BUSCO 4.1.4 is still stuck at Augustus
I am running BUSCO on multiple assemblies to find single copy gene.
some assemblies' analysis has been finished,but two assemblies' analysis has been stuck at augustus.
I run htop
, there is no augustus job.
augustus version 3.3.3
(base) [zch@macaca busco_data]$ tail nohup.out
WARNING: The following job was killed as it was taking too long (>1hr) to complete.
/data/zch/miniconda3/envs/busco_env/bin/augustus --codingseq=1 --proteinprofile=/data/zch/busco_data/lepidoptera_odb10/prfl/1143at7088.prfl --predictionStart=8490009 --predictionEnd=8520242 --species=fly /data/zch/busco_data/sf/run_lepidoptera_odb10/blast_output/sequences/NC_049724.1.temp
WARNING: The following job was killed as it was taking too long (>1hr) to complete.
/data/zch/miniconda3/envs/busco_env/bin/augustus --codingseq=1 --proteinprofile=/data/zch/busco_data/lepidoptera_odb10/prfl/59at7088.prfl --predictionStart=7280259 --predictionEnd=7309819 --species=fly /data/zch/busco_data/sf/run_lepidoptera_odb10/blast_output/sequences/NC_049717.1.temp
INFO: [augustus] 2531 of 6327 task(s) completed
INFO: [augustus] 3164 of 6327 task(s) completed
INFO: [augustus] 3797 of 6327 task(s) completed
INFO: [augustus] 4429 of 6327 task(s) completed
INFO: [augustus] 5062 of 6327 task(s) completed
INFO: [augustus] 5695 of 6327 task(s) completed
(base) [zch@macaca busco_data]$ ps ux
USER PID %CPU %MEM VSZ RSS TTY STAT START TIME COMMAND
zch 32528 0.0 0.0 100052 2016 ? S 23:29 0:00 sshd: zch@pts/1
zch 32529 0.0 0.0 111096 4648 pts/1 Ss 23:29 0:00 -bash
zch 33050 2.0 0.0 110216 1168 pts/1 R+ 23:36 0:00 ps ux
zch 47904 0.0 0.0 100052 1996 ? S 10:54 0:00 sshd: zch@pts/0
zch 47905 0.0 0.0 111204 4728 pts/0 Ss+ 10:54 0:00 -bash
zch 49504 0.0 0.0 3321548 58476 pts/0 Sl 13:46 0:32 python /data/zch/miniconda3/envs/busco_env/bin/busco -m geno -i /data/public/zch/genome/sf/NCBI-Sf/GCF_011064685.1_ZJU_Sf
zch 51436 0.3 0.0 3322752 51684 pts/0 Sl 14:11 1:44 python /data/zch/miniconda3/envs/busco_env/bin/busco -m geno -i /data/public/zch/genome/sf/NCBI-Sf/GCF_011064685.1_ZJU_Sf
zch 51437 0.2 0.0 3323008 51992 pts/0 S 14:11 1:39 python /data/zch/miniconda3/envs/busco_env/bin/busco -m geno -i /data/public/zch/genome/sf/NCBI-Sf/GCF_011064685.1_ZJU_Sf
zch 51438 0.2 0.0 3322752 51788 pts/0 S 14:11 1:40 python /data/zch/miniconda3/envs/busco_env/bin/busco -m geno -i /data/public/zch/genome/sf/NCBI-Sf/GCF_011064685.1_ZJU_Sf
zch 51439 0.2 0.0 3323008 51848 pts/0 S 14:11 1:36 python /data/zch/miniconda3/envs/busco_env/bin/busco -m geno -i /data/public/zch/genome/sf/NCBI-Sf/GCF_011064685.1_ZJU_Sf
zch 51440 0.2 0.0 3323008 51992 pts/0 S 14:11 1:37 python /data/zch/miniconda3/envs/busco_env/bin/busco -m geno -i /data/public/zch/genome/sf/NCBI-Sf/GCF_011064685.1_ZJU_Sf
zch 51441 0.2 0.0 3323008 52044 pts/0 S 14:11 1:41 python /data/zch/miniconda3/envs/busco_env/bin/busco -m geno -i /data/public/zch/genome/sf/NCBI-Sf/GCF_011064685.1_ZJU_Sf
zch 51442 0.2 0.0 3323008 51824 pts/0 S 14:11 1:40 python /data/zch/miniconda3/envs/busco_env/bin/busco -m geno -i /data/public/zch/genome/sf/NCBI-Sf/GCF_011064685.1_ZJU_Sf
zch 51443 0.2 0.0 3323008 52200 pts/0 S 14:11 1:40 python /data/zch/miniconda3/envs/busco_env/bin/busco -m geno -i /data/public/zch/genome/sf/NCBI-Sf/GCF_011064685.1_ZJU_Sf
zch 51444 0.2 0.0 3323008 51816 pts/0 S 14:11 1:40 python /data/zch/miniconda3/envs/busco_env/bin/busco -m geno -i /data/public/zch/genome/sf/NCBI-Sf/GCF_011064685.1_ZJU_Sf
zch 51445 0.2 0.0 3323008 51816 pts/0 S 14:11 1:40 python /data/zch/miniconda3/envs/busco_env/bin/busco -m geno -i /data/public/zch/genome/sf/NCBI-Sf/GCF_011064685.1_ZJU_Sf
zch 51446 0.3 0.0 3323008 51972 pts/0 S 14:11 1:43 python /data/zch/miniconda3/envs/busco_env/bin/busco -m geno -i /data/public/zch/genome/sf/NCBI-Sf/GCF_011064685.1_ZJU_Sf
zch 51447 0.2 0.0 3322752 51832 pts/0 S 14:11 1:38 python /data/zch/miniconda3/envs/busco_env/bin/busco -m geno -i /data/public/zch/genome/sf/NCBI-Sf/GCF_011064685.1_ZJU_Sf
(base) [zch@macaca busco_data]$
Edited by Chunhui Zhang