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Commit 0bf45cab authored by Dominik Brilhaus's avatar Dominik Brilhaus
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add log last run

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1 merge request!2Kallisto cwl
Pipeline #2449 failed
This commit is part of merge request !2. Comments created here will be created in the context of that merge request.
INFO /home/brilator/miniconda3/bin/cwltool 3.1.20240508115724
INFO Resolved '../../workflows/kallisto/kallisto-workflow.cwl' to 'file:///home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/workflows/kallisto/kallisto-workflow.cwl'
INFO [workflow ] start
INFO [workflow ] starting step index
INFO [step index] start
INFO [job index] Using cached output in /home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/c232c80e27f9ac9aff6ffb527ebd4189
INFO [step index] completed success
INFO [workflow ] starting step quant
INFO [step quant] start
INFO [job quant] Output of job will be cached in /home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/04c1d3666d36fb428efa31aedbcef3e7
INFO [job quant] /home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/04c1d3666d36fb428efa31aedbcef3e7$ docker \
run \
-i \
--mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/04c1d3666d36fb428efa31aedbcef3e7,target=/gvSNJe \
--mount=type=bind,source=/tmp/mbmkyli1,target=/tmp \
--mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/c232c80e27f9ac9aff6ffb527ebd4189/Talinum.gm.CDS.nt.kallistoIndex,target=/var/lib/cwl/stg2d88a9bc-457d-4cc9-8603-fe974737cab6/Talinum.gm.CDS.nt.kallistoIndex,readonly \
--mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/assays/Talinum_RNASeq_minimal/dataset/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz,target=/var/lib/cwl/stg9989d547-e38c-4bcd-8449-008e2e4a2d83/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz,readonly \
--workdir=/gvSNJe \
--read-only=true \
--net=none \
--user=1007:1007 \
--rm \
--cidfile=/tmp/lkq3cvxw/20240805135057-308071.cid \
--env=TMPDIR=/tmp \
--env=HOME=/gvSNJe \
quay.io/biocontainers/kallisto:0.50.1--h6de1650_2 \
kallisto \
quant \
--output-dir \
DB_097 \
--bootstrap-samples=30 \
--fragment-length=200 \
--sd \
20 \
--index \
/var/lib/cwl/stg2d88a9bc-457d-4cc9-8603-fe974737cab6/Talinum.gm.CDS.nt.kallistoIndex \
--single \
/var/lib/cwl/stg9989d547-e38c-4bcd-8449-008e2e4a2d83/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz
[quant] fragment length distribution is truncated gaussian with mean = 200, sd = 20
[index] k-mer length: 31
[index] number of targets: 31,434
[index] number of k-mers: 35,149,253
[quant] running in single-end mode
[quant] will process file 1: /var/lib/cwl/stg9989d547-e38c-4bcd-8449-008e2e4a2d83/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz
[quant] finding pseudoalignments for the reads ... [progress] 1M reads processed (69.4% mapped) [progress] 2M reads processed (69.3% mapped) [progress] 3M reads processed (69.2% mapped) [progress] 4M reads processed (69.3% mapped) [progress] 5M reads processed (69.2% mapped) [progress] 6M reads processed (69.2% mapped) [progress] 7M reads processed (69.2% mapped) [progress] 8M reads processed (69.2% mapped) [progress] 9M reads processed (69.2% mapped) [progress] 10M reads processed (69.2% mapped) done
[quant] processed 11,071,656 reads, 7,663,833 reads pseudoaligned
[ em] quantifying the abundances ... done
[ em] the Expectation-Maximization algorithm ran for 460 rounds
