Bismark mapping with Fatal Error exit

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1

Hello Galaxy EU Admin,

I am using Bismark Mapper for alignment of WGBS reads to Arabidopsis reference genome. I was working well for sample 1-5 (Fig 1), but for later samples (sample 6-8), it started to give an error with only simple detail (Fig 2). Could you suggest some possible reasons for this please?

Fig 1: Mapping that went well with its details (which was the same for the later samples that gave failed mapping)

Fig 1: Mapping that went well with its details (which was the same for the later samples that gave failed mapping)
Fig 1: Mapping that went well with its details (which was the same for the later samples that gave failed mapping)1566×1332 349 KB

Fig 2: Error details given for the later samples, when I used the same setting of Bismark Mapper run.

Fig 2: Error details given for the later samples, when I used the same setting of Bismark Mapper run.
Fig 2: Error details given for the later samples, when I used the same setting of Bismark Mapper run.2080×1328 417 KB

Best regards,

Pannaree

2

It was caused by the data uploading problem (likely files not recognised as fastq, not sure why), so I re-uploaded and it works now.

1 Like
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Great! Glad this worked out and thanks for letting is know.

Loading with all default settings in the Upload tool is usually best. Then you can double check the data loading completion, compression, and intact pair status with a tool like Fastq info.

Then, to review the failure closer, the Error tab is a nice summary but the Details tab has the full output logs (down a bit lower, under the input/parameter table). These include technical messages from the underlying job environment and the tool itself and is usually where to start the review. You can also share your history back here for more specific help when troubleshooting (then unshare after!). :slight_smile:

XRef