Possibly inconsistent validation error due to read order #126
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Hi Boas, Did you manage to resolve this issue? I have a colleague who has the same error message cropping up on certain files (forward and reverse) from certain runs. Validation of the sequencing files with external tools did not find any obvious reason for the error, nor did uploading a Phred-score-30 subset of the original files. |
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Hi, @wolthuisr and I are in touch with the ENA helpdesk through email, but so far we haven't been able to upload some files without manually changing them. Does the upload or webin-cli |
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@wolthuisr and I have been trying to validate an upload using the Webin-CLI .jar file for v7.2.1 and v7.3.0, but for some files we get inconsistent errors if the first read pair contains a lot of Ns.
We attached two tiny read sets to illustrate this:
badread_first_R1.fq.gzandbadread_first_R2.fq.gz, where the read pair with many Ns in R2 is listed firstbadread_first_R1.fq.gz
badread_first_R2.fq.gz
badread_last_R1.fq.gzandbadread_last_R2.fq.gz, where the read pair with many Ns in R2 is listed lastbadread_last_R1.fq.gz
badread_last_R2.fq.gz
Only the ordering of the reads differs between these read sets, but badread_first fails the validation with a
ReadsValidationException: Reads must contain only valid IUPAC codes, with no more than 50% of bases being non-AUTCG, while badread_last does not raise this error.The log of our validate commands:
ena_upload_log.txt
Could you please check whether this is intended behaviour and if you have a possible solution for this? Many thanks in advance!
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