[bstrp] running EM for the bootstrap: 1 [bstrp] running EM for the bootstrap: 2 [bstrp] running EM for the bootstrap: 3 [bstrp] running EM for the bootstrap: 4 [bstrp] running EM for the bootstrap: 5 [bstrp] running EM for the bootstrap: 6 [bstrp] running EM for the bootstrap: 7 [bstrp] running EM for the bootstrap: 8 [bstrp] running EM for the bootstrap: 9 [bstrp] running EM for the bootstrap: 10 [bstrp] running EM for the bootstrap: 11 [bstrp] running EM for the bootstrap: 12 [bstrp] running EM for the bootstrap: 13 [bstrp] running EM for the bootstrap: 14 [bstrp] running EM for the bootstrap: 15 [bstrp] running EM for the bootstrap: 16 [bstrp] running EM for the bootstrap: 17 [bstrp] running EM for the bootstrap: 18 [bstrp] running EM for the bootstrap: 19 [bstrp] running EM for the bootstrap: 20 [bstrp] running EM for the bootstrap: 21 [bstrp] running EM for the bootstrap: 22 [bstrp] running EM for the bootstrap: 23 [bstrp] running EM for the bootstrap: 24 [bstrp] running EM for the bootstrap: 25 [bstrp] running EM for the bootstrap: 26 [bstrp] running EM for the bootstrap: 27 [bstrp] running EM for the bootstrap: 28 [bstrp] running EM for the bootstrap: 29 [bstrp] running EM for the bootstrap: 30
INFO [job quant] Max memory used: 283MiB
INFO [job quant] completed success
INFO [step quant] start
INFO [job quant_2] Output of job will be cached in /home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/ca52501ef3b3047551f9124c1d5004b4
INFO [job quant_2] /home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/ca52501ef3b3047551f9124c1d5004b4$ docker \
run \
-i \
--mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/ca52501ef3b3047551f9124c1d5004b4,target=/gvSNJe \
--mount=type=bind,source=/tmp/_x8jqxqc,target=/tmp \
--mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/c232c80e27f9ac9aff6ffb527ebd4189/Talinum.gm.CDS.nt.kallistoIndex,target=/var/lib/cwl/stg19bb2e01-3f1a-4757-8b96-b3736bb62ae2/Talinum.gm.CDS.nt.kallistoIndex,readonly \
--mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/assays/Talinum_RNASeq_minimal/dataset/DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz,target=/var/lib/cwl/stgc8c3c1dc-aa80-4b3c-8c8a-816c343091d2/DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz,readonly \
--workdir=/gvSNJe \
--read-only=true \
--net=none \
--user=1007:1007 \
--rm \
--cidfile=/tmp/1q3__lzr/20240805135536-712649.cid \
--env=TMPDIR=/tmp \
--env=HOME=/gvSNJe \
quay.io/biocontainers/kallisto:0.50.1--h6de1650_2 \
kallisto \
quant \
--output-dir \
DB_099 \
--bootstrap-samples=30 \
--fragment-length=200 \
--sd \
20 \
--index \
/var/lib/cwl/stg19bb2e01-3f1a-4757-8b96-b3736bb62ae2/Talinum.gm.CDS.nt.kallistoIndex \
--single \
/var/lib/cwl/stgc8c3c1dc-aa80-4b3c-8c8a-816c343091d2/DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz
[quant] fragment length distribution is truncated gaussian with mean = 200, sd = 20
[index] k-mer length: 31
[index] number of targets: 31,434
[index] number of k-mers: 35,149,253
[quant] running in single-end mode
[quant] will process file 1: /var/lib/cwl/stgc8c3c1dc-aa80-4b3c-8c8a-816c343091d2/DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz
[quant] finding pseudoalignments for the reads ... [progress] 1M reads processed (70.3% mapped) [progress] 2M reads processed (70.3% mapped) [progress] 3M reads processed (70.2% mapped) [progress] 4M reads processed (70.2% mapped) [progress] 5M reads processed (70.2% mapped) [progress] 6M reads processed (70.2% mapped) [progress] 7M reads processed (70.2% mapped) [progress] 8M reads processed (70.2% mapped) [progress] 9M reads processed (70.3% mapped) [progress] 10M reads processed (70.2% mapped) [progress] 11M reads processed (70.2% mapped) [progress] 12M reads processed (70.3% mapped) [progress] 13M reads processed (70.2% mapped) done
