christophertbrown / fix_assembly_errors Goto Github PK

Hello,
I am trying to get ra2.py up and running and I have installed the dependencies. When I try to execute the command however, I get the following message:

$ python ra2.py -h
Traceback (most recent call last):
  File "ra2.py", line 31, in <module>
    import ctbBio.mapped as map_tool
ModuleNotFoundError: No module named 'ctbBio'

I have already also installed your ctbBio repo with pip install ctbBio, but I'm not sure if I need to do some other step so that ra2.py can access it...
Any help you could provide would be greatly appreciated, thanks!

Now I get this below new error (I'm using python version 3.6.2; is the error related to it?):
(virtualenv3) user@XXXXX:~/tools/fix_assembly_errors/ctbRA$ ./ra2.py -i contigs.fasta -1 read_1.fastq.gz -2 read_2.fastq.gz
Building a SMALL index
Traceback (most recent call last):
File "./ra2.py", line 1119, in
window = window)
File "./ra2.py", line 975, in curate_assembly
allow_orphan = False, allow_orphan_ends = False, save_mapping = save_mapping)
File "./ra2.py", line 915, in check_assembly
mapping, pr_split = map_reads(assembly, scaffolds, pr, threads, multiple, pr_split = pr_split)
File "./ra2.py", line 86, in map_reads
return run_bowtie(assembly, sam, pr, pr_split, sr, threads, multiple, bt_dir) # run bowtie, return sam file
File "./ra2.py", line 66, in run_bowtie
% (matches_command, threads, bt_dir, assembly.rsplit('/', 1)[-1], pr_command, sr_command, sam)
TypeError: not all arguments converted during string formatting

Originally posted by @Anto007 in #3 (comment)

I get the below error when I try to run the ra2.py script. Also is it ok if I leave out shrinksam (difficulty in getting the tool installed and no support from the developer) and modify the bowtie2 command-line to include the --no-unal flag. If I'm not mistaken, this will circumvent the need to use shrinksam? Many thanks for your kind help!

(virtualenv3) user@XXXX:~/tools/fix_assembly_errors/ctbRA$ ./ra2.py
Traceback (most recent call last):
File "./ra2.py", line 36, in
from ctbRA.assemble import velvet as velvet
ModuleNotFoundError: No module named 'ctbRA'

I am getting the following KeyError for some fasta files(1 in 4-5 files, the rest run fine):

Building a SMALL index
Traceback (most recent call last):
File "/opt/bin/bio/ra2.py", line 1117, in
add_Ns = args['add_Ns'], mask = args['mask'], ignore_insert = args['ignore_insert_cov'], window = window)
File "/opt/bin/bio/ra2.py", line 984, in curate_assembly
add_Ns, mask, ignore_insert)
File "/opt/bin/bio/ra2.py", line 782, in merge_assemblies
merged = patch_contig(seq, s2c[id], errors, re_assembled[id], cov_thresh)
KeyError: 'XXXXX(scaffold name)'

Any idea why this is the case? I am running this with the parameters -m 5 -c 6 for read lengths of 250bp. Thanks in advance!