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Getting an error saying E: command failed: CommandException: No URLs matched:
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