[quant] processed 14,332,278 reads, 10,066,684 reads pseudoaligned
[ em] quantifying the abundances ... done
[ em] the Expectation-Maximization algorithm ran for 458 rounds
[bstrp] running EM for the bootstrap: 1 [bstrp] running EM for the bootstrap: 2 [bstrp] running EM for the bootstrap: 3 [bstrp] running EM for the bootstrap: 4 [bstrp] running EM for the bootstrap: 5 [bstrp] running EM for the bootstrap: 6 [bstrp] running EM for the bootstrap: 7 [bstrp] running EM for the bootstrap: 8 [bstrp] running EM for the bootstrap: 9 [bstrp] running EM for the bootstrap: 10 [bstrp] running EM for the bootstrap: 11 [bstrp] running EM for the bootstrap: 12 [bstrp] running EM for the bootstrap: 13 [bstrp] running EM for the bootstrap: 14 [bstrp] running EM for the bootstrap: 15 [bstrp] running EM for the bootstrap: 16 [bstrp] running EM for the bootstrap: 17 [bstrp] running EM for the bootstrap: 18 [bstrp] running EM for the bootstrap: 19 [bstrp] running EM for the bootstrap: 20 [bstrp] running EM for the bootstrap: 21 [bstrp] running EM for the bootstrap: 22 [bstrp] running EM for the bootstrap: 23 [bstrp] running EM for the bootstrap: 24 [bstrp] running EM for the bootstrap: 25 [bstrp] running EM for the bootstrap: 26 [bstrp] running EM for the bootstrap: 27 [bstrp] running EM for the bootstrap: 28 [bstrp] running EM for the bootstrap: 29 [bstrp] running EM for the bootstrap: 30
INFO [job quant_2] Max memory used: 283MiB
INFO [job quant_2] completed success
INFO [step quant] start
INFO [job quant_3] Output of job will be cached in /home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/c4753612931c39e236518d2ca4455d3d
INFO [job quant_3] /home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/c4753612931c39e236518d2ca4455d3d$ docker \
run \
-i \
--mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/c4753612931c39e236518d2ca4455d3d,target=/gvSNJe \
--mount=type=bind,source=/tmp/0idun1z_,target=/tmp \
--mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/c232c80e27f9ac9aff6ffb527ebd4189/Talinum.gm.CDS.nt.kallistoIndex,target=/var/lib/cwl/stg4688cdf5-4be9-4a10-a2da-b72109654518/Talinum.gm.CDS.nt.kallistoIndex,readonly \
--mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/assays/Talinum_RNASeq_minimal/dataset/DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz,target=/var/lib/cwl/stg86fb44d0-f2e4-4049-b4ea-b25fb3cc52ce/DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz,readonly \
--workdir=/gvSNJe \
--read-only=true \
--net=none \
--user=1007:1007 \
--rm \
--cidfile=/tmp/u2m6ez7p/20240805140121-006110.cid \
--env=TMPDIR=/tmp \
--env=HOME=/gvSNJe \
quay.io/biocontainers/kallisto:0.50.1--h6de1650_2 \
kallisto \
quant \
--output-dir \
DB_103 \
--bootstrap-samples=30 \
--fragment-length=200 \
--sd \
20 \
--index \
/var/lib/cwl/stg4688cdf5-4be9-4a10-a2da-b72109654518/Talinum.gm.CDS.nt.kallistoIndex \
--single \
/var/lib/cwl/stg86fb44d0-f2e4-4049-b4ea-b25fb3cc52ce/DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz
[quant] fragment length distribution is truncated gaussian with mean = 200, sd = 20
[index] k-mer length: 31
[index] number of targets: 31,434
[index] number of k-mers: 35,149,253
[quant] running in single-end mode
[quant] will process file 1: /var/lib/cwl/stg86fb44d0-f2e4-4049-b4ea-b25fb3cc52ce/DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz
