Comments (6)
Hi,
What version of AdapterRemoval are you using and what command-line arguments did you use when running it?
from adapterremoval.
Hi,
Thanks for the quick response.
This was a conda install: AdapterRemoval v.2.3.0
Command:
AdapterRemoval --threads 2 --file1 PCS1_S1_L001_R1_001.fastq --file2 PCS1_S1_L001_R2_001.fastq --minalignmentlength 10 --trimns --trimqualities --minquality 20 --collapse --minlength 30 --output1 ./analyis_ready/PCS1.trimmed.R1.fastq --output2 ./analysis_ready/PCS1.trimmed.R2.fastq --outputcollapsed ./analysis_ready/PCS1.trimmed.merged.fastq --settings PCS1_AdapterRemoval.txt --adapter1 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNGCATCTCGTATGCCGTCTTCTGCT --adapter2 AGATCGGAAGAGCGTCGGTAGGGAAAGAGTGTAGTCTGTGGTGTAGATCTCGGTGGTC
from adapterremoval.
I am not sure why the error message is so uninformative, and I am currently exploring how to fix that, but the cause is most likely that AdapterRemoval cannot create the output file, possibly because the directory "analysis_ready" does not exist or because you do not have sufficient permissions to write to it.
Can you check if "analysis_ready" exists and that you have permission to write to it? I.e. what is the output of running the following command in the same folder where you are running AdapterRemoval:
touch ./analyis_ready/PCS1.trimmed.R1.fastq
from adapterremoval.
Actually, this is silly, but apparently this is a simple typo error. I have "analysis_ready" in one spot and "analyis_ready" in another. It is now working. Sorry about that. I should have caught that.
from adapterremoval.
Also, thank you for your time.
from adapterremoval.
You're welcome. I'll release a small update to AdapterRemoval sometime this week to improve the error message; it's easy to make a typo like that, so the error message should at least point in the right direction and not be this uninformative.
from adapterremoval.
Related Issues (20)
- --combined-output generates strange GC% distribution in fastqc reports HOT 4
- stdout and stderr reversed? HOT 1
- homebrew/science was deprecated HOT 1
- Adapter Removal running error HOT 2
- Internal barcodes HOT 5
- Support JSON log output HOT 3
- Add option for singular 'combined' output FASTQ files HOT 5
- Input file is overwritten and cut off HOT 3
- Adapters Not Being Trimmed (Apparently)? HOT 2
- collapse with SE reads HOT 3
- How to demultiplexing paired-end reads in mixed orientation? HOT 4
- installation Adapterremoval with Conda HOT 2
- AdapterRemoval v3 Feedback HOT 12
- remove adapters sequences from BGI/MGI platform HOT 1
- combine with other QC tools HOT 1
- How to interpret the outputs of the multiple inputs after trimming? HOT 4
- New version of catch.hpp needed for glibc >= 2.34 HOT 1
- [feature request] Add support for GNU make's staged install via DESTDIR flag HOT 1
- support .gz format fastq as input HOT 1
- adapterremoval add windows version HOT 2
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