Hi
I was redirected to this Forum when I posted an issue on the github repo.
So I have been trying to use kneaddata with the following command :
kneaddata --bypass-trim --input reads_1.fastq.gz --input reads_2.fastq.gz -db ref/test-db --output kneaddata_output --bowtie2-options="--very-sensitive" --bowtie2-options="-p 4"
And I ran into the following error:
Traceback (most recent call last):
File "/venv/bin/kneaddata", line 11, in <module>
load_entry_point('kneaddata==0.10.0', 'console_scripts', 'kneaddata')()
File "/venv/lib/python3.8/site-packages/kneaddata/knead_data.py", line 453, in main
args.input[index]=utilities.get_reformatted_identifiers(args.input[index],args.output_dir, temp_output_files, args.input)
File "/venv/lib/python3.8/site-packages/kneaddata/utilities.py", line 362, in get_reformatted_identifiers
reformat_file=check_sequence_identifier_format(file)
File "/venv/lib/python3.8/site-packages/kneaddata/utilities.py", line 318, in check_sequence_identifier_format
first_seq_identifiers_list=get_first_n_seq_identifiers(file,num_seq_to_check)
File "/venv/lib/python3.8/site-packages/kneaddata/utilities.py", line 351, in get_first_n_seq_identifiers
lines=next(all_lines)
StopIteration
I was wondering if anybody here can help me understand where I am going wrong. Also , I am using kneaddata for the first time , so I am very sorry if I made any obvious mistakes.
THanks
Ramya