[quant] finding pseudoalignments for the reads ... [progress] 1M reads processed (69.0% mapped) [progress] 2M reads processed (68.9% mapped) [progress] 3M reads processed (68.9% mapped) [progress] 4M reads processed (68.9% mapped) [progress] 5M reads processed (68.9% mapped) [progress] 6M reads processed (68.9% mapped) [progress] 7M reads processed (68.9% mapped) [progress] 8M reads processed (68.9% mapped) [progress] 9M reads processed (68.9% mapped) [progress] 10M reads processed (68.9% mapped) [progress] 11M reads processed (68.9% mapped) [progress] 12M reads processed (68.9% mapped) done
[quant] processed 13,083,957 reads, 9,007,909 reads pseudoaligned
[ em] quantifying the abundances ... done
[ em] the Expectation-Maximization algorithm ran for 806 rounds
[bstrp] running EM for the bootstrap: 1 [bstrp] running EM for the bootstrap: 2 [bstrp] running EM for the bootstrap: 3 [bstrp] running EM for the bootstrap: 4 [bstrp] running EM for the bootstrap: 5 [bstrp] running EM for the bootstrap: 6 [bstrp] running EM for the bootstrap: 7 [bstrp] running EM for the bootstrap: 8 [bstrp] running EM for the bootstrap: 9 [bstrp] running EM for the bootstrap: 10 [bstrp] running EM for the bootstrap: 11 [bstrp] running EM for the bootstrap: 12 [bstrp] running EM for the bootstrap: 13 [bstrp] running EM for the bootstrap: 14 [bstrp] running EM for the bootstrap: 15 [bstrp] running EM for the bootstrap: 16 [bstrp] running EM for the bootstrap: 17 [bstrp] running EM for the bootstrap: 18 [bstrp] running EM for the bootstrap: 19 [bstrp] running EM for the bootstrap: 20 [bstrp] running EM for the bootstrap: 21 [bstrp] running EM for the bootstrap: 22 [bstrp] running EM for the bootstrap: 23 [bstrp] running EM for the bootstrap: 24 [bstrp] running EM for the bootstrap: 25 [bstrp] running EM for the bootstrap: 26 [bstrp] running EM for the bootstrap: 27 [bstrp] running EM for the bootstrap: 28 [bstrp] running EM for the bootstrap: 29 [bstrp] running EM for the bootstrap: 30
INFO [job quant_3] Max memory used: 283MiB
INFO [job quant_3] completed success
INFO [step quant] start
INFO [job quant_4] Output of job will be cached in /home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/7fa99fa2914046d103fe5e619913fef3
INFO [job quant_4] /home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/7fa99fa2914046d103fe5e619913fef3$ docker \
run \
-i \
--mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/7fa99fa2914046d103fe5e619913fef3,target=/gvSNJe \
--mount=type=bind,source=/tmp/qdidmi0d,target=/tmp \
--mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/c232c80e27f9ac9aff6ffb527ebd4189/Talinum.gm.CDS.nt.kallistoIndex,target=/var/lib/cwl/stgd1efd19f-8170-422d-b114-5ea798ac0aec/Talinum.gm.CDS.nt.kallistoIndex,readonly \
--mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/assays/Talinum_RNASeq_minimal/dataset/DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz,target=/var/lib/cwl/stgf263d766-1fa7-41f0-8d5b-d9940c486e06/DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz,readonly \
--workdir=/gvSNJe \
--read-only=true \
--net=none \
--user=1007:1007 \
--rm \
--cidfile=/tmp/fx0nz7uo/20240805140646-758938.cid \
--env=TMPDIR=/tmp \
--env=HOME=/gvSNJe \
quay.io/biocontainers/kallisto:0.50.1--h6de1650_2 \
kallisto \
quant \
--output-dir \
DB_161 \
--bootstrap-samples=30 \
--fragment-length=200 \
--sd \
20 \
--index \
/var/lib/cwl/stgd1efd19f-8170-422d-b114-5ea798ac0aec/Talinum.gm.CDS.nt.kallistoIndex \
--single \
/var/lib/cwl/stgf263d766-1fa7-41f0-8d5b-d9940c486e06/DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz
[quant] fragment length distribution is truncated gaussian with mean = 200, sd = 20
[index] k-mer length: 31
[index] number of targets: 31,434
