cutadapt: error: unrecognized arguments: -f

[samsharr]

Hi, I am running the command trim_galore --paired 2_KC6141-WT_S112_R1_001.fastq.gz 2_KC6141-WT_S112_R2_001.fastq.gz but I keep getting the error:

No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default)

Path to Cutadapt set as: 'cutadapt' (default) 3.4 Cutadapt seems to be working fine (tested command 'cutadapt --version')

AUTO-DETECTING ADAPTER TYPE

Attempting to auto-detect adapter type from the first 1 million sequences of the first file (>> 2_KC6141-WT_S112_R1_001.fastq.gz <<)

Found perfect matches for the following adapter sequences: Adapter type Count Sequence Sequences analysed Percentage Illumina 69762 AGATCGGAAGAGC 1000000 6.98 smallRNA 4 TGGAATTCTCGG 1000000 0.00 Nextera 4 CTGTCTCTTATA 1000000 0.00 Using Illumina adapter for trimming (count: 69762). Second best hit was smallRNA (count: 4)

Writing report to '2_KC6141-WT_S112_R1_001.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS

Input filename: 2_KC6141-WT_S112_R1_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 3.4 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to 2_KC6141-WT_S112_R1_001_trimmed.fq.gz

Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file 2_KC6141-WT_S112_R1_001.fastq.gz <<< This is cutadapt 3.4 with Python 3.6.8 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC 2_KC6141-WT_S112_R1_001.fastq.gz Run "cutadapt --help" to see command-line options. See https://cutadapt.readthedocs.io/ for full documentation.

cutadapt: error: unrecognized arguments: -f 2_KC6141-WT_S112_R1_001.fastq.gz

Cutadapt terminated with exit signal: '512'. Terminating Trim Galore run, please check error message(s) to get an idea what went wrong...

[FelixKrueger]

As a first step, could I ask you to upgrade to the latest version (v0.6.7) and see if you have the same issues?

[samsharr]

Thank you Felix. I believe it’s running now. Will let you know once the process is completed.

Thanks again for your prompt response.

Regards, Samantha

From: Felix Krueger @.> Date: Wednesday, March 2, 2022 at 3:29 PM To: FelixKrueger/TrimGalore @.> Cc: Sharma, Samantha @.>, Author @.> Subject: [External] Re: [FelixKrueger/TrimGalore] cutadapt: error: unrecognized arguments: -f (Issue #128) This message was sent from a non-IU address. Please exercise caution when clicking links or opening attachments from external sources.

As a first step, could I ask you to upgrade to the latest version (v0.6.7) and see if you have the same issues?

— Reply to this email directly, view it on GitHubhttps://github.com/FelixKrueger/TrimGalore/issues/128#issuecomment-1057347535, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AYBA5M7FKTQEW7I6QM5YTE3U57FQ5ANCNFSM5PYQK6OQ. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub. You are receiving this because you authored the thread.Message ID: @.***>

[samsharr]

Hi Felix,

Wanted to update you that the issue was resolved with the updates version.

Thank you for your assistance, Samantha Sharma

From: Sharma, Samantha @.> Date: Wednesday, March 2, 2022 at 4:28 PM To: FelixKrueger/TrimGalore @.>, FelixKrueger/TrimGalore @.> Cc: Author @.> Subject: Re: [External] Re: [FelixKrueger/TrimGalore] cutadapt: error: unrecognized arguments: -f (Issue #128) Thank you Felix. I believe it’s running now. Will let you know once the process is completed.

Thanks again for your prompt response.

Regards, Samantha

From: Felix Krueger @.> Date: Wednesday, March 2, 2022 at 3:29 PM To: FelixKrueger/TrimGalore @.> Cc: Sharma, Samantha @.>, Author @.> Subject: [External] Re: [FelixKrueger/TrimGalore] cutadapt: error: unrecognized arguments: -f (Issue #128) This message was sent from a non-IU address. Please exercise caution when clicking links or opening attachments from external sources.

As a first step, could I ask you to upgrade to the latest version (v0.6.7) and see if you have the same issues?

— Reply to this email directly, view it on GitHubhttps://github.com/FelixKrueger/TrimGalore/issues/128#issuecomment-1057347535, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AYBA5M7FKTQEW7I6QM5YTE3U57FQ5ANCNFSM5PYQK6OQ. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub. You are receiving this because you authored the thread.Message ID: @.***>

[FelixKrueger]

Excellent, glad it all works now!