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### Description of the bug
When using circdna with AmpliconArchitect for a already aligned BAM file, i ran into the following problem:
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Acces…
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Hi Jens,
When I run command:
python /home/programs/AmpliconArchitect-master/src/amplified_intervals.py --ref hg19 --bed /home/output//048_D.clean.sorted.dupmark.merged_CNV_CALLS_pre_filtered.bed…
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## Command
/xxx/software/miniconda3/bin/python3 /xxx/software/AmpliconSuite-pipeline/PrepareAA.py -s xxx -t 10 --cnvkit_dir /xxx/software/cnvkit/cnvkit.py --bam /xxx/bam/xxx.marked.realigned.recal.ba…
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### Description of the bug
I am running circdna with the following command:
`nextflow run nf-core/circdna --input samplesheet_bam.csv --outdir ./output --genome mm10 -profile singularity --circle_id…
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### Description of the bug
Running the following command:
> nextflow run nf-core/circdna -r 1.0.1 --input samplesheet_bam.csv --outdir ./output --genome mm10 -profile singularity --circle_identifier…
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### Description of the bug
The pipeline runs through without problems (on the HPC cluster), but then at the cnvkit step it crashes, saying the file 'GRCh37_cnvkit_filtered_ref.cnn' doesn't exist. It …
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Hello! I have been trying to run the pipeline these days but have not worked it out. I believe the problem was because of the reference genome since the error is "Could not match BAM to a known AA ref…
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Dear AmpliconArchitect Team,
l running AA to create a PDF file that displays the underlying sequence signatures of the amplicon, but my PDF file does not contain different arcs, and my command is as …
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hi,l am running AA, and my commend is:
Commandline: ./software/AmpliconArchitect/src/AmpliconAbed ./cnvkit/skmes1_noref/cnv_5_d.bed
--bam ./skmes1_pe_redup.bam --sensitivems False --ref …
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### Description of the bug
Hi, I ran circdna pipeline on bam files using identifier circle_finder, it broken with exit status 140 while `executing process > 'NFCORE_CIRCDNA:CIRCDNA:SAMTOOLS_SORT_QNAM…