Trimmomatic Error: Unable to detect quality encoding
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0
Entering edit mode
4.3 years ago

Hi,

I am having trouble deciphering why I am getting this error using trimmomatic. I did not have this error before, so I am confused as to why it is occurring. Trimmomatic works for some of the samples, but it does not work with the rest of the samples. This is my code:

rule trim_illumina_Adaptors_fastqs:


And this is my error message:

[Fri Jul 27 15:28:04 2018] rule trim_illumina_Adaptors_fastqs:
[Fri Jul 27 15:28:04 2018] jobid: 0
[Fri Jul 27 15:28:04 2018] wildcards: ds=OM015_2014-09-10

TrimmomaticPE: Started with arguments:
Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
Error: Unable to detect quality encoding
[Fri Jul 27 15:28:05 2018] Error in rule trim_illumina_Adaptors_fastqs:
[Fri Jul 27 15:28:05 2018] jobid: 0

[Fri Jul 27 15:28:05 2018] RuleException:
[Fri Jul 27 15:28:05 2018] CalledProcessError in line 144 of /pine/scr/p/a/parkz/TROUBLESHOOTING/Pv_R_ASAPandCMP_3/Pv_Snaligner.py:
[Fri Jul 27 15:28:05 2018] File "/pine/scr/p/a/parkz/TROUBLESHOOTING/Pv_R_ASAPandCMP_3/Pv_Snaligner.py", line 144, in __rule_trim_illumina_Adaptors_fastqs
[Fri Jul 27 15:28:05 2018] File "/proj/ideel/apps/linuxbrew/opt/python/lib/python3.7/concurrent/futures/thread.py", line 57, in run
[Fri Jul 27 15:28:05 2018] Shutting down, this might take some time.
[Fri Jul 27 15:28:05 2018] Exiting because a job execution failed. Look above for error message


This seems to be the problem:

Error: Unable to detect quality encoding


But I am unable to diagnose the problem with my limited background in coding.

Whether I send the script off as a job on the cluster or I modify the script and run it on the command line, I still get the same error.

Does anyone have any suggestions?

Thank you!

alignment genome sequencing next-gen • 4.1k views
0
Entering edit mode

Hello,

could you please post the fastq data for the first few reads? We should check how the quality values look like.

fin swimmer

1
Entering edit mode
4.3 years ago
h.mon 34k

Trimmomatic uses the first few thousand reads to guess the Phred encoding of the file, looking for unique characters from the Phred+33 or Phred+64 set. If it can't find, it will throw this error. You can pass the encoding on the command-line with the parameters -phred33 or -phred64.