reads Aligned reads (passing E-value): 6202 Runtime sec: 11.9621
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 4 thread 140010917435136 done. Processed 124993 reads. Skipped already processed: 6 reads Aligned reads (passing E-value): 6327 Runtime sec: 12.446
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 5 thread 140010363811584 done. Processed 125000 reads. Skipped already processed: 0 reads Aligned reads (passing E-value): 5950 Runtime sec: 13.5967
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 1 thread 140010229593856 done. Processed 124996 reads. Skipped already processed: 4 reads Aligned reads (passing E-value): 5922 Runtime sec: 13.7651
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 2 thread 140010347026176 done. Processed 124995 reads. Skipped already processed: 4 reads Aligned reads (passing E-value): 6285 Runtime sec: 13.8438
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 0 thread 140010221201152 done. Processed 124991 reads. Skipped already processed: 5 reads Aligned reads (passing E-value): 6151 Runtime sec: 13.992
[next:433] EOF REV reached. Total reads: 62500
[next:433] EOF FWD reached. Total reads: 62500
[align2:133] Processor 3 thread 140010355418880 done. Processed 124997 reads. Skipped already processed: 3 reads Aligned reads (passing E-value): 6344 Runtime sec: 14.0103
[align:220] done index: 5 part: 1 in 14.0488 sec Memory KB: 574
[align:227] Index and References unloaded in 0.0635204 sec. Memory KB: 574
[align:185] Loading index: 6 part: 1/1 Memory KB: 574 ...
[align:190] done in [0.545306] sec Memory KB: 574
[align:193] Loading references ...
[align:197] done in [0.473546] sec. Memory KB: 567
[align2:70] Processor 0 thread 140010330240768 started
[align2:70] Processor 1 thread 140010338633472 started
[align2:70] Processor 2 thread 140010363811584 started
[align2:70] Processor 3 thread 140010917435136 started
[align2:70] Processor 4 thread 140010355418880 started
[align2:70] Processor 5 thread 140010347026176 started
[align2:70] Processor 6 thread 140010229593856 started
[align2:70] Processor 7 thread 140010221201152 started
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 7 thread 140010221201152 done. Processed 124996 reads. Skipped already processed: 4 reads Aligned reads (passing E-value): 6250 Runtime sec: 15.0544
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 1 thread 140010338633472 done. Processed 124996 reads. Skipped already processed: 4 reads Aligned reads (passing E-value): 5967 Runtime sec: 15.0637
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 6 thread 140010229593856 done. Processed 124996 reads. Skipped already processed: 4 reads Aligned reads (passing E-value): 6378 Runtime sec: 15.0709
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 4 thread 140010355418880 done. Processed 124993 reads. Skipped already processed: 6 reads Aligned reads (passing E-value): 6369 Runtime sec: 15.088
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 0 thread 140010330240768 done. Processed 124991 reads. Skipped already processed: 5 reads Aligned reads (passing E-value): 6189 Runtime sec: 15.1061
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 2 thread 140010363811584 done. Processed 124995 reads. Skipped already processed: 4 reads Aligned reads (passing E-value): 6344 Runtime sec: 15.1101
[next:433] EOF REV reached. Total reads: 62500
[next:433] EOF FWD reached. Total reads: 62500
[align2:133] Processor 3 thread 140010917435136 done. Processed 124997 reads. Skipped already processed: 3 reads Aligned reads (passing E-value): 6382 Runtime sec: 15.1477
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 5 thread 140010347026176 done. Processed 125000 reads. Skipped already processed: 0 reads Aligned reads (passing E-value): 6000 Runtime sec: 15.4381
[align:220] done index: 6 part: 1 in 15.4438 sec Memory KB: 567
[align:227] Index and References unloaded in 0.0704959 sec. Memory KB: 555
[align:185] Loading index: 7 part: 1/1 Memory KB: 555 ...
[align:190] done in [0.228702] sec Memory KB: 555
[align:193] Loading references ...
