NicolasProvencher
commented
7 months ago Another issue i run into is when i run the script on multiple files wether using the --input_path or --files argument, if multiple files are given and the list files is bigger than 1, the code is stuck forever after the first cutadapt file has been processed
Total number of input files = 2 Number of bigger files (>=10GB) = 0 Number of smaller files (<10 GB) = 2 number of CPU is 12 Processing 2 files processing file GSM1948925.fastq processing file GSM1608268.fastq Median length of aligned sequences for filename - GSM1948925 is 8.0 Writing BLAST output query subject aligned_seq adapter adapter_length aligned_length evalue qstart sstart 0 19733 4731 AAGCTAAG AAGCTAAG 8 8 1.4 20 24 1 13644 4731 AAGCTAAG AAGCTAAG 8 8 1.3 20 24 2 8250 4731 AAGCTAAG AAGCTAAG 8 8 1.5 20 24 3 12742 4731 AAGCTAAG AAGCTAAG 8 8 1.4 20 24 4 7057 4657 ACCTCGGGC ACCTCGGGC 9 9 0.4 17 20
Putative three prime end adapters for filename - GSM1948925 is ['GTATTAG', 'GCCAAAGC'] Three prime end adapter sequence for filename - GSM1948925 is GTATTAG Trimming with CUTADAPT
cutadapt -q 20 -m 15 -M 50 -a GTATTAG -o /home/noxatras/Desktop/adapt/test1/out/good-mapping/GSM1948925_trimmed.fastq /home/noxatras/Desktop/adapt/test1/in/GSM1948925.fastq > /home/noxatras/Desktop/adapt/test1/out/aux_files/GSM1948925/GSM1948925_cutadapt.txt [---------=8 ] 00:00:28 6,614,307 reads @ 4.3 µs/read; 13.84 M reads/minute len of new_lst is GSM1948925 1764746 len of filtered list is GSM1948925 1177940 Empty DataFrame Columns: [query, subject, aligned_seq, adapter, aligned_length, evalue, qstart, sstart] Index: []
///i used ctrl c here after waiting a good 30 minutes////
^CProcess ForkPoolWorker-1:
Process ForkPoolWorker-7:
Traceback (most recent call last):
File "adapt_find.py", line 996, in
asan-nasa
When specifying a input path, the path given to multiple steps of your script is only the filename which break the code cause it cant find the file in the adapt_find dir [Errno 2] No such file or directory: 'GSM1608268.fastq'
Line 981 -> i added args.input_path + "/" + before the f line 154 line that launch cutadapt etc
another thing i tried is adding os.chdir(cwd)
I am able to fix it myself for myself but since i am not familiar with the overall organisation of your script i though id bring this issue for you so that you can fix it in a way that wont break anything else
so you have a better understanding of whats happening, here is a tree of my setup adapt --adapt_find -----all the file of your git dir --test ----in --------fastq1 --------fastq2 ----out
here is the command line python adapt_find.py ILLUMINA --input_path path/to/adapt/test/in --output_path /path/to/adapt/test/out and i run the line from /path/to/adapt/adapt_find