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trimming.json
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trimming.json
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"name": "Sapporo stderr",
"sha512": "3019e8052340e0afde96cb4fd72bef007f2e9da54d6c55cb85698ad2b00a346efa2e587a1247d4928c4172fa7a6af9efb5ce964fb65439390603234451bba075",
"text": "jq: error (at /home/ubuntu/git/github.com/sapporo-wes/yevis-cli/sapporo-run/f9/f961dd4c-5933-4a6a-b043-bbf03157fc9b/run_request.json:10): null (null) only strings can be parsed\nb qc_2] /tmp/odj_asjx$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/tmp/odj_asjx,target=/ZplaYq \\\n --mount=type=bind,source=/tmp/aijhw610,target=/tmp \\\n --mount=type=bind,source=/home/ubuntu/git/github.com/sapporo-wes/yevis-cli/sapporo-run/f9/f961dd4c-5933-4a6a-b043-bbf03157fc9b/exe/ERR034597_2.small.fq.gz,target=/var/lib/cwl/stg142c1e5b-b91e-4936-b1c1-197344a730ee/ERR034597_2.small.fq.gz,readonly \\\n --workdir=/ZplaYq \\\n --read-only=true \\\n --log-driver=none \\\n --user=0:0 \\\n --rm \\\n --cidfile=/tmp/8r_h46tw/20220912061330-983392.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/ZplaYq \\\n quay.io/biocontainers/fastqc:0.11.9--0 \\\n fastqc \\\n -o \\\n . \\\n --threads \\\n 2 \\\n /var/lib/cwl/stg142c1e5b-b91e-4936-b1c1-197344a730ee/ERR034597_2.small.fq.gz > /tmp/odj_asjx/fastqc-stdout.log 2> /tmp/odj_asjx/fastqc-stderr.log\n\u001b[1;30mINFO\u001b[0m [job qc_2] Max memory used: 144MiB\n\u001b[1;30mINFO\u001b[0m [job qc_2] completed success\n\u001b[1;30mINFO\u001b[0m [step qc_2] completed success\n\u001b[1;30mINFO\u001b[0m [workflow ] starting step trimming\n\u001b[1;30mINFO\u001b[0m [step trimming] start\n\u001b[1;30mINFO\u001b[0m [job trimming] /tmp/tem8s58c$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/tmp/tem8s58c,target=/ZplaYq \\\n --mount=type=bind,source=/tmp/7u4ml8x3,target=/tmp \\\n --mount=type=bind,source=/home/ubuntu/git/github.com/sapporo-wes/yevis-cli/sapporo-run/f9/f961dd4c-5933-4a6a-b043-bbf03157fc9b/exe/ERR034597_1.small.fq.gz,target=/var/lib/cwl/stgda735211-23c6-4134-898c-39199f149921/ERR034597_1.small.fq.gz,readonly \\\n --mount=type=bind,source=/home/ubuntu/git/github.com/sapporo-wes/yevis-cli/sapporo-run/f9/f961dd4c-5933-4a6a-b043-bbf03157fc9b/exe/ERR034597_2.small.fq.gz,target=/var/lib/cwl/stgb93f3246-cd76-4f47-8315-acbf7151f2c4/ERR034597_2.small.fq.gz,readonly \\\n --workdir=/ZplaYq \\\n --read-only=true \\\n --log-driver=none \\\n --user=0:0 \\\n --rm \\\n --cidfile=/tmp/f2p6cfq5/20220912061339-696100.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/ZplaYq \\\n quay.io/biocontainers/trimmomatic:0.38--1 \\\n trimmomatic \\\n PE \\\n -threads \\\n 2 \\\n /var/lib/cwl/stgda735211-23c6-4134-898c-39199f149921/ERR034597_1.small.fq.gz \\\n /var/lib/cwl/stgb93f3246-cd76-4f47-8315-acbf7151f2c4/ERR034597_2.small.fq.gz \\\n ERR034597_1.small.fq.trimmed.1P.fq \\\n ERR034597_1.small.fq.trimmed.1U.fq \\\n ERR034597_1.small.fq.trimmed.2P.fq \\\n ERR034597_1.small.fq.trimmed.2U.fq \\\n ILLUMINACLIP:/usr/local/share/trimmomatic/adapters/TruSeq2-PE.fa:2:40:15 \\\n LEADING:20 \\\n TRAILING:20 \\\n SLIDINGWINDOW:4:15 \\\n MINLEN:36 > /tmp/tem8s58c/trimmomatic-pe-stdout.log 2> /tmp/tem8s58c/trimmomatic-pe-stderr.log\n\u001b[1;30mINFO\u001b[0m [job trimming] Max memory used: 88MiB\n\u001b[1;30mINFO\u001b[0m [job trimming] completed success\n\u001b[1;30mINFO\u001b[0m [step trimming] completed success\n\u001b[1;30mINFO\u001b[0m [workflow ] starting step qc_1\n\u001b[1;30mINFO\u001b[0m [step qc_1] start\n\u001b[1;30mINFO\u001b[0m [job qc_1] /tmp/9s6pjszw$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/tmp/9s6pjszw,target=/ZplaYq \\\n --mount=type=bind,source=/tmp/rccp7i0n,target=/tmp \\\n --mount=type=bind,source=/home/ubuntu/git/github.com/sapporo-wes/yevis-cli/sapporo-run/f9/f961dd4c-5933-4a6a-b043-bbf03157fc9b/exe/ERR034597_1.small.fq.gz,target=/var/lib/cwl/stg1a213db7-41e8-4126-9aab-cb282291688e/ERR034597_1.small.fq.gz,readonly \\\n --workdir=/ZplaYq \\\n --read-only=true \\\n --log-driver=none \\\n --user=0:0 \\\n --rm \\\n --cidfile=/tmp/j6ith35c/20220912061344-112864.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/ZplaYq \\\n quay.io/biocontainers/fastqc:0.11.9--0 \\\n fastqc \\\n -o \\\n . \\\n --threads \\\n 2 \\\n /var/lib/cwl/stg1a213db7-41e8-4126-9aab-cb282291688e/ERR034597_1.small.fq.gz > /tmp/9s6pjszw/fastqc-stdout.log 2> /tmp/9s6pjszw/fastqc-stderr.log\n\u001b[1;30mINFO\u001b[0m [job qc_1] Max memory used: 134MiB\n\u001b[1;30mINFO\u001b[0m [job qc_1] completed success\n\u001b[1;30mINFO\u001b[0m [step qc_1] completed success\n\u001b[1;30mINFO\u001b[0m [workflow ] completed success\n\u001b[1;30mINFO\u001b[0m Final process status is success\n"
}
]
}