[align:197] done in [0.147236] sec. Memory KB: 555
[align2:70] Processor 0 thread 140010221201152 started
[align2:70] Processor 1 thread 140010229593856 started
[align2:70] Processor 7 thread 140010330240768 started
[align2:70] Processor 2 thread 140010347026176 started
[align2:70] Processor 3 thread 140010355418880 started
[align2:70] Processor 6 thread 140010338633472 started
[align2:70] Processor 4 thread 140010917435136 started
[align2:70] Processor 5 thread 140010363811584 started
[next:433] EOF REV reached. Total reads: 62500
[next:433] EOF FWD reached. Total reads: 62500
[align2:133] Processor 3 thread 140010355418880 done. Processed 124997 reads. Skipped already processed: 3 reads Aligned reads (passing E-value): 6382 Runtime sec: 9.78541
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 1 thread 140010229593856 done. Processed 124996 reads. Skipped already processed: 4 reads Aligned reads (passing E-value): 5967 Runtime sec: 9.83089
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 6 thread 140010338633472 done. Processed 124996 reads. Skipped already processed: 4 reads Aligned reads (passing E-value): 6378 Runtime sec: 9.8955
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 7 thread 140010330240768 done. Processed 124996 reads. Skipped already processed: 4 reads Aligned reads (passing E-value): 6250 Runtime sec: 9.92369
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 4 thread 140010917435136 done. Processed 124993 reads. Skipped already processed: 6 reads Aligned reads (passing E-value): 6369 Runtime sec: 9.94304
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 5 thread 140010363811584 done. Processed 125000 reads. Skipped already processed: 0 reads Aligned reads (passing E-value): 6000 Runtime sec: 10.0105
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 2 thread 140010347026176 done. Processed 124995 reads. Skipped already processed: 4 reads Aligned reads (passing E-value): 6344 Runtime sec: 10.1247
[next:433] EOF REV reached. Total reads: 62500
[align2:133] Processor 0 thread 140010221201152 done. Processed 124991 reads. Skipped already processed: 5 reads Aligned reads (passing E-value): 6189 Runtime sec: 10.675
[align:220] done index: 7 part: 1 in 10.6762 sec Memory KB: 556
[align:227] Index and References unloaded in 0.0470631 sec. Memory KB: 556
[align:237] ==== Done alignment in 160.304 sec ====
[store_to_db:292] Stored Reads statistics to DB:
all_reads_count= 1000000 all_reads_len= 99050688 min_read_len= 101 max_read_len= 55 total_aligned= 49909 total_aligned_id= 0 total_aligned_cov= 0 total_aligned_id_cov= 0 total_denovo= 0 num_short= 0 reads_matched_per_db= TODO is_stats_calc= 0 is_total_reads_mapped_cov= 0
[writeSummary:179] ==== Starting summary of alignment statistics ====
[Refstats:60] Index Statistics calculation starts ... done in: 4.45322 sec
[write:62] Using summary file: /home/biocodz/sortmerna/run/out/aligned.log
[writeSummary:185] ==== Done summary in sec [4.45347] ====
[writeReports:160] === Report generation starts ===
[writeReports:175] Restored Readstats from DB: 1
[Refstats:60] Index Statistics calculation starts ... done in: 4.43634 sec
[validate_out_type:139] Output type:
1-file 2-files paired paired_in paired_out out2 sout other otype
+ + + + + 66
[set_num_out:162] num_out: 4
[init:60] num_out: 4
[validate_out_type:139] Output type:
1-file 2-files paired paired_in paired_out out2 sout other otype
+ + + + + 66
[set_num_out:162] num_out: 4
[init:60] num_out: 4
[writeReports:190] loading reference 0 part 1/1 ... done in 0.791885 sec
[report:93] Report Processor: 0 thread: 140010330240768 started. Memory KB: 556
[report:93] Report Processor: 1 thread: 140010338633472 started. Memory KB: 556
[report:93] Report Processor: 2 thread: 140010363811584 started. Memory KB: 556
[report:93] Report Processor: 3 thread: 140010917435136 started. Memory KB: 556
[report:93] Report Processor: 4 thread: 140010355418880 started. Memory KB: 556
[report:93] Report Processor: 5 thread: 140010347026176 started. Memory KB: 556
[report:93] Report Processor: 6 thread: 140010229593856 started. Memory KB: 556
[report:93] Report Processor: 7 thread: 140010221201152 started. Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 1 thread: 140010338633472 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 4 thread: 140010355418880 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 5 thread: 140010347026176 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 2 thread: 140010363811584 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 0 thread: 140010330240768 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 6 thread: 140010229593856 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 7 thread: 140010221201152 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 3 thread: 140010917435136 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[writeReports:211] done reference 0 part: 1 in 24.8879 sec
[writeReports:217] references unloaded in 0.00277428 sec Memory KB: 556
[writeReports:190] loading reference 1 part 1/1 ... done in 0.827815 sec
[report:93] Report Processor: 0 thread: 140010221201152 started. Memory KB: 556
[report:93] Report Processor: 1 thread: 140010229593856 started. Memory KB: 556
[report:93] Report Processor: 2 thread: 140010347026176 started. Memory KB: 556
[report:93] Report Processor: 3 thread: 140010355418880 started. Memory KB: 556
[report:93] Report Processor: 4 thread: 140010917435136 started. Memory KB: 556
[report:93] Report Processor: 5 thread: 140010363811584 started. Memory KB: 556
[report:93] Report Processor: 6 thread: 140010338633472 started. Memory KB: 556
[report:93] Report Processor: 7 thread: 140010330240768 started. Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 1 thread: 140010229593856 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 2 thread: 140010347026176 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 0 thread: 140010221201152 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 6 thread: 140010338633472 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 5 thread: 140010363811584 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 7 thread: 140010330240768 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 3 thread: 140010355418880 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 4 thread: 140010917435136 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[writeReports:211] done reference 1 part: 1 in 4.43556 sec
