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rvolden / Mandalorion-Episode-II

Version II of Mandalorion
MIT License
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Can't get Mandalorion-Episode-II working #1

Closed csijcs closed 6 years ago

csijcs commented 6 years ago

I have been trying to get Mandalorion-Episode-II working for isoform expression of 1D ONT sequencing data and am having trouble. The command I am running is as follows:

python3 defineAndQuantifyWrapper.py \
-c /data/csijcs/nanopore/K562_cytoplasmic_polyA_cDNA_PCR/Mandalorion_isoform_calling/content.txt \
-f /data/csijcs/nanopore/K562_cytoplasmic_polyA_cDNA_PCR/Mandalorion_isoform_calling/config.txt \
-p /data/csijcs/nanopore/K562_cytoplasmic_polyA_cDNA_PCR/Mandalorion_isoform_calling \
-m /home/csijcs/Mandalorion-Episode-II/NUC.4.4.mat \
-g /data/csijcs/hg38/gencode.v28.primary_assembly.annotation.gtf \
-u 5 -d 30 -s 200 -r 0.05 -R 3 -i 0 -t 0 -I 100 -T 60

The config.txt file contains:

poa /home/csijcs/anaconda3/envs/py3/bin/poa
water   /home/csijcs/anaconda3/envs/py3/bin/water
minimap2    /home/csijcs/anaconda3/bin/minimap2
consensus   consensus.py
racon   /home/csijcs/anaconda3/bin/racon
blat    /home/csijcs/anaconda3/envs/py3/bin/blat

The content.txt file contains: /data/csijcs/nanopore/K562_cytoplasmic_polyA_cDNA_PCR/minimap2_alignment/K562_cytoplasmic_polyA_cDNA_PCR_alignment.psl /data/csijcs/nanopore/K562_cytoplasmic_polyA_cDNA_PCR/fastq_20_june_2018/pass/all /data/csijcs/nanopore/K562_cytoplasmic_polyA_cDNA_PCR/fastq_20_june_2018/pass/all /data/csijcs/nanopore/K562_cytoplasmic_polyA_cDNA_PCR/minimap2_alignment/K562_cytoplasmic_polyA_cDNA_PCR_alignment.sam

(I have tried this with and without the .fasta and .fastq extensions and get the same errors)

The errors I receive are:

rm: cannot remove ‘/data/csijcs/nanopore/K562_cytoplasmic_polyA_cDNA_PCR/fastq_20_june_2018/pass/all/parsed_reads/*’: No such file or directory
Traceback (most recent call last):
  File "defineAndQuantifyIsoforms.py", line 245, in <module>
    main()
  File "defineAndQuantifyIsoforms.py", line 239, in main
    splice_dict = splice_dict = collect_splice_events(path)
  File "defineAndQuantifyIsoforms.py", line 33, in collect_splice_events
    for line in open(path + '/SS.bed'):
FileNotFoundError: [Errno 2] No such file or directory: '/data/csijcs/nanopore/K562_cytoplasmic_polyA_cDNA_PCR/Mandalorion_isoform_calling///SS.bed'
Traceback (most recent call last):
  File "createConsensi.py", line 212, in <module>
    for line in open(path + '/isoform_list'):
FileNotFoundError: [Errno 2] No such file or directory: '/data/csijcs/nanopore/K562_cytoplasmic_polyA_cDNA_PCR/fastq_20_june_2018/pass/all/isoform_list'

The pipeline creates a parsed_reads folder, but it is empty. It also creates the files Isoform_Consensi.fasta and Isoform_Consensi_filtered.fasta, but they are both empty. It does not appear to create the SS.bed file or the isofrom_list file.

Can you please tell me what I am doing wrong?