[index] number of k-mers: 35,149,253
[quant] running in single-end mode
[quant] will process file 1: /var/lib/cwl/stgf263d766-1fa7-41f0-8d5b-d9940c486e06/DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz
[quant] finding pseudoalignments for the reads ... [progress] 1M reads processed (71.0% mapped) [progress] 2M reads processed (70.9% mapped) [progress] 3M reads processed (70.9% mapped) [progress] 4M reads processed (70.9% mapped) [progress] 5M reads processed (70.9% mapped) [progress] 6M reads processed (70.8% mapped) [progress] 7M reads processed (70.9% mapped) [progress] 8M reads processed (70.9% mapped) [progress] 9M reads processed (70.9% mapped) [progress] 10M reads processed (70.9% mapped) [progress] 11M reads processed (70.9% mapped) [progress] 12M reads processed (70.9% mapped) done
[quant] processed 12,785,081 reads, 9,058,463 reads pseudoaligned
[ em] quantifying the abundances ... done
[ em] the Expectation-Maximization algorithm ran for 500 rounds
[bstrp] running EM for the bootstrap: 1 [bstrp] running EM for the bootstrap: 2 [bstrp] running EM for the bootstrap: 3 [bstrp] running EM for the bootstrap: 4 [bstrp] running EM for the bootstrap: 5 [bstrp] running EM for the bootstrap: 6 [bstrp] running EM for the bootstrap: 7 [bstrp] running EM for the bootstrap: 8 [bstrp] running EM for the bootstrap: 9 [bstrp] running EM for the bootstrap: 10 [bstrp] running EM for the bootstrap: 11 [bstrp] running EM for the bootstrap: 12 [bstrp] running EM for the bootstrap: 13 [bstrp] running EM for the bootstrap: 14 [bstrp] running EM for the bootstrap: 15 [bstrp] running EM for the bootstrap: 16 [bstrp] running EM for the bootstrap: 17 [bstrp] running EM for the bootstrap: 18 [bstrp] running EM for the bootstrap: 19 [bstrp] running EM for the bootstrap: 20 [bstrp] running EM for the bootstrap: 21 [bstrp] running EM for the bootstrap: 22 [bstrp] running EM for the bootstrap: 23 [bstrp] running EM for the bootstrap: 24 [bstrp] running EM for the bootstrap: 25 [bstrp] running EM for the bootstrap: 26 [bstrp] running EM for the bootstrap: 27 [bstrp] running EM for the bootstrap: 28 [bstrp] running EM for the bootstrap: 29 [bstrp] running EM for the bootstrap: 30
INFO [job quant_4] Max memory used: 283MiB
INFO [job quant_4] completed success
INFO [step quant] start
INFO [job quant_5] Output of job will be cached in /home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/6475ad7bb21ae6103cbbd215f880611a
INFO [job quant_5] /home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/6475ad7bb21ae6103cbbd215f880611a$ docker \
run \
-i \
--mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/6475ad7bb21ae6103cbbd215f880611a,target=/gvSNJe \
--mount=type=bind,source=/tmp/lwmiuppe,target=/tmp \
--mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/c232c80e27f9ac9aff6ffb527ebd4189/Talinum.gm.CDS.nt.kallistoIndex,target=/var/lib/cwl/stg53b39f3b-5476-4170-8c9a-57684344461d/Talinum.gm.CDS.nt.kallistoIndex,readonly \
--mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/assays/Talinum_RNASeq_minimal/dataset/DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz,target=/var/lib/cwl/stgba54becd-ad88-446e-971e-7b50ec97640e/DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz,readonly \
--workdir=/gvSNJe \
--read-only=true \
--net=none \
--user=1007:1007 \
--rm \
--cidfile=/tmp/jf9xn6l5/20240805141155-698481.cid \
--env=TMPDIR=/tmp \
--env=HOME=/gvSNJe \
quay.io/biocontainers/kallisto:0.50.1--h6de1650_2 \
kallisto \
quant \
--output-dir \
DB_163 \
--bootstrap-samples=30 \
--fragment-length=200 \
--sd \
20 \
--index \