[writeReports:217] references unloaded in 0.00518327 sec Memory KB: 556
[writeReports:190] loading reference 2 part 1/1 ... done in 0.719366 sec
[report:93] Report Processor: 0 thread: 140010330240768 started. Memory KB: 556
[report:93] Report Processor: 1 thread: 140010338633472 started. Memory KB: 556
[report:93] Report Processor: 7 thread: 140010221201152 started. Memory KB: 556
[report:93] Report Processor: 6 thread: 140010229593856 started. Memory KB: 556
[report:93] Report Processor: 5 thread: 140010347026176 started. Memory KB: 556
[report:93] Report Processor: 2 thread: 140010363811584 started. Memory KB: 556
[report:93] Report Processor: 4 thread: 140010355418880 started. Memory KB: 556
[report:93] Report Processor: 3 thread: 140010917435136 started. Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 1 thread: 140010338633472 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 4 thread: 140010355418880 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 5 thread: 140010347026176 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 2 thread: 140010363811584 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 3 thread: 140010917435136 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 6 thread: 140010229593856 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 7 thread: 140010221201152 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 0 thread: 140010330240768 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[writeReports:211] done reference 2 part: 1 in 4.91457 sec
[writeReports:217] references unloaded in 0.00132068 sec Memory KB: 556
[writeReports:190] loading reference 3 part 1/1 ... done in 1.05361 sec
[report:93] Report Processor: 0 thread: 140010221201152 started. Memory KB: 556
[report:93] Report Processor: 1 thread: 140010229593856 started. Memory KB: 556
[report:93] Report Processor: 2 thread: 140010347026176 started. Memory KB: 556
[report:93] Report Processor: 3 thread: 140010355418880 started. Memory KB: 556
[report:93] Report Processor: 4 thread: 140010917435136 started. Memory KB: 556
[report:93] Report Processor: 5 thread: 140010363811584 started. Memory KB: 556
[report:93] Report Processor: 6 thread: 140010338633472 started. Memory KB: 556
[report:93] Report Processor: 7 thread: 140010330240768 started. Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 1 thread: 140010229593856 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 2 thread: 140010347026176 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 5 thread: 140010363811584 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 4 thread: 140010917435136 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 3 thread: 140010355418880 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 0 thread: 140010221201152 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 6 thread: 140010338633472 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 7 thread: 140010330240768 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[writeReports:211] done reference 3 part: 1 in 4.36404 sec
[writeReports:217] references unloaded in 0.00403434 sec Memory KB: 556
[writeReports:190] loading reference 4 part 1/1 ... done in 0.0597788 sec
[report:93] Report Processor: 0 thread: 140010330240768 started. Memory KB: 556
[report:93] Report Processor: 1 thread: 140010338633472 started. Memory KB: 556
[report:93] Report Processor: 2 thread: 140010363811584 started. Memory KB: 556
[report:93] Report Processor: 6 thread: 140010229593856 started. Memory KB: 556
[report:93] Report Processor: 7 thread: 140010221201152 started. Memory KB: 556
[report:93] Report Processor: 3 thread: 140010917435136 started. Memory KB: 556
[report:93] Report Processor: 5 thread: 140010347026176 started. Memory KB: 556
[report:93] Report Processor: 4 thread: 140010355418880 started. Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 0 thread: 140010330240768 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 7 thread: 140010221201152 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 6 thread: 140010229593856 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 1 thread: 140010338633472 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 2 thread: 140010363811584 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 3 thread: 140010917435136 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 4 thread: 140010355418880 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 5 thread: 140010347026176 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[writeReports:211] done reference 4 part: 1 in 4.04392 sec
[writeReports:217] references unloaded in 4.0988e-05 sec Memory KB: 556
[writeReports:190] loading reference 5 part 1/1 ... done in 0.229265 sec
[report:93] Report Processor: 0 thread: 140010221201152 started. Memory KB: 556
[report:93] Report Processor: 6 thread: 140010338633472 started. Memory KB: 556
[report:93] Report Processor: 3 thread: 140010355418880 started. Memory KB: 556
[report:93] Report Processor: 5 thread: 140010363811584 started. Memory KB: 556
[report:93] Report Processor: 7 thread: 140010330240768 started. Memory KB: 556
[report:93] Report Processor: 4 thread: 140010917435136 started. Memory KB: 556
[report:93] Report Processor: 1 thread: 140010229593856 started. Memory KB: 556
[report:93] Report Processor: 2 thread: 140010347026176 started. Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 5 thread: 140010363811584 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 3 thread: 140010355418880 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 4 thread: 140010917435136 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 6 thread: 140010338633472 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 0 thread: 140010221201152 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 7 thread: 140010330240768 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 2 thread: 140010347026176 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 1 thread: 140010229593856 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[writeReports:211] done reference 5 part: 1 in 3.89069 sec
[writeReports:217] references unloaded in 0.00141204 sec Memory KB: 556
[writeReports:190] loading reference 6 part 1/1 ... done in 0.494027 sec
[report:93] Report Processor: 0 thread: 140010330240768 started. Memory KB: 556
[report:93] Report Processor: 4 thread: 140010355418880 started. Memory KB: 556
[report:93] Report Processor: 1 thread: 140010338633472 started. Memory KB: 556
[report:93] Report Processor: 5 thread: 140010347026176 started. Memory KB: 556
[report:93] Report Processor: 6 thread: 140010229593856 started. Memory KB: 556
[report:93] Report Processor: 2 thread: 140010363811584 started. Memory KB: 556
[report:93] Report Processor: 7 thread: 140010221201152 started. Memory KB: 556
[report:93] Report Processor: 3 thread: 140010917435136 started. Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 0 thread: 140010330240768 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 1 thread: 140010338633472 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 3 thread: 140010917435136 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 7 thread: 140010221201152 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 5 thread: 140010347026176 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 6 thread: 140010229593856 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 2 thread: 140010363811584 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 4 thread: 140010355418880 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[writeReports:211] done reference 6 part: 1 in 4.31935 sec
[writeReports:217] references unloaded in 0.00583015 sec Memory KB: 556
[writeReports:190] loading reference 7 part 1/1 ... done in 0.151042 sec
[report:93] Report Processor: 0 thread: 140010221201152 started. Memory KB: 556
[report:93] Report Processor: 1 thread: 140010229593856 started. Memory KB: 556
[report:93] Report Processor: 2 thread: 140010347026176 started. Memory KB: 556
[report:93] Report Processor: 3 thread: 140010355418880 started. Memory KB: 556
[report:93] Report Processor: 7 thread: 140010330240768 started. Memory KB: 556
[report:93] Report Processor: 4 thread: 140010917435136 started. Memory KB: 556
[report:93] Report Processor: 6 thread: 140010338633472 started. Memory KB: 556
[report:93] Report Processor: 5 thread: 140010363811584 started. Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 4 thread: 140010917435136 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 7 thread: 140010330240768 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 6 thread: 140010338633472 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 0 thread: 140010221201152 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 2 thread: 140010347026176 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 5 thread: 140010363811584 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 3 thread: 140010355418880 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[next:433] EOF FWD reached. Total reads: 62500
[next:433] EOF REV reached. Total reads: 62500
[report:152] Report processor: 1 thread: 140010229593856 done. Processed reads: 125000 Invalid reads: 0 Memory KB: 556
[writeReports:211] done reference 7 part: 1 in 4.29868 sec
[writeReports:217] references unloaded in 0.0028677 sec Memory KB: 556
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/aligned_paired_fwd_1.fq.gz for reading.
[merge:155] merged /home/biocodz/sortmerna/run/out/aligned_paired_fwd_1.fq.gz -> /home/biocodz/sortmerna/run/out/aligned_paired_fwd_0.fq.gz
[merge:158] deleted /home/biocodz/sortmerna/run/out/aligned_paired_fwd_1.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/aligned_paired_fwd_2.fq.gz for reading.
[merge:155] merged /home/biocodz/sortmerna/run/out/aligned_paired_fwd_2.fq.gz -> /home/biocodz/sortmerna/run/out/aligned_paired_fwd_0.fq.gz
[merge:158] deleted /home/biocodz/sortmerna/run/out/aligned_paired_fwd_2.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/aligned_paired_fwd_3.fq.gz for reading.
[merge:155] merged /home/biocodz/sortmerna/run/out/aligned_paired_fwd_3.fq.gz -> /home/biocodz/sortmerna/run/out/aligned_paired_fwd_0.fq.gz
[merge:158] deleted /home/biocodz/sortmerna/run/out/aligned_paired_fwd_3.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/aligned_paired_fwd_4.fq.gz for reading.
[merge:155] merged /home/biocodz/sortmerna/run/out/aligned_paired_fwd_4.fq.gz -> /home/biocodz/sortmerna/run/out/aligned_paired_fwd_0.fq.gz
[merge:158] deleted /home/biocodz/sortmerna/run/out/aligned_paired_fwd_4.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/aligned_paired_fwd_5.fq.gz for reading.
[merge:155] merged /home/biocodz/sortmerna/run/out/aligned_paired_fwd_5.fq.gz -> /home/biocodz/sortmerna/run/out/aligned_paired_fwd_0.fq.gz
[merge:158] deleted /home/biocodz/sortmerna/run/out/aligned_paired_fwd_5.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/aligned_paired_fwd_6.fq.gz for reading.
[merge:155] merged /home/biocodz/sortmerna/run/out/aligned_paired_fwd_6.fq.gz -> /home/biocodz/sortmerna/run/out/aligned_paired_fwd_0.fq.gz
[merge:158] deleted /home/biocodz/sortmerna/run/out/aligned_paired_fwd_6.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/aligned_paired_fwd_7.fq.gz for reading.
[merge:155] merged /home/biocodz/sortmerna/run/out/aligned_paired_fwd_7.fq.gz -> /home/biocodz/sortmerna/run/out/aligned_paired_fwd_0.fq.gz
[merge:158] deleted /home/biocodz/sortmerna/run/out/aligned_paired_fwd_7.fq.gz
[strip_path_sfx:154] moving /home/biocodz/sortmerna/run/out/aligned_paired_fwd_0.fq.gz -> "/home/biocodz/sortmerna/run/out/aligned_paired_fwd.fq.gz"
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/aligned_paired_rev_1.fq.gz for reading.
[merge:155] merged /home/biocodz/sortmerna/run/out/aligned_paired_rev_1.fq.gz -> /home/biocodz/sortmerna/run/out/aligned_paired_rev_0.fq.gz
[merge:158] deleted /home/biocodz/sortmerna/run/out/aligned_paired_rev_1.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/aligned_paired_rev_2.fq.gz for reading.
[merge:155] merged /home/biocodz/sortmerna/run/out/aligned_paired_rev_2.fq.gz -> /home/biocodz/sortmerna/run/out/aligned_paired_rev_0.fq.gz
[merge:158] deleted /home/biocodz/sortmerna/run/out/aligned_paired_rev_2.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/aligned_paired_rev_3.fq.gz for reading.
