Comments (6)
What does your output graph file look like? Is it empty/truncated?
from arcs.
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.
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.
I have made a pull request : #16
from arcs.
I have just finished my first analysis, the adapted arcs binary seems to work.
from arcs.
This is great, thank you for the fix @jvhaarst !
from arcs.
Related Issues (20)
- About Running ARCS in default mode HOT 3
- GCC version update HOT 1
- arcs-1.2.2: abyss-fixmate-ssq sometimes segfaults HOT 9
- Short read length question: can the tool accept 250? HOT 2
- arcs-long: tiny PE-pairs are produced HOT 3
- Scaffolding Expectations HOT 12
- Running ARCS and ARKS HOT 2
- Parameters for corrected ONT reads HOT 2
- arcs-make in bin HOT 2
- Add optional dependency of pigz HOT 1
- unrecognized option '--fastq' HOT 3
- fastq formatting barcodes in BX tag HOT 8
- ARKS fails to create any links with a highly repetitive input HOT 4
- Parameters for PacBio HiFi data HOT 3
- Can this software use HiC data, or need to use the sequencing technology mentioned in your paper? HOT 1
- `arcs-tigmint` and `arks-tigmint` struggle with input files outside working directory HOT 3
- Incorrect program call? HOT 6
- `arcs-long`/`arks-long` vs `LINKS`? HOT 2
- Understanding specific scaffolding output HOT 4
- tigmint-make 'missing separator' error HOT 8
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from arcs.