Closed sevmurdock closed 2 years ago
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....
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: @.***>
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.
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.
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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
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...