Error while Running Test Example - Consensus Genome #142
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@Samiah-Kanwar Apologies for the slow reply, my colleagues alerted me to this question but I lost track of it in the meantime. Will you please confirm the operating system(s) involved in the environment here? In particular, is Windows involved in some way? The known history of this error message seems related to using Docker on Windows, but it will be interesting if that's not the case here. (Bookmarking source of the error message) |
Hi @mlin thank you for your response. I am using Linux (Ubuntu 21.04), in my case Windows is not involved in any way. The whole system is Linux based. |
@Samiah-Kanwar thanks; this is mysterious, then. Can you post the complete log file? (It should be left behind as |
workflow.log |
@Samiah-Kanwar Thanks, indeed the weird folder name has something to do with it. I can see in the log file that the environment variable
and then We can make some usability improvements in miniwdl to sanity-check the setting of that environment variable so that the error message isn't so confusing. But I can't think of how those control characters could have gotten there. |
Thank you very much @mlin . I tried the command:
And then
I think the error is coming from
Please help me! |
@Samiah-Kanwar Thanks for the update, glad we're at least making progress. I spoke with some of my colleagues today and we think the wiki instructions are probably a little out of date, leading to this problem. We will be going through them to check in the next couple of days and I'll update you here. Sorry for the inconvenience! |
Thank you very much @mlin . Yes and I highly appreciate your efforts. Sure I will be waiting. |
Hi @Samiah-Kanwar thanks for bringing this up, we were missing the |
I successfully installed miniwdl and all other dependencies according to the steps mentioned on GitHub page . Now when I tried to run consensus genome test example using the command:
miniwdl run --verbose consensus-genome/run.wdl docker_image_id=idseq-consensus-genome fastqs_0=idseq-workflows/consensus-genome/test/sample_sars-cov-2_paired_r1.fastq.gz fastqs_1=idseq-workflows/consensus-genome/test/sample_sars-cov-2_paired_r2.fastq.gz sample=sample_sars-cov-2_paired technology=Illumina -i idseq-workflows/consensus-genome/test/local_test.yml
I am getting the following error:
Kindly help me in this regard. I will be available for providing further information
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