Hi all,
I am encountering same issue SIGNAL 9 (KILL). I wonder how you solved this issue.
Anthony h,
Could you describe more detail how you set -k <int> options?
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
Yes, it was running out of memory.
Switched to using -k instead of -a and it completed.
Leave a comment:
-
How much memory does you system have?
System may kill processes if there is severe resource starvation; i.e. no memory available.
Leave a comment:
-
What happens when you use --local --very-sensitive-local at the same time? I assume it picks one and keeps on going?
Leave a comment:
-
I was thinking a memory issue when I first read this. Have a look at the requirement on there website. Failing that drop them an email.
Leave a comment:
-
Also getting KILL
I am also getting this when I turn on the -a option.
Without -a my file of ~7M reads gets mapped against human genome hg19 successfully. With -a it bombs out even if I truncate to 200k reads. Maybe the process is using too much memory and the OS is killing it?
Leave a comment:
-
Bowtie signal 9 (KILL) error
I'm aligning a bunch of Illumina runs using Bowtie2 and I'm getting a frustrating error with only a few of the fastq files.
I run them with the following command:
bowtie2 -p 10 -x mm10_genome -1 SRR594396_1.fastq -2 SRR594396_2.fastq --local --very-sensitive-local --no-mixed --no-discordant | samtools view -uS - | samtools sort -m 10000000000 - SRR594393_genome
Here are the outputs I get for a few fastq file pairs:
SRR594399_genome
[samopen] SAM header is present: 22 sequences.
Parse error at line 111594048: missing colon in auxiliary data
[bam_sort_core] merging from 2 files...
SRR594400_genome
[samopen] SAM header is present: 22 sequences.
bowtie2-align died with signal 9 (KILL)
[sam_read1] reference 'SRR59' is recognized as '*'.
[main_samview] truncated file.
[bam_sort_core] merging from 2 files...
SRR594401_genome
[samopen] SAM header is present: 22 sequences.
Parse error at line 111266936: sequence and quality are inconsistent
[bam_sort_core] merging from 2 files...
SRR594396_genome
[samopen] SAM header is present: 22 sequences.
bowtie2-align died with signal 9 (KILL)
Parse error at line 111938538: missing colon in auxiliary data
[bam_sort_core] merging from 2 files...
SRR594415_genome
[samopen] SAM header is present: 22 sequences.
bowtie2-align died with signal 9 (KILL)
Parse error at line 112131890: missing colon in auxiliary data
[bam_sort_core] merging from 2 files...
SRR594417_genome
[samopen] SAM header is present: 22 sequences.
bowtie2-align died with signal 9 (KILL)
Parse error at line 112044487: sequence and quality are inconsistent
[bam_sort_core] merging from 2 files...
I can't find anything about this KILL error and googling the parse errors isn't helping much. I think the parsing has something to do with bowtie failing and then the sam->bam operation subsequently failing on the last line.
Can anyone help with this KILL business?Tags: None
Latest Articles
Collapse
-
by seqadmin
The first FDA-approved CRISPR-based therapy marked the transition of therapeutic gene editing from a dream to reality1. CRISPR technologies have streamlined gene editing, and CRISPR screens have become an important approach for identifying genes involved in disease processes2. This technique introduces targeted mutations across numerous genes, enabling large-scale identification of gene functions, interactions, and pathways3. Identifying the full range...-
Channel: Articles
08-27-2024, 04:44 AM -
-
by seqadmin
Sequencing mRNA provides a snapshot of cellular activity, allowing researchers to study the dynamics of cellular processes, compare gene expression across different tissue types, and gain insights into the mechanisms of complex diseases. “mRNA’s central role in the dogma of molecular biology makes it a logical and relevant focus for transcriptomic studies,” stated Sebastian Aguilar Pierlé, Ph.D., Application Development Lead at Inorevia. “One of the major hurdles for...-
Channel: Articles
08-07-2024, 12:11 PM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 08-27-2024, 04:40 AM
|
0 responses
16 views
0 likes
|
Last Post
by seqadmin
08-27-2024, 04:40 AM
|
||
New Single-Molecule Sequencing Platform Introduces Advanced Features for High-Throughput Genomics
by seqadmin
Started by seqadmin, 08-22-2024, 05:00 AM
|
0 responses
293 views
0 likes
|
Last Post
by seqadmin
08-22-2024, 05:00 AM
|
||
Started by seqadmin, 08-21-2024, 10:49 AM
|
0 responses
135 views
0 likes
|
Last Post
by seqadmin
08-21-2024, 10:49 AM
|
||
Started by seqadmin, 08-19-2024, 05:12 AM
|
0 responses
124 views
0 likes
|
Last Post
by seqadmin
08-19-2024, 05:12 AM
|
Leave a comment: