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yyoshiaki / VIRTUS

A bioinformatics pipeline for viral transcriptome detection and quantification considering splicing.
https://github.com/yyoshiaki/VIRTUS/wiki
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create index failed #32

Open km-2021 opened 2 years ago

km-2021 commented 2 years ago

Hello,

I tried to create index, however, the process has failed at the stage to get transcripts.fa. The command and log is as follows:

:~$ createindex.cwl https://raw.githubusercontent.com/yyoshiaki/VIRTUS/master/workflow/createindex.job.yaml INFO /usr/bin/cwltool 2.0.20200224214940 INFO Resolved './VIRTUS/bin/createindex.cwl' to 'file:///home/acc/VIRTUS/bin/createindex.cwl' VIRTUS/bin/createindex.cwl:39:5: object id VIRTUS/bin/createindex.cwl#createindex/salmon_index_human previously defined VIRTUS/bin/createindex.cwl:39:5: object id VIRTUS/bin/createindex.cwl#createindex/salmon_index_human previously defined VIRTUS/bin/createindex.cwl:148:9: object id VIRTUS/bin/createindex.cwl#createindex/salmon_index_human/index previously defined VIRTUS/tool/salmon-cwl/salmon-index.cwl:8:5: object id VIRTUS/tool/salmon-cwl/salmon-index.cwl#index previously defined INFO [workflow ] start INFO [workflow ] starting step wget_transcipt INFO [step wget_transcipt] start INFO [job wget_transcipt] /tmp/m9d6eydr$ docker \ run \ -i \ --mount=type=bind,source=/tmp/m9d6eydr,target=/rElFSG \ --mount=type=bind,source=/tmp/4dll8gk3,target=/tmp \ --workdir=/rElFSG \ --read-only=true \ --user=1000:1000 \ --rm \ --env=TMPDIR=/tmp \ --env=HOME=/rElFSG \ --cidfile=/tmp/hrtpxeac/20211214084330-306019.cid \ inutano/wget:1.20.3-r1 \ wget \ --output-document=gencode.v33.transcripts.fa.gz \ ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_33/gencode.v33.transcripts.fa.gz 2> /tmp/m9d6eydr/wget-stderr.log INFO [job wget_transcipt] Max memory used: 0MiB WARNING [job wget_transcipt] completed permanentFail WARNING [step wget_transcipt] completed permanentFail INFO [workflow ] completed permanentFail { "downloaded_virus": null, "starIndex_virus": null, "starIndex_human": null, "downloaded_genomefasta_human": null, "salmon_index_human": null, "downloaded": { "location": "file:///home/acc/gencode.v33.transcripts.fa.gz", "basename": "gencode.v33.transcripts.fa.gz", "class": "File", "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", "size": 0, "path": "/home/acc/gencode.v33.transcripts.fa.gz" } } WARNING Final process status is permanentFail

Would you mind giving us sdvices?

yyoshiaki commented 2 years ago

Hi!

This looks like an error relating to CWL or docker. Do your docker and CWL work appropriately? For CWL, this conformance test would be helpful. https://www.commonwl.org/v1.2/

km-2021 commented 2 years ago

Hello,

Is this pipeline used by pulling an image from docker hub or by creating a linux-based container and cloning the repository in it?

yyoshiaki commented 2 years ago

Hi,

This pipeline pulls docker images from docker-hub.

km-2021 commented 2 years ago

Thank you for your reply,

Would you mind telling us the name of the docker image to pull?

yyoshiaki commented 2 years ago

As described in each tool file, VIRTUS is using many containers, such as;

What are you concerned about?

km-2021 commented 2 years ago

Thank you for your reply,

In other words, am I correct in understanding that Virtus pipeline works in an environment with multiple containers pulled together? I would appreciate it if you could provide me with the minimum IMAGE required for running VIRTUS.

yyoshiaki commented 2 years ago

No, VIRTUS automatically pulls all required images. For example, how about using another environment such as GCP or AWS for testing VIRTUS?

ruthangelina commented 1 year ago

I'm having the same issue as km-2021.. I ran conformist test. Everything seems to be installed correctly.

yyoshiaki commented 1 year ago

I could not reproduce the situation. Because VIRTUS2 https://github.com/yyoshiaki/VIRTUS2 is not using salmon, one option may be switching to VIRTUS2.

ruthangelina commented 1 year ago

Thanks for your reply. That's odd... This was the same repository I used. I get the same message running the test script... Permanent fail. I thought it was a memory issue, but the same thing happens afterI modifying the RAM In docker

On Fri, Aug 26, 2022, 10:36 PM Yoshiaki Yasumizu @.***> wrote:

I could not reproduce the situation. Because VIRTUS2 https://github.com/yyoshiaki/VIRTUS2 is not using salmon, one option may be switching to VIRTUS2.

— Reply to this email directly, view it on GitHub https://github.com/yyoshiaki/VIRTUS/issues/32#issuecomment-1229104954, or unsubscribe https://github.com/notifications/unsubscribe-auth/AI4VU7HB6S73DDZUQUILHMTV3F5K7ANCNFSM5J7ZQKSQ . You are receiving this because you commented.Message ID: @.***>