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TypeError _call_() takes 3 positional arguments but 5 were given #393

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SusanaFreitas opened this issue Aug 8, 2019 · 5 comments

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@SusanaFreitas
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commented Aug 8, 2019

Dear all
I am trying to run cutadapt with the command below but I keep getting the same error:
TypeErrror: call() takes 3 positional arguments but 5 were given.
The cutadapt and python versions are:
cutadapt version 2.4
python 3.7.2

I am using cutadapt on the university server and it was installed by the IT team (we upload it via module system).
I found this issue here:
#203
so I tried to remove all possible options, but I always get the same error.
Do you think you could help??

Thanks!!!

cutadapt -b GATCGGAAGAGCACACGTCTGAACTCCAGTCAC -b ATCTCGTATGCCGTCTTCTGCTTG -B AATGATACGGCGACCACCGAGATCTACAC -B ACACTCTTTCCCTACACGACGCTCTTCCGATCT -e 0.2 -n 3 --discard-trimmed --info-file read1.txt -q 20 -m 40 -o read1-trimmed1.fastq.gz -p read2-trimmed2.fastq.gz AH3TLYBBXX_lane4-s324-index--CACCTTAC-CTTCGCCT-84-505_S324_L004_R1_001.fastq.gz AH3TLYBBXX_lane4-s324-index--CACCTTAC-CTTCGCCT-84-505_S324_L004_R2_001.fastq.gz

@marcelm

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commented Aug 8, 2019

Can you please post the full error message? (Not only the last line with the TypeError?)

@SusanaFreitas

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commented Aug 8, 2019

Here it is:

This is cutadapt 2.4 with Python 3.7.2
Command line parameters: -b GATCGGAAGAGCACACGTCTGAACTCCAGTCAC -b ATCTCGTATGCCGTCTTCTGCTTG -B AATGATACGGCGACCACCGAGATCTACAC -B ACACTCTTTCCCTACACGACGCTCTTCCGATCT -e 0.2 -n 3 --discard-trimmed --info-file read1.txt -q 20 -m 40 -o read1-trimmed1.fastq.gz -p read2-trimmed2.fastq.gz AH3TLYBBXX_lane4-s324-index--CACCTTAC-CTTCGCCT-84-505_S324_L004_R1_001.fastq.gz AH3TLYBBXX_lane4-s324-index--CACCTTAC-CTTCGCCT-84-505_S324_L004_R2_001.fastq.gz
Processing reads on 1 core in paired-end mode ...
Traceback (most recent call last):
File "/mnt/software/.local/easybuild/software/lang/Python/3.7.2/bin/cutadapt", line 10, in
sys.exit(main())
File "/mnt/software/.local/easybuild/software/lang/Python/3.7.2/lib/python3.7/site-packages/cutadapt/main.py", line 848, in main
stats = runner.run()
File "/mnt/software/.local/easybuild/software/lang/Python/3.7.2/lib/python3.7/site-packages/cutadapt/pipeline.py", line 737, in run
(n, total1_bp, total2_bp) = self._pipeline.process_reads(progress=self.progress)
File "/mnt/software/.local/easybuild/software/lang/Python/3.7.2/lib/python3.7/site-packages/cutadapt/pipeline.py", line 331, in process_reads
if filter
(read1, read2, matches1, matches2):
TypeError: call() takes 3 positional arguments but 5 were given

@marcelm

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commented Aug 8, 2019

Thanks, I’ll look into this. It appears that using --info-file is the problem here.

marcelm added a commit that referenced this issue Aug 8, 2019

@marcelm marcelm closed this in c05a870 Aug 9, 2019

@marcelm

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commented Aug 9, 2019

I’ve fixed the crash. The problem was that the --info-file option did not work when processing paired-end data. Note that in the fixed version, the info file will still only contain data about R1, and everything that happens to R2 will simply be ignored. That is, there is at the moment no --paired-info-file option or similar. If you are interested in that, please file a new issue!

And for completeness: The same crash would also have occurred for the options --wildcard-file and --rest-file. This has also been fixed.

If you want to test this, please install the development version of Cutadapt.

@SusanaFreitas

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commented Aug 9, 2019

Thanks!!
I tried without the --info-file option and it worked.

Best
Susana

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