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straightlab / charseq-pipelines

Pipelines to process raw ChAR-seq data
MIT License
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Missing file remove_short_reads_SE #1

Open jadeenright opened 2 years ago

jadeenright commented 2 years ago

Can't run remove_short_reads_SE step because we are missing filter_short_reads_pairs.sh.

climouse commented 2 years ago

Hi @jadeenright , Thanks, I added the missing script to the companion chartools-dev repo. Let me know if it works. FYI this repo is under active dev. The pipeline works but we are working on testing/improving portability. A more detailed documentation of the installation and run steps will also come out soon.

jadeenright commented 2 years ago

Hi! Thank you, that did work. We are now experiencing the following error message: "Error in job decon_RNA_SE while creating output files Charseq_pilot_R2/split_chimeras/SE_merge_pear/long.decon/rna.fastq.gz, Charseq_pilot_R2/split_chimeras/SE_merge_pear/long.contaminants/rna.fastq.gz, Charseq_pilot_R2/split_chimeras/SE_merge_pear/long.contaminants/rna.bam, Charseq_pilot_R2/split_chimeras/SE_merge_pear/long.contaminants/rna.stats.txt. RuleException: CalledProcessError in line 267 of /Volumes/Sequencing_Data/Jade/pipeline.smk: Command ' bowtie2 -p 1 -q --very-sensitive --norc -x /Volumes/Sequencing_Data/Jade/GRCm39/annotations_musbase/bowtie_rRNA/rRNA --rg-id Charseq_pilot_R2:SE_merge_pear/long/rna --rg SM:Charseq_pilot_R2 -U Charseq_pilot_R2/split_chimeras/SE_merge_pear/long/rna.fastq.gz 2>Charseq_pilot_R2/split_chimeras/SE_merge_pear/long.contaminants/rna.stats.txt | picard SortSam I=/dev/stdin O=Charseq_pilot_R2/split_chimeras/SE_merge_pear/long.contaminants/rna.bam SORT_ORDER=queryname && bash /Volumes/Sequencing_Data/Jade/decon_reads_pairs.sh Charseq_pilot_R2/split_chimeras/SE_merge_pear/long/rna.fastq.gz Charseq_pilot_R2/split_chimeras/SE_merge_pear/long.contaminants/rna.bam rna Charseq_pilot_R2/split_chimeras/SE_merge_pear/long 1 ' returned non-zero exit status 1. File "/Volumes/Sequencing_Data/Jade/pipeline.smk", line 267, in __rule_decon_RNA_SE File "/opt/anaconda3/envs/charseq/lib/python3.6/concurrent/futures/thread.py", line 56, in run Removing output files of failed job decon_RNA_SE since they might be corrupted: Charseq_pilot_R2/split_chimeras/SE_merge_pear/long.contaminants/rna.bam, Charseq_pilot_R2/split_chimeras/SE_merge_pear/long.contaminants/rna.stats.txt Will exit after finishing currently running jobs. Exiting because a job execution failed. Look above for error message"

Which we then determine is caused by: "Error: Read A00325:476:HHWTJDSX3:2:1523:4508:24706 1:N:0:CATGTGACTG+ATGCGGATCC has more quality values than read characters. libc++abi: terminating with uncaught exception of type int (ERR): bowtie2-align died with signal 6 (ABRT)"

We'd appreciate any help you could give with this, thank you!