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Getting an error saying E: command failed: CommandException: No URLs matched:
DivyKangeyan
Member, Broadie ✭
I have been updating the bismark_wgbs method configuration in aryee-lab/dna-methylation workspace for visualizing the BAM files. BAM files are generated without a problem but when I try to generate BAM index file with the samtools I am getting the following error.
2018/02/15 17:57:46 I: Running command: sudo gsutil -q -m cp -L /var/log/google-genomics/out.log /mnt/local-disk/8_HL77WBBXX-8-TCCGGAGA_GCCTCTAT.bam.bai gs://fc-6eb91be1-054c-4af6-81d3-1b81d1a94ce6/611b0957-7af6-44d1-a106-ddc0700f1098/call_bismark/573e13ce-7fde-4689-8dc5-ed6f0687152c/call-step1_bismark_wgbs/8_HL77WBBXX-8-TCCGGAGA_GCCTCTAT.bam.bai
2018/02/15 17:57:47 E: command failed: CommandException: No URLs matched: /mnt/local-disk/8_HL77WBBXX-8-TCCGGAGA_GCCTCTAT.bam.bai
CommandException: 1 file/object could not be transferred.
(exit status 1)
I use the samtools to sort the BAM file in the WDL file, it seems to work fine but samtools index is not working
Best Answer
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I think this is because of an old version of samtools, after updating the samtools in docker I was able to generate the bam index file.
Answers
The line that stands out to me most in that error message is:
No URLs matched: /mnt/local-disk/8_HL77WBBXX-8-TCCGGAGA_GCCTCTAT.bam.baiTo me, that indicates that that URL is either incorrect (mistyped, an old link that might've missed being updated, etc.) or the file was supposed to be generated in the workflow, but hasn't because that step failed. Could you double check to verify the file listed above exists where you expect it to, and that it isn't mistyped in any way?
I don't see the bam.bai file in the directory while I see all the other files that should be there. It doesn't look like the bam index file was generated but it is not clear to me why that step failed based on the log file.
One thing that I noticed from exec.sh file is that the line generating the bam index file has additional indentation, I am not sure whether this is the reason for the error. But looks aligned well in my WDL file
These are same lines from my WDL file. @KateN Any idea why the lines would me misaligned in exec.sh and whether this would be the reason for failing to generate the bai file.
I take that back even when the code is aligned correctly I get the error saying No URL matched.
I'm so sorry for the delay; I'm looking into this but I don't yet have an answer for you. Thank you for your patience.
Alright, I think I'm going to need to take a look at the actual workspace. Could you share
aryee-lab/dna-methylationwith[email protected], and also give the submission ID and workflow ID where you see this error?I share the workspace with you. This is one of the workflow ID
02574062-00a7-4c59-89e7-b1ec1ac34b51and submission ID is4c015951-a419-4636-93c8-f616669e956bI have tried running the same workflow locally with cromwell hoping to get more information on this error. But all I get is that the
.baifile couldn't be found and no more information on why it was not generated.I think this is because of an old version of samtools, after updating the samtools in docker I was able to generate the bam index file.
Good to know, thank you for getting back to me! I've had three developers scouring the error readouts to try to figure it out.
@KateN Thank you for the help, convey my gratitude to all the developers working in this problem!