Cutadapt doesn't seem to recognize adapter specific parameters

Question

[kyusikkim]

Hello all! I'm using cutadapt 3.4 via Docker. (quay.io/biocontainers/cutadapt:3.4--py37h73a75cf_1) on a cluster

I'm trying to trim specific adapters from my paired end read files. For some reason, Cutadapt doesn't seem to recognize the adapter specific error parameters. Here is my command below

cutadapt -j 8 -a "CTGTAGGCACCATCAAT;max_error_rate=0.1;min_overlap=12" --discard-untrimmed -o "$dir"/r1.fastq.gz -p "$dir"/r2.fastq.gz "$dir"/F.fastq.gz "$dir"/R.fastq.gz


> 3.4--py37h73a75cf_1: Pulling from biocontainers/cutadapt cefc4d495539: Pulling fs layer 4ca545ee6d5d: Pulling fs layer 07a90f10ce03: Pulling
> fs layer 4ca545ee6d5d: Waiting cefc4d495539: Verifying Checksum
> cefc4d495539: Download complete 4ca545ee6d5d: Verifying Checksum
> 4ca545ee6d5d: Download complete cefc4d495539: Pull complete
> 4ca545ee6d5d: Pull complete Traceback (most recent call last):   File
> "/opt/ibm/lsfsuite/lsf/10.1/linux2.6-glibc2.3-x86_64/etc/docker1_monitor.py",
> line 379, in <module>
>     main(sys.argv[1:])   File "/opt/ibm/lsfsuite/lsf/10.1/linux2.6-glibc2.3-x86_64/etc/docker1_monitor.py",
> line 372, in main
>     if driverMonitor.start_monitor() < 0 :   File "/opt/ibm/lsfsuite/lsf/10.1/linux2.6-glibc2.3-x86_64/etc/docker1_monitor.py",
> line 163, in start_monitor
>     if self.__collect_rusage() < 0 :   File "/opt/ibm/lsfsuite/lsf/10.1/linux2.6-glibc2.3-x86_64/etc/docker1_monitor.py",
> line 194, in __collect_rusage
>     self.log.debug("Couldn't read container UUID from %s: %s" % ( self.uuidFile, e )) NameError: global name 'e' is not defined
> 07a90f10ce03: Verifying Checksum 07a90f10ce03: Download complete
> 07a90f10ce03: Pull complete Digest:
> sha256:12e96e635cf387b7969a2cfefadfe79d893bb3ad33cb03dc500451900111a6dc
> Status: Downloaded newer image for
> quay.io/biocontainers/cutadapt:3.4--py37h73a75cf_1
> quay.io/biocontainers/cutadapt:3.4--py37h73a75cf_1 This is cutadapt
> 3.4 with Python 3.7.10 Command line parameters: -j 8 -a CTGTAGGCACCATCAAT Run "cutadapt --help" to see command-line options.
> See https://cutadapt.readthedocs.io/ for full documentation.
> 
> cutadapt: error: You did not provide any input file names. Please give
> me something to do! line 8: --discard-untrimmed: command not found

Any ideas and help would be greatly appreciated!

[cpad0112]

Seems you are using cutadapt docker. I have tried the function you posted with local cutadapt (v 3.4; python 3.8 conda on debian 11) and no issues with function (command) per se. However, please check the part of " cutadapt: error: You did not provide any input file names"

[kyusikkim]

Cutadapt works fine and as intended without the adapter specific parameter. It’s only when I add it that it stops working

[cpad0112]

I tested as posted in OP. Didn't change a thing and it worked.

[kyusikkim]

Maybe it's something to do with docker then. I'll do some testing by moving the quotation marks around

Answer 1

[kyusikkim]

Solved. Needed to add quotation marks around the -a parameter as below

"-a CTGTAGGCACCATCAAT;max_error_rate=0.1;min_overlap=12"

Not sure why. If anyone would like to comment, please do :)