/var/lib/cwl/stg53b39f3b-5476-4170-8c9a-57684344461d/Talinum.gm.CDS.nt.kallistoIndex \
--single \
/var/lib/cwl/stgba54becd-ad88-446e-971e-7b50ec97640e/DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz
[quant] fragment length distribution is truncated gaussian with mean = 200, sd = 20
[index] k-mer length: 31
[index] number of targets: 31,434
[index] number of k-mers: 35,149,253
[quant] running in single-end mode
[quant] will process file 1: /var/lib/cwl/stgba54becd-ad88-446e-971e-7b50ec97640e/DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz
[quant] finding pseudoalignments for the reads ... [progress] 1M reads processed (70.4% mapped) [progress] 2M reads processed (70.3% mapped) [progress] 3M reads processed (70.3% mapped) [progress] 4M reads processed (70.3% mapped) [progress] 5M reads processed (70.3% mapped) [progress] 6M reads processed (70.3% mapped) [progress] 7M reads processed (70.2% mapped) [progress] 8M reads processed (70.3% mapped) [progress] 9M reads processed (70.3% mapped) [progress] 10M reads processed (70.3% mapped) [progress] 11M reads processed (70.3% mapped) [progress] 12M reads processed (70.3% mapped) [progress] 13M reads processed (70.3% mapped) done
[quant] processed 14,312,514 reads, 10,054,587 reads pseudoaligned
[ em] quantifying the abundances ... done
[ em] the Expectation-Maximization algorithm ran for 583 rounds
[bstrp] running EM for the bootstrap: 1 [bstrp] running EM for the bootstrap: 2 [bstrp] running EM for the bootstrap: 3 [bstrp] running EM for the bootstrap: 4 [bstrp] running EM for the bootstrap: 5 [bstrp] running EM for the bootstrap: 6 [bstrp] running EM for the bootstrap: 7 [bstrp] running EM for the bootstrap: 8 [bstrp] running EM for the bootstrap: 9 [bstrp] running EM for the bootstrap: 10 [bstrp] running EM for the bootstrap: 11 [bstrp] running EM for the bootstrap: 12 [bstrp] running EM for the bootstrap: 13 [bstrp] running EM for the bootstrap: 14 [bstrp] running EM for the bootstrap: 15 [bstrp] running EM for the bootstrap: 16 [bstrp] running EM for the bootstrap: 17 [bstrp] running EM for the bootstrap: 18 [bstrp] running EM for the bootstrap: 19 [bstrp] running EM for the bootstrap: 20 [bstrp] running EM for the bootstrap: 21 [bstrp] running EM for the bootstrap: 22 [bstrp] running EM for the bootstrap: 23 [bstrp] running EM for the bootstrap: 24 [bstrp] running EM for the bootstrap: 25 [bstrp] running EM for the bootstrap: 26 [bstrp] running EM for the bootstrap: 27 [bstrp] running EM for the bootstrap: 28 [bstrp] running EM for the bootstrap: 29 [bstrp] running EM for the bootstrap: 30
INFO [job quant_5] Max memory used: 283MiB
INFO [job quant_5] completed success
INFO [step quant] start
INFO [job quant_6] Output of job will be cached in /home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/64cab5af8057447efd20f0d6b5bc5235
INFO [job quant_6] /home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/64cab5af8057447efd20f0d6b5bc5235$ docker \
run \
-i \
--mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/64cab5af8057447efd20f0d6b5bc5235,target=/gvSNJe \
--mount=type=bind,source=/tmp/n2t1f_d1,target=/tmp \
--mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/c232c80e27f9ac9aff6ffb527ebd4189/Talinum.gm.CDS.nt.kallistoIndex,target=/var/lib/cwl/stg34703b5f-6fb1-4f01-9926-b3250461e42b/Talinum.gm.CDS.nt.kallistoIndex,readonly \
--mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/assays/Talinum_RNASeq_minimal/dataset/DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz,target=/var/lib/cwl/stg48c813d5-839d-404e-84c6-ba7a313e084f/DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz,readonly \
