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Commit 9b5b0bf8 authored by Dominik Brilhaus's avatar Dominik Brilhaus
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kallisto quant test run

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......@@ -5,3 +5,5 @@ _publication/Data[[:space:]]Sheet[[:space:]]1.xlsx filter=lfs diff=lfs merge=lfs
studies/arabidopsis-reference/resources/Araport11_genes.201606.cdna.fasta filter=lfs diff=lfs merge=lfs -text
runs/kallisto_index/out/kallisto_index filter=lfs diff=lfs merge=lfs -text
studies/arabidopsis-reference/resources/Arabidopsis_thaliana.TAIR10.28.cdna.all.fa filter=lfs diff=lfs merge=lfs -text
runs/kallisto_quant-pe/out/50-WT-D_S21_L002/abundance.h5 filter=lfs diff=lfs merge=lfs -text
runs/kallisto_quant-pe/out/50-WT-D_S21_L002/abundance.tsv filter=lfs diff=lfs merge=lfs -text
runs/kallisto_quant-pe/out/50-WT-D_S21_L002/abundance.h5 0 → 100644 LFS
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runs/kallisto_quant-pe/out/50-WT-D_S21_L002/abundance.tsv 0 → 100644 LFS
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source diff could not be displayed: it is stored in LFS. Options to address this: view the blob.
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{
"n_targets": 41392,
"n_bootstraps": 30,
"n_processed": 30869744,
"kallisto_version": "0.43.0",
"index_version": 10,
"start_time": "Thu Jan 25 13:20:21 2024",
"call": "kallisto quant -b 30 -t 4 -i /var/lib/cwl/stgbd0fc0c0-3b39-4d0b-8c87-5618da767205/kallisto_index -o ./out/50-WT-D_S21_L002 /var/lib/cwl/stg4036b29a-e463-4614-bf7a-fb2f022f00ca/dataset/50-WT-D_S21_L002_R1_001.fastq.gz /var/lib/cwl/stg4036b29a-e463-4614-bf7a-fb2f022f00ca/dataset/50-WT-D_S21_L002_R2_001.fastq.gz"
}
runs/kallisto_quant-pe/run.log 0 → 100644
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INFO /Users/dominikbrilhaus/opt/anaconda3/bin/cwltool 3.1.20240112164112
INFO Resolved 'run.cwl' to 'file:///Users/dominikbrilhaus/gitlab_dataplant/hhu-plant-biochemistry/2018_SamuilovBrilhaus_BOU_DB/runs/kallisto_quant-pe/run.cwl'
INFO [job run.cwl] /private/tmp/docker_tmpbbc44k52$ docker \
run \
-i \
--mount=type=bind,source=/private/tmp/docker_tmpbbc44k52,target=/KHFwkx \
--mount=type=bind,source=/private/tmp/docker_tmpaqm0vcus,target=/tmp \
--mount=type=bind,source=/Users/dominikbrilhaus/gitlab_dataplant/hhu-plant-biochemistry/2018_SamuilovBrilhaus_BOU_DB/workflows/kallisto_quant-pe/kallisto_quant-pe.sh,target=/var/lib/cwl/stgea2c243e-7dc5-42e1-8073-b054c37b123f/kallisto_quant-pe.sh,readonly \
--mount=type=bind,source=/Users/dominikbrilhaus/gitlab_dataplant/hhu-plant-biochemistry/2018_SamuilovBrilhaus_BOU_DB/runs/kallisto_index/out/kallisto_index,target=/var/lib/cwl/stgbd0fc0c0-3b39-4d0b-8c87-5618da767205/kallisto_index,readonly \
--mount=type=bind,source=/Users/dominikbrilhaus/gitlab_dataplant/hhu-plant-biochemistry/2018_SamuilovBrilhaus_BOU_DB/assays/rna-seq/dataset,target=/var/lib/cwl/stg4036b29a-e463-4614-bf7a-fb2f022f00ca/dataset,readonly \
--workdir=/KHFwkx \
--read-only=true \
--net=none \
--user=502:20 \
--rm \
--cidfile=/private/tmp/docker_tmprgaby8b9/20240125142021-081142.cid \
--env=TMPDIR=/tmp \
--env=HOME=/KHFwkx \
quay.io/biocontainers/kallisto:0.43.0--hdf51.8.17_2 \
bash \
/var/lib/cwl/stgea2c243e-7dc5-42e1-8073-b054c37b123f/kallisto_quant-pe.sh \
./out \
/var/lib/cwl/stgbd0fc0c0-3b39-4d0b-8c87-5618da767205/kallisto_index \
/var/lib/cwl/stg4036b29a-e463-4614-bf7a-fb2f022f00ca/dataset \
30 \
4
50-WT-D_S21_L002
[quant] fragment length distribution will be estimated from the data
[index] k-mer length: 31
[index] number of targets: 41,392
[index] number of k-mers: 47,713,570
[index] number of equivalence classes: 115,412
[quant] running in paired-end mode
[quant] will process pair 1: /var/lib/cwl/stg4036b29a-e463-4614-bf7a-fb2f022f00ca/dataset/50-WT-D_S21_L002_R1_001.fastq.gz
/var/lib/cwl/stg4036b29a-e463-4614-bf7a-fb2f022f00ca/dataset/50-WT-D_S21_L002_R2_001.fastq.gz
[quant] finding pseudoalignments for the reads ... done
[quant] processed 30,869,744 reads, 29,573,099 reads pseudoaligned
[quant] estimated average fragment length: 152.005
[ em] quantifying the abundances ... done
[ em] the Expectation-Maximization algorithm ran for 976 rounds
[bstrp] number of EM bootstraps complete: 1 [bstrp] number of EM bootstraps complete: 2 [bstrp] number of EM bootstraps complete: 3 [bstrp] number of EM bootstraps complete: 4 [bstrp] number of EM bootstraps complete: 5 [bstrp] number of EM bootstraps complete: 6 [bstrp] number of EM bootstraps complete: 7 [bstrp] number of EM bootstraps complete: 8 [bstrp] number of EM bootstraps complete: 9 [bstrp] number of EM bootstraps complete: 10 [bstrp] number of EM bootstraps complete: 11 [bstrp] number of EM bootstraps complete: 12 [bstrp] number of EM bootstraps complete: 13 [bstrp] number of EM bootstraps complete: 14 [bstrp] number of EM bootstraps complete: 15 [bstrp] number of EM bootstraps complete: 16 [bstrp] number of EM bootstraps complete: 17 [bstrp] number of EM bootstraps complete: 18 [bstrp] number of EM bootstraps complete: 19 [bstrp] number of EM bootstraps complete: 20 [bstrp] number of EM bootstraps complete: 21 [bstrp] number of EM bootstraps complete: 22 [bstrp] number of EM bootstraps complete: 23 [bstrp] number of EM bootstraps complete: 24 [bstrp] number of EM bootstraps complete: 25 [bstrp] number of EM bootstraps complete: 26 [bstrp] number of EM bootstraps complete: 27 [bstrp] number of EM bootstraps complete: 28 [bstrp] number of EM bootstraps complete: 29 [bstrp] number of EM bootstraps complete: 30
Kallisto done
INFO [job run.cwl] Max memory used: 3563MiB
INFO [job run.cwl] completed success
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}INFO Final process status is success
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