Open Songq-20 opened 2 months ago
Could you please read the Basalt_checkpoint.txt file and tell us where the software stopped? I may need to check the error occurred in which step. Thank you very much. You may also re-run the program. BASALT will keep running the incomplete job continuously.
Thank you for your reply,the Basalt_checkpoint.txt
:
1st autobinner done!
2nd bin selection within group done!
3rd bin selection within multiple groups done!
4th outlier removal done!
5th contig retrieve did not perform!
6th secondary de-repplication done!
7th Skip contig retrieve within group! BestBinset_outlier_refined_filtrated_retrieved
我的运行似乎也在“7th Skip contig retrieve within group! BestBinset_outlier_refined_filtrated_retrieved”这一步停止 我的输入代码是 “#!/bin/bash source /home/zhongpei/miniconda3/bin/activate BASALT BASALT -a Unknown_CA010-001R0004.fastp_megahit_contigs.fa,Unknown_CA010-001R0005.fastp_megahit_contigs.fa,Unknown_CA010-001R0006.fastp_megahit_contigs.fa\ -s Unknown_CA010-001R0004.fastp.1.fq.gz,Unknown_CA010-001R0004.fastp.2.fq.gz/Unknown_CA010-001R0005.fastp.1.fq.gz,Unknown_CA010-001R0005.fastp.2.fq.gz/Unknown_CA010-001R0006.fastp.1.fq.gz,Unknown_CA010-001R0006.fastp.2.fq.gz\ -t 90 -m 350 -qc checkm --autopara sensitive --refinepara deep”
Hi both,
From the checkpoint file provided by Songq-20, it seems that BASALT stopped running at the gap filling step. Could you please check:
If the above described status are true, please stop BASALT and re-run the program, BASALT will continue and finish the program. Alternatively, please download the latest BASALT (v1.0.2), as this bug has fixed in this version.
Thanks for using BASALT!
Dear BASALT Team: I submitted the task through Slurm. Slurm shows that the task is still running, but when I checked the server CPU usage, I found that the task was not actually running. This is my command:
The Slurm:
How can I slove this problem? Thanks!