I see this : <div class="snippet-clipboard-content notranslate position-relative o

So far that seems to work, I don't get an error : <div class="snippet-clipboard-co

I have made a pull request : <a class="issue-link js-issue-link" data-error-text="Fail

This is great, thank you for the fix <a class="user-mention notranslate" data-hovercar

Too large BAM file ? about arcs HOT 6 CLOSED

bcgsc commented on June 13, 2024

Too large BAM file ?

from arcs.

Comments (6)

sarahyeo commented on June 13, 2024

What does your output graph file look like? Is it empty/truncated?

from arcs.

jvhaarst commented on June 13, 2024

I don't know, I restarted the run after changing the linecount variable from an int to a long long int.
It has now passed the line where it failed befote, I'll let you know how it ends.

from arcs.

jvhaarst commented on June 13, 2024

So far that seems to work, I don't get an error :

Running: arcs 1.0.1
 pid 26911
 -f XXXX.fasta
 -a fof.in
 -s 98
 -c 5
 -l 0
 -z 500
 -b XXXX.fasta
 Min index multiplicity: 50
 Max index multiplicity: 10000
 -d 0
 -e 0
 -r 0.05
 -v 1

=>Getting scaffold sizes... Wed May 17 15:17:12 2017
Saw 31431 sequences.

=>Starting to read BAM files... Wed May 17 15:17:20 2017
Reading bam XXXX.faa.sorted.bam
On line 10000000
On line 20000000
On line 30000000
On line 40000000
<SNIP>
On line 2120000000
On line 2130000000
On line 2140000000
On line 2150000000
On line 2160000000
On line 2170000000
On line 2180000000
On line 2190000000
On line 2200000000
On line 2210000000
On line 2220000000
On line 2230000000
On line 2240000000
On line 2250000000

=>Starting pairing of scaffolds... Wed May 17 20:02:39 2017

=>Starting to create graph... Wed May 17 20:11:46 2017

=>Starting to write graph file... Wed May 17 20:12:35 2017

      Max Degree (-d) set to: 0. Will not delete any verticies from graph.
      Writting graph file to XXXX.fasta_original.gv...

=>Done. Thu May 18 00:31:43 2017

from arcs.

jvhaarst commented on June 13, 2024

I have made a pull request : #16

from arcs.

jvhaarst commented on June 13, 2024

I have just finished my first analysis, the adapted arcs binary seems to work.

from arcs.