[merge:155] merged /home/biocodz/sortmerna/run/out/aligned_paired_rev_3.fq.gz -> /home/biocodz/sortmerna/run/out/aligned_paired_rev_0.fq.gz
[merge:158] deleted /home/biocodz/sortmerna/run/out/aligned_paired_rev_3.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/aligned_paired_rev_4.fq.gz for reading.
[merge:155] merged /home/biocodz/sortmerna/run/out/aligned_paired_rev_4.fq.gz -> /home/biocodz/sortmerna/run/out/aligned_paired_rev_0.fq.gz
[merge:158] deleted /home/biocodz/sortmerna/run/out/aligned_paired_rev_4.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/aligned_paired_rev_5.fq.gz for reading.
[merge:155] merged /home/biocodz/sortmerna/run/out/aligned_paired_rev_5.fq.gz -> /home/biocodz/sortmerna/run/out/aligned_paired_rev_0.fq.gz
[merge:158] deleted /home/biocodz/sortmerna/run/out/aligned_paired_rev_5.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/aligned_paired_rev_6.fq.gz for reading.
[merge:155] merged /home/biocodz/sortmerna/run/out/aligned_paired_rev_6.fq.gz -> /home/biocodz/sortmerna/run/out/aligned_paired_rev_0.fq.gz
[merge:158] deleted /home/biocodz/sortmerna/run/out/aligned_paired_rev_6.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/aligned_paired_rev_7.fq.gz for reading.
[merge:155] merged /home/biocodz/sortmerna/run/out/aligned_paired_rev_7.fq.gz -> /home/biocodz/sortmerna/run/out/aligned_paired_rev_0.fq.gz
[merge:158] deleted /home/biocodz/sortmerna/run/out/aligned_paired_rev_7.fq.gz
[strip_path_sfx:154] moving /home/biocodz/sortmerna/run/out/aligned_paired_rev_0.fq.gz -> "/home/biocodz/sortmerna/run/out/aligned_paired_rev.fq.gz"
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/aligned_singleton_fwd_1.fq.gz for reading.
[merge:155] merged /home/biocodz/sortmerna/run/out/aligned_singleton_fwd_1.fq.gz -> /home/biocodz/sortmerna/run/out/aligned_singleton_fwd_0.fq.gz
[merge:158] deleted /home/biocodz/sortmerna/run/out/aligned_singleton_fwd_1.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/aligned_singleton_fwd_2.fq.gz for reading.
[merge:155] merged /home/biocodz/sortmerna/run/out/aligned_singleton_fwd_2.fq.gz -> /home/biocodz/sortmerna/run/out/aligned_singleton_fwd_0.fq.gz
[merge:158] deleted /home/biocodz/sortmerna/run/out/aligned_singleton_fwd_2.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/aligned_singleton_fwd_3.fq.gz for reading.
[merge:155] merged /home/biocodz/sortmerna/run/out/aligned_singleton_fwd_3.fq.gz -> /home/biocodz/sortmerna/run/out/aligned_singleton_fwd_0.fq.gz
[merge:158] deleted /home/biocodz/sortmerna/run/out/aligned_singleton_fwd_3.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/aligned_singleton_fwd_4.fq.gz for reading.
[merge:155] merged /home/biocodz/sortmerna/run/out/aligned_singleton_fwd_4.fq.gz -> /home/biocodz/sortmerna/run/out/aligned_singleton_fwd_0.fq.gz
[merge:158] deleted /home/biocodz/sortmerna/run/out/aligned_singleton_fwd_4.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/aligned_singleton_fwd_5.fq.gz for reading.
[merge:155] merged /home/biocodz/sortmerna/run/out/aligned_singleton_fwd_5.fq.gz -> /home/biocodz/sortmerna/run/out/aligned_singleton_fwd_0.fq.gz
[merge:158] deleted /home/biocodz/sortmerna/run/out/aligned_singleton_fwd_5.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/aligned_singleton_fwd_6.fq.gz for reading.
[merge:155] merged /home/biocodz/sortmerna/run/out/aligned_singleton_fwd_6.fq.gz -> /home/biocodz/sortmerna/run/out/aligned_singleton_fwd_0.fq.gz
[merge:158] deleted /home/biocodz/sortmerna/run/out/aligned_singleton_fwd_6.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/aligned_singleton_fwd_7.fq.gz for reading.
[merge:155] merged /home/biocodz/sortmerna/run/out/aligned_singleton_fwd_7.fq.gz -> /home/biocodz/sortmerna/run/out/aligned_singleton_fwd_0.fq.gz
[merge:158] deleted /home/biocodz/sortmerna/run/out/aligned_singleton_fwd_7.fq.gz
[strip_path_sfx:154] moving /home/biocodz/sortmerna/run/out/aligned_singleton_fwd_0.fq.gz -> "/home/biocodz/sortmerna/run/out/aligned_singleton_fwd.fq.gz"
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/aligned_singleton_rev_1.fq.gz for reading.
[merge:155] merged /home/biocodz/sortmerna/run/out/aligned_singleton_rev_1.fq.gz -> /home/biocodz/sortmerna/run/out/aligned_singleton_rev_0.fq.gz
[merge:158] deleted /home/biocodz/sortmerna/run/out/aligned_singleton_rev_1.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/aligned_singleton_rev_2.fq.gz for reading.
