Skip to content

Instantly share code, notes, and snippets.

@yuifu
Created September 12, 2020 01:39
Show Gist options
  • Save yuifu/b6b617e7fcca4f169cf48435424e053c to your computer and use it in GitHub Desktop.
Save yuifu/b6b617e7fcca4f169cf48435424e053c to your computer and use it in GitHub Desktop.
/home/harukao/anaconda3/bin/cwltool 1.0.20190228155703
https://schema.org/docs/!DOCTYPE html does not look like a valid URI, trying to serialize this will break.
html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en" does not look like a valid URI, trying to serialize this will break.
Could not load extension schema https://schema.org/docs/schema_org_rdfa.html: RDFa parsing Error! mismatched tag: line 21, column 2
Workflow checker warning:
https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/master/workflows/download-fastq/download-fastq.cwl:12:5: Source 'nthreads'
of type ["null",
"int"] may be
incompatible
https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/master/workflows/download-fastq/download-fastq.cwl:39:7: with sink
'nthreads' of type
"int"
https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/master/workflows/download-fastq/download-fastq.cwl:17:5: Source 'repo' of
type ["null",
"string"] may be
incompatible
https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/master/workflows/download-fastq/download-fastq.cwl:31:7: with sink 'repo'
of type "string"
[workflow ] initialized from https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/master/workflows/download-fastq/download-fastq.cwl
[workflow ] start
[workflow ] {
"run_ids": [
"SRR12594136"
],
"repo": "ebi",
"nthreads": 4
}
[workflow ] job step https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/master/workflows/download-fastq/download-fastq.cwl#pfastq_dump not ready
[workflow ] starting step download_sra
[job step download_sra] job input {
"https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/master/workflows/download-fastq/download-fastq.cwl#download_sra/repo": "ebi",
"https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/master/workflows/download-fastq/download-fastq.cwl#download_sra/run_ids": [
"SRR12594136"
]
}
[job step download_sra] evaluated job input to {
"https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/master/workflows/download-fastq/download-fastq.cwl#download_sra/repo": "ebi",
"https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/master/workflows/download-fastq/download-fastq.cwl#download_sra/run_ids": [
"SRR12594136"
]
}
[step download_sra] start
[job download_sra] initializing from https://github.com/pitagora-network/pitagora-cwl/raw/master/tools/download-sra/download-sra.cwl as part of step download_sra
[job download_sra] {
"repo": "ebi",
"run_ids": [
"SRR12594136"
]
}
[job download_sra] path mappings is {}
[job download_sra] command line bindings is [
{
"position": [
-1000000,
0
],
"datum": "download-sra"
},
{
"position": [
1,
"repo"
],
"prefix": "-r",
"datum": "ebi"
},
{
"position": [
2,
"run_ids"
],
"datum": [
"SRR12594136"
]
},
{
"position": [
2,
"run_ids",
0,
0,
"run_ids",
"run_ids"
],
"datum": "SRR12594136"
}
]
[job download_sra] initial work dir {}
[job download_sra] /tmp/9id49viu$ docker \
run \
-i \
--volume=/tmp/9id49viu:/ogbbFJ:rw \
--volume=/tmp/ynpu5y_9:/tmp:rw \
--workdir=/ogbbFJ \
--read-only=true \
--user=10011:10000 \
--rm \
--env=TMPDIR=/tmp \
--env=HOME=/ogbbFJ \
--cidfile=/tmp/71xe8q60/20200912103727-306707.cid \
quay.io/inutano/download-sra:0.2.1 \
download-sra \
-r \
ebi \
SRR12594136
--2020-09-12 01:37:29-- ftp://ftp.sra.ebi.ac.uk/vol1/srr/SRR125/SRR12594136
=> 'SRR12594136.sra'
Resolving ftp.sra.ebi.ac.uk... 193.62.197.74
Connecting to ftp.sra.ebi.ac.uk|193.62.197.74|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done. ==> PWD ... done.
==> TYPE I ... done. ==> CWD (1) /vol1/srr/SRR125 ... done.
==> SIZE SRR12594136 ... done.
==> PASV ... done. ==> RETR SRR12594136 ...
No such file 'SRR12594136'.
[job download_sra] Max memory used: 0MiB
[job download_sra] completed permanentFail
[job download_sra] {
"sraFiles": [
{
"location": "file:///tmp/9id49viu/SRR12594136.sra",
"basename": "SRR12594136.sra",
"nameroot": "SRR12594136",
"nameext": ".sra",
"class": "File",
"checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
"size": 0,
"http://commonwl.org/cwltool#generation": 0
}
]
}
[step download_sra] produced output {
"https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/master/workflows/download-fastq/download-fastq.cwl#download_sra/sraFiles": [
{
"location": "file:///tmp/9id49viu/SRR12594136.sra",
"basename": "SRR12594136.sra",
"nameroot": "SRR12594136",
"nameext": ".sra",
"class": "File",
"checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
"size": 0,
"http://commonwl.org/cwltool#generation": 0
}
]
}
[step download_sra] completed permanentFail
[job download_sra] Removing input staging directory /tmp/21apo9gn
[job download_sra] Removing temporary directory /tmp/ynpu5y_9
[workflow ] completed permanentFail
[workflow ] {
"fastq_files": null
}
{
"fastq_files": null
}
Final process status is permanentFail
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment