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marcelm, cutadapt, untrimpiperfastq, reads, untrimmedoutput, work, sign, pairedend, instance, issue, forwardrfastqgz, reverserfastqgz, interleaved, untrimmed, pairadapters, filefwdtagsfasta, filerevtagsfasta, file, commented, owner, deadlock, ill, opens, navigation, pull, requests, actions, security, piping, cutdapt, closed, opened, instances, option, dont, files, ive, inputrfastqgz, inputrfastq, error, command, doesnt, fix, process, writing, waits, side, didnt, bba, development,

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untrimmed-output/--untrimmed-paired-output options demultiplex paired-end reads trimming paired-end reads interleaved --untrimmed-output untrimmed reads marcelm closed comment metadata assignees untrimmed-output output files reverse_r1 fastq cutadapt open short-output long-output trim adapters reads 3bb88a2 sign cutadapt interleaved option separate files mkfifo untrim_pipe_r1 issue fastq untrim_pipe_r2 interleaved file revcomp option perfectly fine process opens fifo blocks chlige added assigned labels labels projects projects milestone milestone relationships fastq & wait side opens opened fix interleaving �user error” development version github ll investigate deadlock occurs command doesn r1 file r2 file untrim_pipe_r2 untrim_pipe_r1 reverse_r1 gz fastq error

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DiscussionForumPosting:
      context:https://schema.org
      headline:Piping untrimmed paired-end reads to another instance of cutdapt
      articleBody:Cutadapt 2.8 with Python 3.6.7 installed via conda I'm trying to pipe together different instances of cutadapt to trim adapters and demultiplex paired-end reads which may be in either orientation. I'm aware of the --revcomp option, but I don't want to use it because I'd prefer to keep the two orientations in separate files, because I will treat them somewhat differently later in the pipeline. Here's what I've tried: ```bash mkfifo untrim_pipe_R1.fastq untrim_pipe_R2.fastq cutadapt \ --pair-adapters\ -a file:fwd_tags.fasta\ -A file:rev_tags.fasta\ -o forward_R1.fastq.gz\ -p forward_R2.fastq.gz\ --untrimmed-output untrim_pipe_R1.fastq \ --untrimmed-paired-output untrim_pipe_R2.fastq \ input_R1.fastq.gz \ input_R2.fastq.gz & cutadapt \ --pair-adapters\ -a file:fwd_tags.fasta\ -A file:rev_tags.fasta\ -o reverse_R2.fastq.gz\ -p reverse_R1.fastq.gz\ untrim_pipe_R2.fastq \ untrim_pipe_R1.fastq & wait ``` However, no reads are processed. The output files `reverse_R1.fastq.gz` and `reverse_R2.fastq.gz` are created (with no contents), but not `forward_R1.fastq.gz` and `forward_R2.fastq.gz`. I assume the problem is that the second instance of cutadapt is waiting for input on `untrim_pipe_R2.fastq` while the first instance is trying to write to `untrim_pipe_R1.fastq`, so both are blocking. Using an interleaved file, with a script between the two instances to switch the order of the reads, might be a solution, but it appears that this isn't supported for the untrimmed reads: ```bash cutadapt \ --pair-adapters\ --interleaved\ -a file:fwd_tags.fasta\ -A file:rev_tags.fasta\ -m 1\ -o forward.fastq.gz\ --untrimmed-output untrim.fastq\ input_R1.fastq input_R2.fastq ``` ``` cutadapt: error: When trimming paired-end reads, you must use either none or both of the --untrimmed-output/--untrimmed-paired-output options. ```
      author:
         url:https://github.com/brendanf
         type:Person
         name:brendanf
      datePublished:2020-03-25T16:54:13.000Z
      interactionStatistic:
         type:InteractionCounter
         interactionType:https://schema.org/CommentAction
         userInteractionCount:3
      url:https://github.com/450/cutadapt/issues/450
      context:https://schema.org
      headline:Piping untrimmed paired-end reads to another instance of cutdapt
      articleBody:Cutadapt 2.8 with Python 3.6.7 installed via conda I'm trying to pipe together different instances of cutadapt to trim adapters and demultiplex paired-end reads which may be in either orientation. I'm aware of the --revcomp option, but I don't want to use it because I'd prefer to keep the two orientations in separate files, because I will treat them somewhat differently later in the pipeline. Here's what I've tried: ```bash mkfifo untrim_pipe_R1.fastq untrim_pipe_R2.fastq cutadapt \ --pair-adapters\ -a file:fwd_tags.fasta\ -A file:rev_tags.fasta\ -o forward_R1.fastq.gz\ -p forward_R2.fastq.gz\ --untrimmed-output untrim_pipe_R1.fastq \ --untrimmed-paired-output untrim_pipe_R2.fastq \ input_R1.fastq.gz \ input_R2.fastq.gz & cutadapt \ --pair-adapters\ -a file:fwd_tags.fasta\ -A file:rev_tags.fasta\ -o reverse_R2.fastq.gz\ -p reverse_R1.fastq.gz\ untrim_pipe_R2.fastq \ untrim_pipe_R1.fastq & wait ``` However, no reads are processed. The output files `reverse_R1.fastq.gz` and `reverse_R2.fastq.gz` are created (with no contents), but not `forward_R1.fastq.gz` and `forward_R2.fastq.gz`. I assume the problem is that the second instance of cutadapt is waiting for input on `untrim_pipe_R2.fastq` while the first instance is trying to write to `untrim_pipe_R1.fastq`, so both are blocking. Using an interleaved file, with a script between the two instances to switch the order of the reads, might be a solution, but it appears that this isn't supported for the untrimmed reads: ```bash cutadapt \ --pair-adapters\ --interleaved\ -a file:fwd_tags.fasta\ -A file:rev_tags.fasta\ -m 1\ -o forward.fastq.gz\ --untrimmed-output untrim.fastq\ input_R1.fastq input_R2.fastq ``` ``` cutadapt: error: When trimming paired-end reads, you must use either none or both of the --untrimmed-output/--untrimmed-paired-output options. ```
      author:
         url:https://github.com/brendanf
         type:Person
         name:brendanf
      datePublished:2020-03-25T16:54:13.000Z
      interactionStatistic:
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         interactionType:https://schema.org/CommentAction
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      url:https://github.com/450/cutadapt/issues/450
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      url:https://github.com/brendanf
      name:brendanf
      url:https://github.com/brendanf
      name:brendanf
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