BigDataBiology
Error: Running hmmsearch fail
Hi, great job of binning.
Recently when I use Semibin2 to do the scaffolds binnning, a problem occurred in some samples. The first line is my command. Could you please help me to solve that? Thanks
`(semibin) [huwa@localhost: SRR21518485_spades_raw] SemiBin2 single_easy_bin --environment human_oral -i scaffolds.fasta -b SRR21518485_vamb/bam_path/SRR21518485_28131_sorted_mapped.bam -o SRR21518485_semibin_bam 2024-08-04 15:16:55 localhost.localdomain SemiBin[2188044] INFO Setting number of CPUs to 104 2024-08-04 15:16:55 localhost.localdomain SemiBin[2188044] INFO Binning for short_read 2024-08-04 15:16:58 localhost.localdomain SemiBin[2188044] INFO Did not detect GPU, using CPU. 2024-08-04 15:16:58 localhost.localdomain SemiBin[2188044] INFO Generating training data... 2024-08-04 15:16:59 localhost.localdomain SemiBin[2188044] INFO Calculating coverage for every sample. 2024-08-04 15:17:02 localhost.localdomain SemiBin[2188044] INFO Processed: SRR21518485_vamb/bam_path/SRR21518485_28131_sorted_mapped.bam 2024-08-04 15:17:02 localhost.localdomain SemiBin[2188044] INFO Start binning. 2024-08-04 15:17:03 localhost.localdomain SemiBin[2188044] INFO Number of bins prior to reclustering: 0 2024-08-04 15:17:04 localhost.localdomain SemiBin[2188044] INFO Running naive ORF finder
Error: Sequence file /tmp/tmpydq2w4yn/orfs.faa is empty or misformatted
Error: Running hmmsearch fail`
SemiBin should not have generated an error here (or at least a more informative error), but it found 0 bins in this sample (see the message Number of bins prior to reclustering: 0)
Either something is wrong with the files or could this have been a very shallow/empty sample?
I am having the same issue and also it says it can't find GPU despite I explicitly running job on gpu node.
024-08-13 21:51:46 agq013 SemiBin[86060] INFO Setting number of CPUs to 32 2024-08-13 21:51:46 agq013 SemiBin[86060] INFO Binning for short_read 2024-08-13 21:51:46 agq013 SemiBin[86060] INFO SemiBin will run in self supervised mode 2024-08-13 21:52:01 agq013 SemiBin[86060] INFO Did not detect GPU, using CPU. 2024-08-13 21:52:07 agq013 SemiBin[86060] INFO Generating training data... 2024-08-13 21:58:16 agq013 SemiBin[86060] INFO Calculating coverage for every sample. 2024-08-13 22:10:13 agq013 SemiBin[86060] INFO Processed: /bamfiles/0_sorted.bam 2024-08-13 22:10:21 agq013 SemiBin[86060] INFO Processed: /bamfiles/1_sorted.bam 2024-08-13 22:10:21 agq013 SemiBin[86060] INFO Processed: /bamfiles/2_sorted.bam 2024-08-13 22:10:28 agq013 SemiBin[86060] INFO Processed: /bamfiles/3_sorted.bam 2024-08-13 22:10:28 agq013 SemiBin[86060] INFO Processed: /bamfiles/4_sorted.bam 2024-08-13 22:10:28 agq013 SemiBin[86060] INFO Processed: /bamfiles/5_sorted.bam 2024-08-13 22:10:28 agq013 SemiBin[86060] INFO Processed: /bamfiles/6_sorted.bam 2024-08-13 22:10:28 agq013 SemiBin[86060] INFO Processed: /bamfiles/7_sorted.bam 2024-08-13 22:10:28 agq013 SemiBin[86060] INFO Processed: /bamfiles/8_sorted.bam 2024-08-13 22:10:28 agq013 SemiBin[86060] INFO Processed: /bamfiles/9_sorted.bam 2024-08-13 22:10:55 agq013 SemiBin[86060] INFO Start training from a single sample. 2024-08-13 22:11:10 agq013 SemiBin[86060] INFO Training model... 100%|██████████| 15/15 [1:11:22<00:00, 285.51s/it] 2024-08-13 23:22:48 agq013 SemiBin[86060] INFO Training finished. 2024-08-13 23:22:48 agq013 SemiBin[86060] INFO Start binning. 2024-08-13 23:24:52 agq013 SemiBin[86060] INFO Number of bins prior to reclustering: 0 2024-08-13 23:24:53 agq013 SemiBin[86060] INFO Running naive ORF finder
Error: Sequence file /semibin_tmp/tmpoh16qf07/orfs.faa is empty or misformatted
Error: Running hmmsearch fail Command exited with non-zero status 1
Any help is much appreciated.
