jfy133
commented
2 years ago Output files indicate that this is eager1, so this is the wrong repository. I'll ask @apeltzer if there is a quick answer, but eager1 isn't supported anymore, so no promises... (Sprry)!)
I’m running a sample with EAGER and I want to get no-merged data, following the instructions below: -For the input file upload two Fastq (reads 1 e 2) and select the Single-End Data -General settings: FastQC analysis; Adapter RM/Merging : CLIP&Merge (Perform only adapter clipping); Mapping: CircularMapper; Complexity Estimation; Remove Duplicates with DeDup; Damage calculation with mapDamage; But the analysis dies when trying to remove the duplicates. The .log file reports: SamtoolsSortDeDup was executed with the following commandline: “samtools sort -[@ 10]() -m 3G /../OUTPUT/5-DeDup/file_name.fastq.fq.MT_realigned.mappedonly.sorted.qF.sorted.cleaned_rmdup.bam -o /../ OUTPUT/INPUT/5-DeDup/file_name.fastq.fq.MT_realigned.mappedonly.sorted.qF.sorted.cleaned_rmdup.sorted.bam “ “samtools sort: truncated file. Aborting” Furthermore I can still find the following 10 multiple bam files in the 5-DeDup directory even if they should disappear once the final file(file_name.fastq.fq.MT_realigned.mappedonly.sorted.qF.sorted.cleaned_rmdup.sorted.bam. ) is created: -fastq.fq.MT_realigned.mappedonly.sorted.qF.sorted.cleaned_rmdup.sorted.bam.tmp.0000.bam ( this is an example of one of the 10 files) How can I manage this issue? Should I start again the analysis from the beginning or is there a way to skip the steps that went right? I was also wandering if there is a way to know if the 10 files in the 5-DeDup directory are complete. Lastly, I only manage to get the report file if I run more samples in a row, how can I get it analysing only one file?