Command split_fa failed return code: 2 #139
Comments
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Hi Kathy, Did you ever get a response or figure out how to fix your problem? I have a very similar error upon submitting run_purge_dups.py. Some of the messages I received seem to be duplicated. In addition, I get a subsequent minimap error. But when I run the minimap command as shown, it seems to run ok. My slurm-xxx.out file has the following info: command /beegfs_agamede/gscratch/bgppermp/conda/env/purge_dups/bin/split_fa /beegfs_agamede/gscratch/bgppermp/flye_2_results/phlomis_all_trimmedQ7_gt5Kbp_gtQ7_assembly.fa > /beegfs_agamede/gscratch/bgppermp/purge_dups_phlomis/phlomis_all_trimmedQ7_gt5Kbp_gtQ7_assembly/split_aln/phlomis_all_trimmedQ7_gt5Kbp_gtQ7_assembly.split.fa failed, return code: 2 Here are the contents of the config file I used: Please post any understanding you have of this, and what you did to make progress. :-) --Peter |
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Hello, this script was only tested on Sanger farm, which use LSF, based on your description, you might be using slurm? So it may not work. I recommend you write a bash script descriped in README. Best, Dengfeng.
… On Nov 19, 2024, at 20:03, Peter B. Pearman ***@***.***> wrote:
Hi Kathy, Did you ever get a response or figure out how to fix your problem? I have a very similar error upon submitting run_purge_dups.py. Some of the messages I received seem to be duplicated. In addition, I get a subsequent minimap error. But when I run the minimap command as shown, it seems to run ok. My slurm-xxx.out file has the following info:
Job runing on nh001
Choosing scratch ...
Forced gscratch selection
/gscratch/bgppermp/64214
/gscratch/bgppermp/64214 directory
/usr/bin/time -p /beegfs_agamede/gscratch/bgppermp/conda/env/purge_dups/bin/run_purge_dups.py /beegfs_agamede/gscratch/bgppermp/purge_dups_phlomis/phlomis_flye_Q7_purge_dups_config2.json /beegfs_agamede/gscratch/bgppermp/conda/env/purge_dups/bin Phlomis
calculate coverage and self-alignment
Unknown option: K
Unknown option: K
Unknown option: R"select[mem>5000] rusage[mem
Unknown option: R"select[mem>30000] rusage[mem
Usage:
Usage:
bsub [-cwd Working Directory Path] [-e Error Path] [-I Interactive Mode]
[-m Node List] [-M Memory Limit] [-n Min Process] [-o Output Path] [-q
Queue Name] [-W Time] [-x Exclusive] [-h] [script]
bsub [-cwd Working Directory Path] [-e Error Path] [-I Interactive Mode]
[-m Node List] [-M Memory Limit] [-n Min Process] [-o Output Path] [-q
Queue Name] [-W Time] [-x Exclusive] [-h] [script]
command /beegfs_agamede/gscratch/bgppermp/conda/env/purge_dups/bin/split_fa /beegfs_agamede/gscratch/bgppermp/flye_2_results/phlomis_all_trimmedQ7_gt5Kbp_gtQ7_assembly.fa > /beegfs_agamede/gscratch/bgppermp/purge_dups_phlomis/phlomis_all_trimmedQ7_gt5Kbp_gtQ7_assembly/split_aln/phlomis_all_trimmedQ7_gt5Kbp_gtQ7_assembly.split.fa failed, return code: 2
unkown error, please check error log
command minimap2 -I 10G -x map-ont -t 12 /beegfs_agamede/gscratch/bgppermp/flye_2_results/phlomis_all_trimmedQ7_gt5Kbp_gtQ7_assembly.fa /beegfs_agamede/gscratch/bgppermp/all_trimmedQ7_gt5Kbp_gtQ7.fastq >/beegfs_agamede/gscratch/bgppermp/purge_dups_phlomis/phlomis_all_trimmedQ7_gt5Kbp_gtQ7_assembly/coverage/all_trimmedQ7_gt5Kbp_gtQ7.paf failed, return code: 2
unkown error, please check error log
Here are the contents of the config file I used:
{
"cc": {
"fofn": "/beegfs_agamede/gscratch/bgppermp/purge_dups_phlomis/pb.fofn",
"isdip": 1,
"core": 12,
"mem": 30000,
"queue": "normal",
"mnmp_opt": "-x map-ont",
"bwa_opt": "",
"ispb": 1,
"skip": 0
},
"sa": {
"core": 12,
"mem": 30000,
"queue": "normal"
},
"busco": {
"core": 12,
"mem": 30000,
"queue": "long",
"skip": 0,
"lineage": "/beegfs_agamede/gscratch/bgppermp/busco_data/eudicots_odb10",
"prefix": "phlomis_all_trimmedQ7_gt5Kbp_gtQ7_assembly_purged",
"tmpdir": "busco_tmp"
},
"pd": {
"mem": 30000,
"queue": "normal"
},
"gs": {
"mem": 30000,
"oe": 0
},
"kcp": {
"core": 12,
"mem": 30000,
"fofn": "/beegfs_agamede/gscratch/bgppermp/purge_dups_phlomis/pb.fofn",
"prefix": "phlomis_all_trimmedQ7_gt5Kbp_gtQ7_assembly_purged_kcm",
"tmpdir": "kcp_tmp",
"skip": 0
},
"ref": "/beegfs_agamede/gscratch/bgppermp/flye_2_results/phlomis_all_trimmedQ7_gt5Kbp_gtQ7_assembly.fa",
"out_dir": "/beegfs_agamede/gscratch/bgppermp/purge_dups_phlomis/phlomis_all_trimmedQ7_gt5Kbp_gtQ7_assembly"
}
Please post any understanding you have of this, and what you did to make progress. :-) --Peter
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Thank you, Dengfeng. I'm running the two 'Step 1' parts of the pipeline now. So far, so good. Cheers, Peter |
Hello,
I'm having some trouble getting purge_dups to run. No output or intermediate files are created in the process and this is the output in the .txt file:
calculate coverage and self-alignment
command /N/slate/kdarrag/programs/purge_dups/bin/split_fa /N/slate/kdarrag/Costus/allenii/PB1055_KK0154_SpiralGinger_HiFiv3_Revio_cell1/Fasta_Fastq_7335/outputs/run2/allenii.ASM.p_ctg.fa > allenii.ASM.p_ctg/split_aln/allenii.ASM.p_ctg.split.fa failed, return code: 2
unkown error, please check error log
purge duplicates
and in the .err file:
Unknown option: K
Unknown option: R"select[mem>5000] rusage[mem
Usage:
bsub [-cwd Working Directory Path] [-e Error Path] [-I Interactive Mode]
[-m Node List] [-M Memory Limit] [-n Min Process] [-o Output Path] [-q
Queue Name] [-W Time] [-x Exclusive] [-h] [script]
slurmstepd: error: Detected 1 oom_kill event in StepId=3300451.batch. Some of the step tasks have been OOM Killed.
I am running with 480Gb for a 1.1Gb genome.
Is there some way that by split_fa failing this is causing the oom by not splitting up the genome? Any idea what return code 2 is? There is no error log information to check.
Thank you,
Kathy
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