[merge:155] merged /home/biocodz/sortmerna/run/out/aligned_singleton_rev_2.fq.gz -> /home/biocodz/sortmerna/run/out/aligned_singleton_rev_0.fq.gz
[merge:158] deleted /home/biocodz/sortmerna/run/out/aligned_singleton_rev_2.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/aligned_singleton_rev_3.fq.gz for reading.
[merge:155] merged /home/biocodz/sortmerna/run/out/aligned_singleton_rev_3.fq.gz -> /home/biocodz/sortmerna/run/out/aligned_singleton_rev_0.fq.gz
[merge:158] deleted /home/biocodz/sortmerna/run/out/aligned_singleton_rev_3.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/aligned_singleton_rev_4.fq.gz for reading.
[merge:155] merged /home/biocodz/sortmerna/run/out/aligned_singleton_rev_4.fq.gz -> /home/biocodz/sortmerna/run/out/aligned_singleton_rev_0.fq.gz
[merge:158] deleted /home/biocodz/sortmerna/run/out/aligned_singleton_rev_4.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/aligned_singleton_rev_5.fq.gz for reading.
[merge:155] merged /home/biocodz/sortmerna/run/out/aligned_singleton_rev_5.fq.gz -> /home/biocodz/sortmerna/run/out/aligned_singleton_rev_0.fq.gz
[merge:158] deleted /home/biocodz/sortmerna/run/out/aligned_singleton_rev_5.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/aligned_singleton_rev_6.fq.gz for reading.
[merge:155] merged /home/biocodz/sortmerna/run/out/aligned_singleton_rev_6.fq.gz -> /home/biocodz/sortmerna/run/out/aligned_singleton_rev_0.fq.gz
[merge:158] deleted /home/biocodz/sortmerna/run/out/aligned_singleton_rev_6.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/aligned_singleton_rev_7.fq.gz for reading.
[merge:155] merged /home/biocodz/sortmerna/run/out/aligned_singleton_rev_7.fq.gz -> /home/biocodz/sortmerna/run/out/aligned_singleton_rev_0.fq.gz
[merge:158] deleted /home/biocodz/sortmerna/run/out/aligned_singleton_rev_7.fq.gz
[strip_path_sfx:154] moving /home/biocodz/sortmerna/run/out/aligned_singleton_rev_0.fq.gz -> "/home/biocodz/sortmerna/run/out/aligned_singleton_rev.fq.gz"
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/other_paired_fwd_1.fq.gz for reading.
[merge:130] merged /home/biocodz/sortmerna/run/out/other_paired_fwd_1.fq.gz -> /home/biocodz/sortmerna/run/out/other_paired_fwd_0.fq.gz
[merge:133] deleted /home/biocodz/sortmerna/run/out/other_paired_fwd_1.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/other_paired_fwd_2.fq.gz for reading.
[merge:130] merged /home/biocodz/sortmerna/run/out/other_paired_fwd_2.fq.gz -> /home/biocodz/sortmerna/run/out/other_paired_fwd_0.fq.gz
[merge:133] deleted /home/biocodz/sortmerna/run/out/other_paired_fwd_2.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/other_paired_fwd_3.fq.gz for reading.
[merge:130] merged /home/biocodz/sortmerna/run/out/other_paired_fwd_3.fq.gz -> /home/biocodz/sortmerna/run/out/other_paired_fwd_0.fq.gz
[merge:133] deleted /home/biocodz/sortmerna/run/out/other_paired_fwd_3.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/other_paired_fwd_4.fq.gz for reading.
[merge:130] merged /home/biocodz/sortmerna/run/out/other_paired_fwd_4.fq.gz -> /home/biocodz/sortmerna/run/out/other_paired_fwd_0.fq.gz
[merge:133] deleted /home/biocodz/sortmerna/run/out/other_paired_fwd_4.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/other_paired_fwd_5.fq.gz for reading.
[merge:130] merged /home/biocodz/sortmerna/run/out/other_paired_fwd_5.fq.gz -> /home/biocodz/sortmerna/run/out/other_paired_fwd_0.fq.gz
[merge:133] deleted /home/biocodz/sortmerna/run/out/other_paired_fwd_5.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/other_paired_fwd_6.fq.gz for reading.
[merge:130] merged /home/biocodz/sortmerna/run/out/other_paired_fwd_6.fq.gz -> /home/biocodz/sortmerna/run/out/other_paired_fwd_0.fq.gz
[merge:133] deleted /home/biocodz/sortmerna/run/out/other_paired_fwd_6.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/other_paired_fwd_7.fq.gz for reading.
[merge:130] merged /home/biocodz/sortmerna/run/out/other_paired_fwd_7.fq.gz -> /home/biocodz/sortmerna/run/out/other_paired_fwd_0.fq.gz
[merge:133] deleted /home/biocodz/sortmerna/run/out/other_paired_fwd_7.fq.gz
[strip_path_sfx:154] moving /home/biocodz/sortmerna/run/out/other_paired_fwd_0.fq.gz -> "/home/biocodz/sortmerna/run/out/other_paired_fwd.fq.gz"
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/other_paired_rev_1.fq.gz for reading.
