Hello auve my submit directory is: /net/cn-1/mnt/SCRATCH/bin420-21/TuesdaySession/Results/dram_annotation this is the job: 13643801 I am running on: cn-3 I am running with: 14 cpus Today is: Fri Oct 22 17:24:56 CEST 2021 auve exists on /home/work copying files to /home/work/auve/tmpDir_of.13643801 copying MAGs to /home/work/auve/tmpDir_of.13643801 DRAM started at 22 Oct 17:24:56 /net/cn-1/mnt/SCRATCH/bin420-21/condaenvironments/metaG/DRAM/lib/python3.9/site-packages/mag_annotator/annotate_bins.py:120: PerformanceWarning: DataFrame is highly fragmented. This is usually the result of calling `frame.insert` many times, which has poor performance. Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()` hits[forward_hit] = [row.tId, rbh, row.seqIdentity, row.bitScore, row.eVal] /net/cn-1/mnt/SCRATCH/bin420-21/condaenvironments/metaG/DRAM/lib/python3.9/site-packages/mag_annotator/annotate_bins.py:595: UserWarning: No rRNAs were detected, no rrnas.tsv file will be created. warnings.warn('No rRNAs were detected, no rrnas.tsv file will be created.') /net/cn-1/mnt/SCRATCH/bin420-21/condaenvironments/metaG/DRAM/lib/python3.9/site-packages/mag_annotator/annotate_bins.py:120: PerformanceWarning: DataFrame is highly fragmented. This is usually the result of calling `frame.insert` many times, which has poor performance. Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()` hits[forward_hit] = [row.tId, rbh, row.seqIdentity, row.bitScore, row.eVal] /net/cn-1/mnt/SCRATCH/bin420-21/condaenvironments/metaG/DRAM/lib/python3.9/site-packages/mag_annotator/annotate_bins.py:595: UserWarning: No rRNAs were detected, no rrnas.tsv file will be created. warnings.warn('No rRNAs were detected, no rrnas.tsv file will be created.') /net/cn-1/mnt/SCRATCH/bin420-21/condaenvironments/metaG/DRAM/lib/python3.9/site-packages/mag_annotator/annotate_bins.py:120: PerformanceWarning: DataFrame is highly fragmented. This is usually the result of calling `frame.insert` many times, which has poor performance. Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()` hits[forward_hit] = [row.tId, rbh, row.seqIdentity, row.bitScore, row.eVal] /net/cn-1/mnt/SCRATCH/bin420-21/condaenvironments/metaG/DRAM/lib/python3.9/site-packages/mag_annotator/annotate_bins.py:595: UserWarning: No rRNAs were detected, no rrnas.tsv file will be created. warnings.warn('No rRNAs were detected, no rrnas.tsv file will be created.') /net/cn-1/mnt/SCRATCH/bin420-21/condaenvironments/metaG/DRAM/lib/python3.9/site-packages/mag_annotator/annotate_bins.py:595: UserWarning: No rRNAs were detected, no rrnas.tsv file will be created. warnings.warn('No rRNAs were detected, no rrnas.tsv file will be created.') /net/cn-1/mnt/SCRATCH/bin420-21/condaenvironments/metaG/DRAM/lib/python3.9/site-packages/mag_annotator/annotate_bins.py:595: UserWarning: No rRNAs were detected, no rrnas.tsv file will be created. warnings.warn('No rRNAs were detected, no rrnas.tsv file will be created.') /net/cn-1/mnt/SCRATCH/bin420-21/condaenvironments/metaG/DRAM/lib/python3.9/site-packages/mag_annotator/annotate_bins.py:595: UserWarning: No rRNAs were detected, no rrnas.tsv file will be created. warnings.warn('No rRNAs were detected, no rrnas.tsv file will be created.') 6 fastas found 2021-10-22 17:25:03.927077: Annotation started 0:00:00.024452: Retrieved database locations and descriptions 0:00:00.024487: Annotating bins21.1 0:00:48.970558: Turning genes from prodigal to mmseqs2 db 0:00:51.844836: Getting hits from kofam 0:17:21.584136: Getting forward best hits from peptidase 0:17:32.018664: Getting reverse best hits from peptidase 0:17:35.449816: Getting descriptions of hits from peptidase 0:17:37.769174: Getting hits from pfam 0:17:54.121393: Getting hits from dbCAN 0:18:06.940621: Getting hits from VOGDB 0:23:51.814925: Merging ORF annotations 0:24:09.082906: Annotating bins21.3 0:24:53.608712: Turning genes from prodigal to mmseqs2 db 0:24:56.483806: Getting hits from kofam 0:49:02.189209: Getting forward best hits from peptidase 0:49:16.223654: Getting reverse best hits from peptidase 0:49:17.782374: Getting descriptions of hits from peptidase 0:49:19.849959: Getting hits from pfam 0:49:37.823034: Getting hits from dbCAN 0:49:58.599386: Getting hits from VOGDB 0:58:29.808155: Merging ORF annotations 0:58:54.953275: Annotating bins21.4 0:59:17.184321: