Trimmomatic FileNotFoundException

Question

[awhale01]

Hi, I am trying to run TrimmomaticPE as part of a workflow. I have ended up feeding my short reads directly from the input params, so I know they exist, and have given them full paths, however, Trimmomatic still has a file not found exception being thrown. I'm not sure what else to try. Any help is appreciated.

Thank you!

Error executing process > 'trimSR (Trimmomatic on Short Reads)'

Caused by:
  Process `trimSR (Trimmomatic on Short Reads)` terminated with an error exit status (1)

Command executed:

  java -jar /Trimmomatic-0.39/trimmomatic-0.39.jar PE -threads 4 /home/ahale/ProjData/testing/sr/00-473_S9_L001_R1_001.fastq.gz /home/ahale/ProjData/testing/sr/00-473_S9_L001_R2_001.fastq.gz -baseout 00-473.fastq.gz SLIDINGWINDOW:10:20 MINLEN:100 > 00-473.trim.stats.txt

Command exit status:
  1

Command output:
  (empty)

Command error:
  WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
  TrimmomaticPE: Started with arguments:
   -threads 4 /home/ahale/ProjData/testing/sr/00-473_S9_L001_R1_001.fastq.gz /home/ahale/ProjData/testing/sr/00-473_S9_L001_R2_001.fastq.gz -baseout 00-473.fastq.gz SLIDINGWINDOW:10:20 MINLEN:100
  Using templated Output files: 00-473_1P.fastq.gz 00-473_1U.fastq.gz 00-473_2P.fastq.gz 00-473_2U.fastq.gz
  Exception in thread "main" java.io.FileNotFoundException: /home/ahale/ProjData/testing/sr/00-473_S9_L001_R1_001.fastq.gz (No such file or directory)
    at java.base/java.io.FileInputStream.open0(Native Method)
    at java.base/java.io.FileInputStream.open(FileInputStream.java:219)
    at java.base/java.io.FileInputStream.<init>(FileInputStream.java:157)
    at org.usadellab.trimmomatic.fastq.FastqParser.parse(FastqParser.java:135)
    at org.usadellab.trimmomatic.TrimmomaticPE.process(TrimmomaticPE.java:265)
    at org.usadellab.trimmomatic.TrimmomaticPE.run(TrimmomaticPE.java:555)
  rk dirat org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:80)

Work dir:
  /home/ahale/ProjData/testing/work/19/a406d0c75058cf5ede19c14ed674ee

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

[Mensur Dlakic]

Computers have no sense of humor, and yours will not say that the file is not there just to prank you. Either the file isn't there, or it can't be read.

What is the output of these commands?

file /home/ahale/ProjData/testing/sr/00-473_S9_L001_R1_001.fastq.gz
ls -al /home/ahale/ProjData/testing/sr/00-473_S9_L001_R1_001.fastq.gz

[awhale01]

So for file I get:

 the path followed by its filetype, its name, and when it was last modified

As for ls -la:

rwxrwxrwx 1 ahale ahale.

[Mensur Dlakic]

This doesn't answer the question. Please paste the whole screen output of the above two commands. By this I mean not of the command ls -la but instead of:

ls -al /home/ahale/ProjData/testing/sr/00-473_S9_L001_R1_001.fastq.gz

[awhale01]

My apologies,

ahale@RSJ_TLP_2:~/ProjData$ ls -al ~/ProjData/testing/sr/00-473_S9_L001_R1_001.fastq.gz 
-rwxrwxrwx 1 ahale ahale 136127308 Jul 28 16:09 /home/ahale/ProjData/testing/sr/00-473_S9_L001_R1_001.fastq.gz
ahale@RSJ_TLP_2:~/ProjData$ file ~/ProjData/testing/sr/00-473_S9_L001_R1_001.fastq.gz 
/home/ahale/ProjData/testing/sr/00-473_S9_L001_R1_001.fastq.gz: gzip compressed data, was "00-473_S9_L001_R1_001.fastq", last modified: Tue Jun 14 16:36:16 2022, from Unix

[Pierre Lindenbaum]

are you run NF on a cluster ? are the cluster nodes able to see the file ?

can you please add the following lines in your nextflow before invoking java -jar, and re-run nextflow.

set -x
ls -la  /home/
ls -la  /home/ahale/
ls -la  /home/ahale/ProjData/
ls -la  /home/ahale/ProjData/testing/
ls -la  /home/ahale/ProjData/testing/sr/
ls -la  /home/ahale/ProjData/testing/sr/00-473_S9_L001_R1_001.fastq.gz 

[Pierre Lindenbaum]

 /home/ahale/ProjData/testing/sr/00-473_S9_L001_R1_001.fastq.gz (No such file or directory)

Check your path. Can you run ls /home/ahale/ProjData/testing/sr/00-473_S9_L001_R1_001.fastq.gz?