Hi, I have a problem with using both usegalaxy.org and usegalaxy.eu, and i have no more ideas how to overcome it.
I use the standard pipeline fastq-dump > Trimmomatic > BWA-MEM … Some time ago it stopped working for collections.
I have established that fastq-dump generates now list of pairs and BWA-MEM results in error if the workflow is used. Manually, BWA-MEM works on such collection, however, it results in two separate BAM files, and I suppose that alignments were performed separately for left and right ends. I tried all the variants of inputs. Earlier, fastq-dump from SRR list resulted in collection of single Fastq files for paired-end experiments, and no such issue happened.
I tried to use list with 5 SRRs that I have already tested long ago, but, I obtained novel error - fastq-dump generated empty list.
Single SRR retrieval works perfectly.
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@Zimenkov is it possible that you share a history with us? Thanks!
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