Turning genes from prodigal to mmseqs2 db 0:59:20.019100: Getting hits from kofam 1:18:10.598457: Getting forward best hits from peptidase 1:18:21.228211: Getting reverse best hits from peptidase 1:18:22.643871: Getting descriptions of hits from peptidase 1:18:24.688377: Getting hits from pfam 1:18:41.265450: Getting hits from dbCAN 1:18:54.495537: Getting hits from VOGDB 1:25:30.712760: Merging ORF annotations 1:25:41.960795: Annotating bins21.5 1:25:48.329436: Turning genes from prodigal to mmseqs2 db 1:25:50.946707: Getting hits from kofam 1:31:36.616576: Getting forward best hits from peptidase 1:31:39.683745: Getting reverse best hits from peptidase 1:31:40.848627: Getting descriptions of hits from peptidase 1:31:41.071161: Getting hits from pfam 1:31:54.464233: Getting hits from dbCAN 1:31:58.928054: Getting hits from VOGDB 1:34:03.148602: Merging ORF annotations 1:34:10.541491: Annotating bins21.6 1:34:17.285158: Turning genes from prodigal to mmseqs2 db 1:34:20.056306: Getting hits from kofam 1:40:36.759055: Getting forward best hits from peptidase 1:40:39.844730: Getting reverse best hits from peptidase 1:40:40.973469: Getting descriptions of hits from peptidase 1:40:41.175140: Getting hits from pfam 1:40:54.681530: Getting hits from dbCAN 1:40:59.416042: Getting hits from VOGDB 1:43:13.896836: Merging ORF annotations 1:43:17.216725: Annotating bins21.7 1:43:21.602432: Turning genes from prodigal to mmseqs2 db 1:43:24.351326: Getting hits from kofam 1:52:26.127516: Getting forward best hits from peptidase 1:52:30.144402: Getting reverse best hits from peptidase 1:52:31.353257: Getting descriptions of hits from peptidase 1:52:31.855017: Getting hits from pfam 1:52:45.824918: Getting hits from dbCAN 1:52:52.830208: Getting hits from VOGDB 1:56:08.023279: Merging ORF annotations 1:56:24.484689: Annotations complete, processing annotations 1:56:25.243297: Completed annotations real 116m32.673s user 184m44.040s sys 14m21.874s Distilling... Traceback (most recent call last): File "/net/cn-1/mnt/SCRATCH/bin420-21/condaenvironments/metaG/DRAM/bin/DRAM.py", line 168, in args.func(**args_dict) File "/net/cn-1/mnt/SCRATCH/bin420-21/condaenvironments/metaG/DRAM/lib/python3.9/site-packages/mag_annotator/summarize_genomes.py", line 575, in summarize_genomes rrna_frame = pd.read_csv(rrna_path, sep='\t') File "/net/cn-1/mnt/SCRATCH/bin420-21/condaenvironments/metaG/DRAM/lib/python3.9/site-packages/pandas/util/_decorators.py", line 311, in wrapper return func(*args, **kwargs) File "/net/cn-1/mnt/SCRATCH/bin420-21/condaenvironments/metaG/DRAM/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 586, in read_csv return _read(filepath_or_buffer, kwds) File "/net/cn-1/mnt/SCRATCH/bin420-21/condaenvironments/metaG/DRAM/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 482, in _read parser = TextFileReader(filepath_or_buffer, **kwds) File "/net/cn-1/mnt/SCRATCH/bin420-21/condaenvironments/metaG/DRAM/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 811, in __init__ self._engine = self._make_engine(self.engine) File "/net/cn-1/mnt/SCRATCH/bin420-21/condaenvironments/metaG/DRAM/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1040, in _make_engine return mapping[engine](self.f, **self.options) # type: ignore[call-arg] File "/net/cn-1/mnt/SCRATCH/bin420-21/condaenvironments/metaG/DRAM/lib/python3.9/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 51, in __init__ self._open_handles(src, kwds) File "/net/cn-1/mnt/SCRATCH/bin420-21/condaenvironments/metaG/DRAM/lib/python3.9/site-packages/pandas/io/parsers/base_parser.py", line 222, in _open_handles self.handles = get_handle( File "/net/cn-1/mnt/SCRATCH/bin420-21/condaenvironments/metaG/DRAM/lib/python3.9/site-packages/pandas/io/common.py", line 702, in get_handle handle = open( FileNotFoundError: [Errno 2] No such file or directory: 'dram.annotation.MAGs.dir/rrnas.tsv' real 0m5.135s user 0m2.590s sys 0m1.599s DRAM finished at 22 Oct 19:21:34 mv: cannot stat ‘dram.genome_summaries.MAGs.dir’: No such file or directory moving results to /net/cn-1/mnt/SCRATCH/bin420-21/TuesdaySession/Results/dram_annotation/MAGs real 0m0.472s user 0m0.000s sys 0m0.067s DRAM results are in: /net/cn-1/mnt/SCRATCH/bin420-21/TuesdaySession/Results/dram_annotation/MAGs/DRAM.Results.dir.MAGs.dir I've done at Fri Oct 22 19:21:35 CEST 2021