--workdir=/gvSNJe \
--read-only=true \
--net=none \
--user=1007:1007 \
--rm \
--cidfile=/tmp/_nyrkq_n/20240805141801-155673.cid \
--env=TMPDIR=/tmp \
--env=HOME=/gvSNJe \
quay.io/biocontainers/kallisto:0.50.1--h6de1650_2 \
kallisto \
quant \
--output-dir \
DB_165 \
--bootstrap-samples=30 \
--fragment-length=200 \
--sd \
20 \
--index \
/var/lib/cwl/stg34703b5f-6fb1-4f01-9926-b3250461e42b/Talinum.gm.CDS.nt.kallistoIndex \
--single \
/var/lib/cwl/stg48c813d5-839d-404e-84c6-ba7a313e084f/DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz
[quant] fragment length distribution is truncated gaussian with mean = 200, sd = 20
[index] k-mer length: 31
[index] number of targets: 31,434
[index] number of k-mers: 35,149,253
[quant] running in single-end mode
[quant] will process file 1: /var/lib/cwl/stg48c813d5-839d-404e-84c6-ba7a313e084f/DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz
[quant] finding pseudoalignments for the reads ... [progress] 1M reads processed (70.0% mapped) [progress] 2M reads processed (69.8% mapped) [progress] 3M reads processed (69.8% mapped) [progress] 4M reads processed (69.8% mapped) [progress] 5M reads processed (69.8% mapped) [progress] 6M reads processed (69.8% mapped) [progress] 7M reads processed (69.8% mapped) [progress] 8M reads processed (69.8% mapped) [progress] 9M reads processed (69.8% mapped) [progress] 10M reads processed (69.8% mapped) [progress] 11M reads processed (69.8% mapped) [progress] 12M reads processed (69.8% mapped) [progress] 13M reads processed (69.8% mapped) done
[quant] processed 13,679,479 reads, 9,552,610 reads pseudoaligned
[ em] quantifying the abundances ... done
[ em] the Expectation-Maximization algorithm ran for 514 rounds
[bstrp] running EM for the bootstrap: 1 [bstrp] running EM for the bootstrap: 2 [bstrp] running EM for the bootstrap: 3 [bstrp] running EM for the bootstrap: 4 [bstrp] running EM for the bootstrap: 5 [bstrp] running EM for the bootstrap: 6 [bstrp] running EM for the bootstrap: 7 [bstrp] running EM for the bootstrap: 8 [bstrp] running EM for the bootstrap: 9 [bstrp] running EM for the bootstrap: 10 [bstrp] running EM for the bootstrap: 11 [bstrp] running EM for the bootstrap: 12 [bstrp] running EM for the bootstrap: 13 [bstrp] running EM for the bootstrap: 14 [bstrp] running EM for the bootstrap: 15 [bstrp] running EM for the bootstrap: 16 [bstrp] running EM for the bootstrap: 17 [bstrp] running EM for the bootstrap: 18 [bstrp] running EM for the bootstrap: 19 [bstrp] running EM for the bootstrap: 20 [bstrp] running EM for the bootstrap: 21 [bstrp] running EM for the bootstrap: 22 [bstrp] running EM for the bootstrap: 23 [bstrp] running EM for the bootstrap: 24 [bstrp] running EM for the bootstrap: 25 [bstrp] running EM for the bootstrap: 26 [bstrp] running EM for the bootstrap: 27 [bstrp] running EM for the bootstrap: 28 [bstrp] running EM for the bootstrap: 29 [bstrp] running EM for the bootstrap: 30
INFO [job quant_6] Max memory used: 283MiB
INFO [job quant_6] completed success
INFO [step quant] completed success
INFO [workflow ] starting step collectResults
INFO [step collectResults] start
INFO [step collectResults] start
INFO [step collectResults] start
INFO [step collectResults] start
INFO [step collectResults] start
INFO [step collectResults] start
INFO [step collectResults] completed success
INFO [workflow ] completed success
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}INFO Final process status is success
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