[merge:130] merged /home/biocodz/sortmerna/run/out/other_paired_rev_1.fq.gz -> /home/biocodz/sortmerna/run/out/other_paired_rev_0.fq.gz
[merge:133] deleted /home/biocodz/sortmerna/run/out/other_paired_rev_1.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/other_paired_rev_2.fq.gz for reading.
[merge:130] merged /home/biocodz/sortmerna/run/out/other_paired_rev_2.fq.gz -> /home/biocodz/sortmerna/run/out/other_paired_rev_0.fq.gz
[merge:133] deleted /home/biocodz/sortmerna/run/out/other_paired_rev_2.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/other_paired_rev_3.fq.gz for reading.
[merge:130] merged /home/biocodz/sortmerna/run/out/other_paired_rev_3.fq.gz -> /home/biocodz/sortmerna/run/out/other_paired_rev_0.fq.gz
[merge:133] deleted /home/biocodz/sortmerna/run/out/other_paired_rev_3.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/other_paired_rev_4.fq.gz for reading.
[merge:130] merged /home/biocodz/sortmerna/run/out/other_paired_rev_4.fq.gz -> /home/biocodz/sortmerna/run/out/other_paired_rev_0.fq.gz
[merge:133] deleted /home/biocodz/sortmerna/run/out/other_paired_rev_4.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/other_paired_rev_5.fq.gz for reading.
[merge:130] merged /home/biocodz/sortmerna/run/out/other_paired_rev_5.fq.gz -> /home/biocodz/sortmerna/run/out/other_paired_rev_0.fq.gz
[merge:133] deleted /home/biocodz/sortmerna/run/out/other_paired_rev_5.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/other_paired_rev_6.fq.gz for reading.
[merge:130] merged /home/biocodz/sortmerna/run/out/other_paired_rev_6.fq.gz -> /home/biocodz/sortmerna/run/out/other_paired_rev_0.fq.gz
[merge:133] deleted /home/biocodz/sortmerna/run/out/other_paired_rev_6.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/other_paired_rev_7.fq.gz for reading.
[merge:130] merged /home/biocodz/sortmerna/run/out/other_paired_rev_7.fq.gz -> /home/biocodz/sortmerna/run/out/other_paired_rev_0.fq.gz
[merge:133] deleted /home/biocodz/sortmerna/run/out/other_paired_rev_7.fq.gz
[strip_path_sfx:154] moving /home/biocodz/sortmerna/run/out/other_paired_rev_0.fq.gz -> "/home/biocodz/sortmerna/run/out/other_paired_rev.fq.gz"
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/other_singleton_fwd_1.fq.gz for reading.
[merge:130] merged /home/biocodz/sortmerna/run/out/other_singleton_fwd_1.fq.gz -> /home/biocodz/sortmerna/run/out/other_singleton_fwd_0.fq.gz
[merge:133] deleted /home/biocodz/sortmerna/run/out/other_singleton_fwd_1.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/other_singleton_fwd_2.fq.gz for reading.
[merge:130] merged /home/biocodz/sortmerna/run/out/other_singleton_fwd_2.fq.gz -> /home/biocodz/sortmerna/run/out/other_singleton_fwd_0.fq.gz
[merge:133] deleted /home/biocodz/sortmerna/run/out/other_singleton_fwd_2.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/other_singleton_fwd_3.fq.gz for reading.
[merge:130] merged /home/biocodz/sortmerna/run/out/other_singleton_fwd_3.fq.gz -> /home/biocodz/sortmerna/run/out/other_singleton_fwd_0.fq.gz
[merge:133] deleted /home/biocodz/sortmerna/run/out/other_singleton_fwd_3.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/other_singleton_fwd_4.fq.gz for reading.
[merge:130] merged /home/biocodz/sortmerna/run/out/other_singleton_fwd_4.fq.gz -> /home/biocodz/sortmerna/run/out/other_singleton_fwd_0.fq.gz
[merge:133] deleted /home/biocodz/sortmerna/run/out/other_singleton_fwd_4.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/other_singleton_fwd_5.fq.gz for reading.
[merge:130] merged /home/biocodz/sortmerna/run/out/other_singleton_fwd_5.fq.gz -> /home/biocodz/sortmerna/run/out/other_singleton_fwd_0.fq.gz
[merge:133] deleted /home/biocodz/sortmerna/run/out/other_singleton_fwd_5.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/other_singleton_fwd_6.fq.gz for reading.
[merge:130] merged /home/biocodz/sortmerna/run/out/other_singleton_fwd_6.fq.gz -> /home/biocodz/sortmerna/run/out/other_singleton_fwd_0.fq.gz
[merge:133] deleted /home/biocodz/sortmerna/run/out/other_singleton_fwd_6.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/other_singleton_fwd_7.fq.gz for reading.
[merge:130] merged /home/biocodz/sortmerna/run/out/other_singleton_fwd_7.fq.gz -> /home/biocodz/sortmerna/run/out/other_singleton_fwd_0.fq.gz
[merge:133] deleted /home/biocodz/sortmerna/run/out/other_singleton_fwd_7.fq.gz
[strip_path_sfx:154] moving /home/biocodz/sortmerna/run/out/other_singleton_fwd_0.fq.gz -> "/home/biocodz/sortmerna/run/out/other_singleton_fwd.fq.gz"
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/other_singleton_rev_1.fq.gz for reading.
