rm index

runs/kallisto_index/run.log

-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_index/run.cwl'
-INFO [job run.cwl] /private/tmp/docker_tmp7lobn46w$ docker \
-    run \
-    -i \
-    --mount=type=bind,source=/private/tmp/docker_tmp7lobn46w,target=/OoJBhI \
-    --mount=type=bind,source=/private/tmp/docker_tmp18wvdt5m,target=/tmp \
-    --mount=type=bind,source=/Users/dominikbrilhaus/gitlab_dataplant/hhu-plant-biochemistry/2018_SamuilovBrilhaus_BOU_DB/workflows/kallisto_index/kallisto_index.sh,target=/var/lib/cwl/stg35dff622-c131-4e27-9e17-aff52d5d1d4a/kallisto_index.sh,readonly \
-    --mount=type=bind,source=/Users/dominikbrilhaus/gitlab_dataplant/hhu-plant-biochemistry/2018_SamuilovBrilhaus_BOU_DB/studies/arabidopsis-reference/resources/Araport11_genes.201606.cdna.fasta,target=/var/lib/cwl/stg1613bcd4-6884-48ed-9ab4-94385e70a5e6/Araport11_genes.201606.cdna.fasta,readonly \
-    --workdir=/OoJBhI \
-    --read-only=true \
-    --net=none \
-    --user=502:20 \
-    --rm \
-    --cidfile=/private/tmp/docker_tmp1e1fablo/20240125124956-101533.cid \
-    --env=TMPDIR=/tmp \
-    --env=HOME=/OoJBhI \
-    quay.io/biocontainers/kallisto:0.43.0--hdf51.8.17_2 \
-    bash \
-    /var/lib/cwl/stg35dff622-c131-4e27-9e17-aff52d5d1d4a/kallisto_index.sh \
-    /var/lib/cwl/stg1613bcd4-6884-48ed-9ab4-94385e70a5e6/Araport11_genes.201606.cdna.fasta \
-    ./out
-kallisto, version 0.43.0
-When using this program in your research, please cite
-
-  Bray, N. L., Pimentel, H., Melsted, P. & Pachter, L.
-  Near-optimal probabilistic RNA-seq quantification, 
-  Nature Biotechnology 34, 525-527(2016), doi:10.1038/nbt.3519
-
-
-[build] loading fasta file /var/lib/cwl/stg1613bcd4-6884-48ed-9ab4-94385e70a5e6/Araport11_genes.201606.cdna.fasta
-[build] k-mer length: 31
-[build] warning: clipped off poly-A tail (longer than 10)
-        from 14 target sequences
-[build] warning: replaced 11 non-ACGUT characters in the input sequence
-        with pseudorandom nucleotides
-[build] counting k-mers ... done.
-[build] building target de Bruijn graph ...  done 
-[build] creating equivalence classes ...  done
-[build] target de Bruijn graph has 173467 contigs and contains 45546882 k-mers 
-
-INFO [job run.cwl] Max memory used: 4869MiB
-INFO [job run.cwl] completed success
-{
-    "outdir": [
-        {
-            "location": "file:///Users/dominikbrilhaus/gitlab_dataplant/hhu-plant-biochemistry/2018_SamuilovBrilhaus_BOU_DB/runs/kallisto_index/out",
-            "basename": "out",
-            "class": "Directory",
-            "listing": [
-                {
-                    "class": "File",
-                    "location": "file:///Users/dominikbrilhaus/gitlab_dataplant/hhu-plant-biochemistry/2018_SamuilovBrilhaus_BOU_DB/runs/kallisto_index/out/kallisto_index",
-                    "basename": "kallisto_index",
-                    "size": 973267848,
-                    "checksum": "sha1$e7b7f9828f01a754b0373aaaa793089585580172",
-                    "path": "/Users/dominikbrilhaus/gitlab_dataplant/hhu-plant-biochemistry/2018_SamuilovBrilhaus_BOU_DB/runs/kallisto_index/out/kallisto_index"
-                }
-            ],
-            "path": "/Users/dominikbrilhaus/gitlab_dataplant/hhu-plant-biochemistry/2018_SamuilovBrilhaus_BOU_DB/runs/kallisto_index/out"
-        }
-    ]
-}INFO Final process status is success