Problem running makeTSVfile.py about arcs HOT 9 CLOSED

is the arcs_test_original.gv file empty?

from arcs.

No. 422155 lines of the following.

head arcs_test_original.gv
graph G {
0 [id=1];
1 [id=58];
2 [id=107];
3 [id=610];
4 [id=691];
5 [id=744];
6 [id=1019];
7 [id=1176];
8 [id=1327];

tail arcs_test_original.gv
446--4157 [label=2, weight=1];
4156--7197 [label=0, weight=1];
11166--2331 [label=0, weight=3];
10678--10475 [label=0, weight=1];
19656--7384 [label=0, weight=1];
4235--4157 [label=2, weight=1];
5964--4768 [label=3, weight=1];
4768--2541 [label=2, weight=1];
19060--428 [label=2, weight=1];
}

from arcs.

How are the headers of your FASTA file formatted? The script makeTSVfile.py expects headers to be in the form:

>12345 other_info

where 12345 is a unique sequence id.

If there are strings in your seq id (ex. >abc123efg4) ARCS will try to extract all the digits from the name (abc123efg4 becomes 1234).

If this is the case does replacing lines 24-26 in makeTSVfile.py with:

test = re.findall(r'\d+', line.rstrip().split()[0])
counter += 1
links_numbering["".join(test)] = str(counter)

fix the problem?

from arcs.

from arcs.

If you renumbered the headers to only contain a unique ID, you will have to rerun ARCS using the renumbered FASTA to ensure the seq ID's remain consistent throughout the pipeline. Likewise you many need to rerun the alignments to generate a bam file with the correct renumbered seq IDs to input to ARCS.

from arcs.

from arcs.

Yes that might be the case. I just pushed a bug fix to the "develop" branch which allows the use of strings for seq IDs instead of ints. Let me know if that resolves the issue!

from arcs.

Hi Sarah and others, I am trying to run the makeTSVfile.py script (using the new version from the develop branch), and although I am not getting any error messages, it is taking a very long time. Last run I had to abort after 5 days, is it normal for it to take this long? My input graph file is not huge (around 15 000 lines), but my assembly is quite fragmented..
It would be great to hear your experiences about running this script! Thanks!

from arcs.

Closing this old issue -- feel free to re-open if you still have questions.

from arcs.