[merge:130] merged /home/biocodz/sortmerna/run/out/other_singleton_rev_1.fq.gz -> /home/biocodz/sortmerna/run/out/other_singleton_rev_0.fq.gz
[merge:133] deleted /home/biocodz/sortmerna/run/out/other_singleton_rev_1.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/other_singleton_rev_2.fq.gz for reading.
[merge:130] merged /home/biocodz/sortmerna/run/out/other_singleton_rev_2.fq.gz -> /home/biocodz/sortmerna/run/out/other_singleton_rev_0.fq.gz
[merge:133] deleted /home/biocodz/sortmerna/run/out/other_singleton_rev_2.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/other_singleton_rev_3.fq.gz for reading.
[merge:130] merged /home/biocodz/sortmerna/run/out/other_singleton_rev_3.fq.gz -> /home/biocodz/sortmerna/run/out/other_singleton_rev_0.fq.gz
[merge:133] deleted /home/biocodz/sortmerna/run/out/other_singleton_rev_3.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/other_singleton_rev_4.fq.gz for reading.
[merge:130] merged /home/biocodz/sortmerna/run/out/other_singleton_rev_4.fq.gz -> /home/biocodz/sortmerna/run/out/other_singleton_rev_0.fq.gz
[merge:133] deleted /home/biocodz/sortmerna/run/out/other_singleton_rev_4.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/other_singleton_rev_5.fq.gz for reading.
[merge:130] merged /home/biocodz/sortmerna/run/out/other_singleton_rev_5.fq.gz -> /home/biocodz/sortmerna/run/out/other_singleton_rev_0.fq.gz
[merge:133] deleted /home/biocodz/sortmerna/run/out/other_singleton_rev_5.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/other_singleton_rev_6.fq.gz for reading.
[merge:130] merged /home/biocodz/sortmerna/run/out/other_singleton_rev_6.fq.gz -> /home/biocodz/sortmerna/run/out/other_singleton_rev_0.fq.gz
[merge:133] deleted /home/biocodz/sortmerna/run/out/other_singleton_rev_6.fq.gz
[openfr:114] Opened output file /home/biocodz/sortmerna/run/out/other_singleton_rev_7.fq.gz for reading.
[merge:130] merged /home/biocodz/sortmerna/run/out/other_singleton_rev_7.fq.gz -> /home/biocodz/sortmerna/run/out/other_singleton_rev_0.fq.gz
[merge:133] deleted /home/biocodz/sortmerna/run/out/other_singleton_rev_7.fq.gz
[strip_path_sfx:154] moving /home/biocodz/sortmerna/run/out/other_singleton_rev_0.fq.gz -> "/home/biocodz/sortmerna/run/out/other_singleton_rev.fq.gz"
[merge:67] merged /home/biocodz/sortmerna/run/out/aligned_1.blast.gz -> /home/biocodz/sortmerna/run/out/aligned_0.blast.gz
[merge:70] deleted /home/biocodz/sortmerna/run/out/aligned_1.blast.gz
[merge:67] merged /home/biocodz/sortmerna/run/out/aligned_2.blast.gz -> /home/biocodz/sortmerna/run/out/aligned_0.blast.gz
[merge:70] deleted /home/biocodz/sortmerna/run/out/aligned_2.blast.gz
[merge:67] merged /home/biocodz/sortmerna/run/out/aligned_3.blast.gz -> /home/biocodz/sortmerna/run/out/aligned_0.blast.gz
[merge:70] deleted /home/biocodz/sortmerna/run/out/aligned_3.blast.gz
[merge:67] merged /home/biocodz/sortmerna/run/out/aligned_4.blast.gz -> /home/biocodz/sortmerna/run/out/aligned_0.blast.gz
[merge:70] deleted /home/biocodz/sortmerna/run/out/aligned_4.blast.gz
[merge:67] merged /home/biocodz/sortmerna/run/out/aligned_5.blast.gz -> /home/biocodz/sortmerna/run/out/aligned_0.blast.gz
[merge:70] deleted /home/biocodz/sortmerna/run/out/aligned_5.blast.gz
[merge:67] merged /home/biocodz/sortmerna/run/out/aligned_6.blast.gz -> /home/biocodz/sortmerna/run/out/aligned_0.blast.gz
[merge:70] deleted /home/biocodz/sortmerna/run/out/aligned_6.blast.gz
[merge:67] merged /home/biocodz/sortmerna/run/out/aligned_7.blast.gz -> /home/biocodz/sortmerna/run/out/aligned_0.blast.gz
[merge:70] deleted /home/biocodz/sortmerna/run/out/aligned_7.blast.gz
[strip_path_sfx:154] moving /home/biocodz/sortmerna/run/out/aligned_0.blast.gz -> "/home/biocodz/sortmerna/run/out/aligned.blast.gz"
[writeReports:259] === done Reports in 64.4271 sec ===
[run] Run time: 294.6793098449707
Testing num_reads: 1000000 Expected: 1000000
Testing num_hits: 49909 Expected: 49909
Testing num_fail: 950091 Expected: 950091
processing Blast file: /home/biocodz/sortmerna/run/out/aligned.blast.gz
[process_blast] TODO: implement gz processing