Error while executing the Bisulfite bisulphite-mapping about gembs

[heathsc]

Thanks for the feedback. I will make the suggested changes. Simon

…

On 14 Mar 2019, at 15:34, Ismail Moghul ***@***.***> wrote: Okay found a fix: After adding a log-line to see the mapping process, I see that it attempts to run: /home/ucbtmog/.pyenv/versions/3.5.3/lib/python3.5/site-packages/gemBS/gemBSbinaries/gem-mapper -I /home/ucbtmog/d/nugen/t/ref_indexes/hg37.BS.gem -i PCa_45_01b_S19_R1.fastq.gz -t 70 --report-file /home/ucbtmog/d/nugen/t/mapping/PCa_45_01b_S19/PCa_45_01b_S19.json -r @rg\\tID:PCa_45_01b_S19\\tSM:PCa_45_01b_S19\\tBC:PCa_45_01b_S19\\tPU:PCa_45_01b_S19 This gives me the following error message: GEM::FatalError (fm.c:193,fm_open_file) Could not open file 'PCa_45_01b_S19_R1.fastq.gz' Would be nice if this was reported in the error logs or in STDOUT So the issue is that the full path to the input file is not passed to the tool. Here is a fix: https://github.com/heathsc/gemBS/blob/fca06d59931a6639fee89839009847d84a08824a/gemBS/production.py#L480-L503 <https://github.com/heathsc/gemBS/blob/fca06d59931a6639fee89839009847d84a08824a/gemBS/production.py#L480-L503> Specifically Line 490 should be changed to: if not skip: inputFiles.append(os.path.join(input_dir,file)) This is similar to what is done with paired-end reads - see lines 499 & 451 above — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#46 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADHPd8ufkjWfVfcgNC-w_S9xnBd05dDzks5vWl3kgaJpZM4b0SJt>.

[IsmailM]

Okay found a fix:

After adding a log-line to see the mapping process, I see that it attempts to run:

/home/ucbtmog/.pyenv/versions/3.5.3/lib/python3.5/site-packages/gemBS/gemBSbinaries/gem-mapper -I /home/ucbtmog/d/nugen/t/ref_indexes/hg37.BS.gem -i PCa_45_01b_S19_R1.fastq.gz -t 70 --report-file /home/ucbtmog/d/nugen/t/mapping/PCa_45_01b_S19/PCa_45_01b_S19.json -r @RG\\tID:PCa_45_01b_S19\\tSM:PCa_45_01b_S19\\tBC:PCa_45_01b_S19\\tPU:PCa_45_01b_S19

This gives me the following error message:

GEM::FatalError (fm.c:193,fm_open_file)
 Could not open file 'PCa_45_01b_S19_R1.fastq.gz'

Would be nice if this was reported in the error logs or in STDOUT

So the issue is that the full path to the input file is not passed to the tool.

Here is a fix:

gemBS/gemBS/production.py

Lines 480 to 503 in fca06d5

	if len(mlist) == 1:
	(file, m) = mlist[0]
	skip = false
	if ftype is None:
	if m.group(4).lower() in ['SAM', 'BAM']:
	ftype = 'BAM' if m.group(4).lower == 'BAM' else 'SAM'
	else:
	ftype = 'INTERLEAVED' if self.paired else 'SINGLE'
	elif ftype == 'PAIRED' or (ftype == 'SAM' and m.group(4).lower != 'sam') or (ftype == 'BAM' and m.group(4).lower() != 'bam'): skip = True
	if not skip: inputFiles.append(file)
	elif len(mlist) == 2:
	(file1, m1) = mlist[0]
	(file2, m2) = mlist[1]
	for ix in [1, 2, 4]:
	if m1.group(ix) != m2.group(ix): break
	else:
	if (ftype == None or ftype == 'PAIRED') and m1.group(4) in ['fastq', 'fq', 'fasta', 'fa']:
	if m1.group(3) == '1' and m2.group(3) == '2':
	inputFiles = [os.path.join(input_dir,file1), os.path.join(input_dir,file2)]
	elif m1.group(3) == '2' and m2.group(3) == '1':
	inputFiles = [os.path.join(input_dir,file2), os.path.join(input_dir,file1)]
	self.ftype = 'PAIRED'
	self.paired = True

Specifically Line 490 should be changed to:

if not skip: inputFiles.append(os.path.join(input_dir,file))

This is similar to what is done with paired-end reads - see lines 499 & 451 above

[heathsc]

Fix applied.