cutadapt: error: unrecognized arguments: -f P2_A01_M_0001.fastq Cutadapt terminated with exit signal: '512'.

[sevmurdock]

I keep getting the same error messages cutadapt: error: unrecognized arguments: -f P2_A01_M_0001.fastq Cutadapt terminated with exit signal: '512'.

This is my origional code trim_galore -q 30 --phred33 --gzip --length 36 --fastqc P2_A01_M_0001.fastq -o trimmed_reads_P2

I even tried just running trim_galore P2_A01_M_0001.fastq -o trimmed_reads_P2 and I am still getting the same error messages.

Run information shown below ....

Minimum required sequence length before a sequence gets removed: 36 bp Running FastQC on the data once trimming has completed Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to P2_A01_M_0001_trimmed.fq.gz

Now performing quality (cutoff 30) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file P2_A01_M_0001.fastq <<< This is cutadapt 4.1 with Python 3.10.5 Command line parameters: -f fastq -e 0.1 -q 30 -O 1 -a AGATCGGAAGAGC P2_A01_M_0001.fastq Run "cutadapt --help" to see command-line options. See https://cutadapt.readthedocs.io/ for full documentation.

cutadapt: error: unrecognized arguments: -f P2_A01_M_0001.fastq

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

[FelixKrueger]

This is very odd indeed, since at no point in your command line I can see the option -f P2_A01_M_0001.fastq.

I just copied your command but changed the input file to a test file that ships with Trim Galore:

trim_galore -q 30 --phred33 --gzip --length 36 --fastqc illumina_10K.fastq.gz -o trimmed_reads_P2

And it completes just fine. My guess would be that something is wrong with --fastqc, maybe you copy-pasted it from a PDF document or something similar where there might be invisible characters somewhere? I would suggest typing the command once more from scratch, and see if the issue is still there....

[sevmurdock]

Thanks !! I will give that a try!!

On Wed, Sep 21, 2022 at 3:19 AM Felix Krueger @.***> wrote:

This is very odd indeed, since at no point in your command line I can see the option -f P2_A01_M_0001.fastq.

I just copied your command but changed the input file to a test file that ships with Trim Galore:

trim_galore -q 30 --phred33 --gzip --length 36 --fastqc illumina_10K.fastq.gz -o trimmed_reads_P2

And it completes just fine. My guess would be that something is wrong with --fastqc, maybe you copy-pasted it from a PDF document or something similar where there might be invisible characters somewhere? I would suggest typing the command once more from scratch, and see if the issue is still there....

— Reply to this email directly, view it on GitHub https://github.com/FelixKrueger/TrimGalore/issues/141#issuecomment-1253500635, or unsubscribe https://github.com/notifications/unsubscribe-auth/AY5656YZX6LQ4CDZO7SBMC3V7LOJPANCNFSM6AAAAAAQQRPOSM . You are receiving this because you authored the thread.Message ID: @.***>

[cbcptdtptp]

Hey, I met exactly the same problem and found that it was because the version 4.1 of cutadapt is not accepted by trim_galore. I installed cutadapt 1.18 and the problem is solved.

[sevmurdock]

Thanks for letting me know. Oddly enough, I think I ran conda update Trim-galore and the problem went away. I will keep this in the back of my mind for my next round of samples that come in.

Warm regards, Savanna

On Wed, Sep 28, 2022 at 6:52 AM cbcptdtptp @.***> wrote:

Hey, I met exactly the same problem and found that it was because the version 4.1 of cutadapt is not accepted by trim_galore. I installed cutadapt 1.18 and the problem is solved.

— Reply to this email directly, view it on GitHub https://github.com/FelixKrueger/TrimGalore/issues/141#issuecomment-1260949111, or unsubscribe https://github.com/notifications/unsubscribe-auth/AY56563HEEIDE6MINGVFIYTWAREQ3ANCNFSM6AAAAAAQQRPOSM . You are receiving this because you authored the thread.Message ID: @.***>