Closed mdehollander closed 9 years ago
I am running this command:
groopm extract binning/groopm/database.gm -b 6 -m reads --threads 16 spades/bwa/*-s.bam -v ******************************************************************************* [[GroopM 0.3.4]] Running in 'reads' extraction mode... ******************************************************************************* Loading data from: binning/groopm/database.gm GroopM DB version (5) up to date Loaded indices with condition: ((length >= 0) & (bid == 6)) Working with: 619 contigs Loading coverage profiles Loading PCA kmer sigs (42 dimensional space) Loading PCA kmer variance (total variance: 0.80) Loading contig names Loading contig lengths (Total: 5893597 BP) Loading contig GC ratios (Average GC: 0.335) Creating color map Loading bin assignments Reticulating splines Making bin objects Loaded 1 bins from database { THIS: 0:00:01.000 || TOTAL: 0:00:01.001 } Extracting reads Thread_0 Preparing to extract reads from file: C1-s Thread_1 Preparing to extract reads from file: C2-s Thread_2 Preparing to extract reads from file: C3-s Thread_3 Preparing to extract reads from file: C4-s Thread_4 Preparing to extract reads from file: S1-s Thread_6 Preparing to extract reads from file: S2-s Thread_5 Preparing to extract reads from file: S3-s Thread_7 Preparing to extract reads from file: SR1-s Thread_8 Preparing to extract reads from file: SR2-s Thread_10 Preparing to extract reads from file: SR3-s
but no files are written to disk.
The target bin is not empty:
groopm print binning/groopm/database.gm -b 6 "bin id" "Likely chimeric" "length (bp)" "# seqs" "GC mean" "GC std" "Coverage 1 mean" "Coverage 1 std" "Coverage 2 mean" "Coverage 2 std" "Coverage 3 mean" "Coverage 3 std" "Coverage 4 mean" "Coverage 4 std" "Coverage 5 mean" "Coverage 5 std" "Coverage 6 mean" "Coverage 6 std" "Coverage 7 mean" "Coverage 7 std" "Coverage 8 mean" "Coverage 8 std" "Coverage 9 mean" "Coverage 9 std" "Coverage 10 mean" "Coverage 10 std" 6 False 5893597 619 0.3332 0.0222 0.0107 0.0790 0.0282 0.1230 0.4013 0.2556 1.0898 0.5213 0.0692 0.3295 1.6939 0.6566 1.6240 0.6854 3.5212 1.2434 0.0977 0.3936 0.0315 0.1601
When I look at the dumo output for contigs and see if there are any reads mapping to this contig in the sam file there is a match:
groopm print binning/groopm/database.gm -b 6 -f contigs #"bid" "cid" "length" "GC" 6 NODE_10007_length_2698_cov_3.04851_ID_20013 2698 0.3047 grep 'NODE_10007_length_2698_cov_3.04851_ID_20013' spades/bwa/*.sam spades/bwa/SR2.sam:M01910:32:000000000-ADVL1:1:2116:6494:11842 163 NODE_10007_length_2698_cov_3.04851_ID_20013 584 60 214M = 1045 713 GTAAAGTCGGCAATTGTAACCGATTTTATACTTTCTGTAGAAATTGTAATTATCGCTTTAGGAACCGTAATCGGAAAACCATTGGTTTCTCAAATTATCACAGTTTCAATCATCGCATTAATTGCAACAATTGGCGTTTACGGAATCGTAGCGCTTATTGTTCGTATGGATGAAGTAGGTTTCAAAATGATTAAAAGCAGTAAAAAAGAAAACA CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGF@FGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGGGGGGFFFFCFGGGGGGGGGGDDGGGGFCGGEEGCGGGGGGGGGGFGD8=FGGGGGGGGGGGCFGGGGGGFDGGGFGGCFFGFFF5FFFA NM:i:0 MD:Z:214 AS:i:214 XS:i:0
Is there a way to get the individual reads written to disk?
I realised that this is a BamM issue, so continue there
I am running this command:
but no files are written to disk.
The target bin is not empty:
When I look at the dumo output for contigs and see if there are any reads mapping to this contig in the sam file there is a match:
Is there a way to get the individual reads written to disk?