Comments (6)
Hi Raphael,
My md5sum is the same.
I am able to reproduce this on another machine. I hope I will be able to fix this as fast as possible.
from colord.
Hi Raphael,
It should now be fixed with 3e87a22
Please try to verify this. I have also created a new release (1.2.1) containing this fix if you, for some reason, cannot compile the code.
Let me know if it works in your environment now.
from colord.
Hi,
I cannot reproduce this :(
This is how I run it:
./pbindex ../m64017_191213_003759.hifi_reads.bam
./bam2fastq -o m64017_191213_003759.hifi_reads ../m64017_191213_003759.hifi_reads.bam
The first run was without ref seq:
colord/bin/colord compress-pbhifi --qual org --threads 8 m64017_191213_003759.hifi_reads.fastq.gz m64017_191213_003759.hifi_reads.fastq.colord
Counting k-mers.
Stage 1: 100%
Stage 2: 100%
Filtering k-mers.
100%
Running compression.
100%
DNA size : 968988426
Quality size : 7181648469
Header size : 1203516
Meta size : 54
Info size : 203
Total time : 948.253s
And for the second, I downloaded ref. seq (Is this the same file you have used?):
wget https://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/GRCh38_reference_genome/GRCh38_full_analysis_set_plus_decoy_hla.fa
mv GRCh38_full_analysis_set_plus_decoy_hla.fa hs38DH.fa
And then:
/usr/bin/time -v colord/bin/colord compress-pbhifi --qual org --threads 8 --reference-genome hs38DH.fa m64017_191213_003759.hifi_reads.fastq.gz m64017_191213_003759.hifi_reads.fastq.colord+ref
Counting k-mers.
Stage 1: 100%
Stage 2: 100%
Filtering k-mers.
100%
Running compression.
100%8%
DNA size : 279460182
Quality size : 7180109405
Header size : 1203515
Meta size : 83
Info size : 236
Total time : 3842.36s
Command being timed: "colord/bin/colord compress-pbhifi --qual org --threads 8 --reference-genome hs38DH.fa m64017_191213_003759.hifi_reads.fastq.gz m64017_191213_003759.hifi_reads.fastq.colord+ref"
User time (seconds): 21653.69
System time (seconds): 81.94
Percent of CPU this job got: 565%
Elapsed (wall clock) time (h:mm:ss or m:ss): 1:04:02
Average shared text size (kbytes): 0
Average unshared data size (kbytes): 0
Average stack size (kbytes): 0
Average total size (kbytes): 0
Maximum resident set size (kbytes): 12528628
Average resident set size (kbytes): 0
Major (requiring I/O) page faults: 48
Minor (reclaiming a frame) page faults: 18038895
Voluntary context switches: 3727105
Involuntary context switches: 22179
Swaps: 0
File system inputs: 7128
File system outputs: 0
Socket messages sent: 0
Socket messages received: 0
Signals delivered: 0
Page size (bytes): 4096
Exit status: 0
I have run this on WSL.
Let me know your operating system and hardware environment and if you can try it in a different environment.
Best
Marek
from colord.
Hi Marek, thanks for your reply.
I can get colord to run without a reference genome, but as soon as I specify one I get the Segmentation fault (I've tried the one you mentioned, plus hs38DH.fa
and the standard hg38.fa
). Interestingly, it works when I specify the reference genome AND only use a single thread. Two and three threads works fine too, but more than 4 leads to the Segmentation fault.
I'm running it on Rocky Linux 9.2, with AMD Epyc 7742 CPUs.
Best,
Raphael
Edit: I have the following md5sum:
3c0a0006322b140e6e39bb02cdf207a2 m64017_191213_003759.hifi_reads.fastq.gz
from colord.
Hi @marekkokot,
I can confirm that the bug is fixed, thanks for the quick fix.
Best,
Raphael
from colord.
Great, I am closing this.
from colord.
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