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BinPro / CONCOCT

Clustering cONtigs with COverage and ComposiTion
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Concoct Error Could not retrieve index file #319

Open howla1ke opened 1 year ago

howla1ke commented 1 year ago

Hello, I am trying to run concoct, I successfully used this script: cut_up_fasta.py 58D_contigs-fixed.fa -c 10000 -o 0 --merge_last -b contigs_10K.bed > E58_contigs_10K.fa I then go to create the coverage table and I get errors. I have a bam file, sorted.bam, and bam.bai files and I get an error saying that it cannot open the indexed files. All of the mapping was done using BWA, against the original contigs file (58D_contigs-fixed.fa) can you please tell me what I am doing wrong here. I followed the advice of others ie renaming sample.sorted.bam to sample.bam. I also moved the sorted and indexed bam files into a directory. Nothing is working for me.

concoct_coverage_table.py contigs_10K.bed mapping/D_A20-E58-D3.interleave.bam > coverage_table.tsv [E::hts_open_format] Failed to open file "mapping/D_A20-E58-D3.interleave.bam" : No such file or directory ERROR: fail to open index BAM file 'mapping/D_A20-E58-D3.interleave.bam' Traceback (most recent call last): File "/opt/software/CONCOCT/1.1.0-foss-2020b-Python-2.7.18/bin/concoct_coverage_table.py", line 91, in generate_input_table(args.bedfile, args.bamfiles, samplenames=samplenames) File "/opt/software/CONCOCT/1.1.0-foss-2020b-Python-2.7.18/bin/concoct_coverage_table.py", line 42, in generate_input_table sys.stderr.write(err) TypeError: expected a string or other character buffer object $ concoct_coverage_table.py contigs_10K.bed D_A20-E58-D3.interleave.bam > coverage_table.tsv [E::idx_find_and_load] Could not retrieve index file for 'D_A20-E58-D3.interleave.bam' ERROR: fail to open index BAM file 'D_A20-E58-D3.interleave.bam' Traceback (most recent call last): File "/opt/software/CONCOCT/1.1.0-foss-2020b-Python-2.7.18/bin/concoct_coverage_table.py", line 91, in generate_input_table(args.bedfile, args.bamfiles, samplenames=samplenames) File "/opt/software/CONCOCT/1.1.0-foss-2020b-Python-2.7.18/bin/concoct_coverage_table.py", line 42, in generate_input_table sys.stderr.write(err) TypeError: expected a string or other character buffer object $ ls 58D_contigs-fixed.fa D_A20-E58-D3.interleave.bam E58_contigs_10K.fa contigs_10K.bed D_A20-E58-D3_S8_L001.interleave.fq.bam coverage_table.tsv D_A20-E58-D3_S8_L001.interleave.fq.sorted.bam.bai [howla1keCMICH@dev-intel14-k20 E58_Concoct2]$ mv D_A20-E58-D3_S8_L001.interleave.fq.sorted.bam.bai D_A20-E58-D3.interleave.bam.bai $ ls 58D_contigs-fixed.fa D_A20-E58-D3.interleave.bam E58_contigs_10K.fa contigs_10K.bed D_A20-E58-D3.interleave.bam.bai coverage_table.tsv D_A20-E58-D3_S8_L001.interleave.fq.bam $ mkdir bam $ cd bam/ $ pwd

$ cd .. $ mv D_A20-E58-D3.interleave.bam /mnt/gs21/scratch//E58_Concoct2/bam $ mv D_A20-E58-D3.interleave.bam.bai mv: missing destination file operand after ‘D_A20-E58-D3.interleave.bam.bai’ Try 'mv --help' for more information. $ mv D_A20-E58-D3.interleave.bam.bai /mnt/gs21/scratch/E58_Concoct2/bam $ ls 58D_contigs-fixed.fa contigs_10K.bed D_A20-E58-D3_S8_L001.interleave.fq.bam bam coverage_table.tsv E58_contigs_10K.fa $ rm -r coverage_table.tsv $ concoct_coverage_table.py contigs_10K.bed mapping/~/bam > coverage_table.tsv [E::hts_open_format] Failed to open file "mapping/~/bam" : No such file or directory ERROR: fail to open index BAM file 'mapping/~/bam' Traceback (most recent call last): File "/opt/software/CONCOCT/1.1.0-foss-2020b-Python-2.7.18/bin/concoct_coverage_table.py", line 91, in generate_input_table(args.bedfile, args.bamfiles, samplenames=samplenames) File "/opt/software/CONCOCT/1.1.0-foss-2020b-Python-2.7.18/bin/concoct_coverage_table.py", line 42, in generate_input_table sys.stderr.write(err) TypeError: expected a string or other character buffer object $ concoct_coverage_table.py contigs_10K.bed ~/bam > coverage_table.tsv [E::hts_open_format] Failed to open file "/mnt/home/howla1keCMICH/bam" : No such file or directory ERROR: fail to open index BAM file '/mnt/home/howla1keCMICH/bam' Traceback (most recent call last): File "/opt/software/CONCOCT/1.1.0-foss-2020b-Python-2.7.18/bin/concoct_coverage_table.py", line 91, in generate_input_table(args.bedfile, args.bamfiles, samplenames=samplenames) File "/opt/software/CONCOCT/1.1.0-foss-2020b-Python-2.7.18/bin/concoct_coverage_table.py", line 42, in generate_input_table sys.stderr.write(err) TypeError: expected a string or other character buffer object $ concoct_coverage_table.py contigs_10K.bed ~/mnt/gs21/scratch/E58_Concoct2/bam > coverage_table.tsv [E::hts_open_format] Failed to open file "/mnt/home/mnt/gs21/scratch/E58_Concoct2/bam" : No such file or directory ERROR: fail to open index BAM file '/mnt/home/howla1keCMICH/mnt/gs21/scratch/E58_Concoct2/bam' Traceback (most recent call last): File "/opt/software/CONCOCT/1.1.0-foss-2020b-Python-2.7.18/bin/concoct_coverage_table.py", line 91, in generate_input_table(args.bedfile, args.bamfiles, samplenames=samplenames) File "/opt/software/CONCOCT/1.1.0-foss-2020b-Python-2.7.18/bin/concoct_coverage_table.py", line 42, in generate_input_table sys.stderr.write(err) TypeError: expected a string or other character buffer object

arijitnus commented 1 year ago

The same issue is being faced by me, and can't figure out the reason @howla1ke . A similar discussion is found here https://github.com/BinPro/CONCOCT/issues/307 Let's try this, if that helps us solve

howla1ke commented 1 year ago

Hi, thank you! Let me know if you try this please. I am going to use Concoct through Anvio to see if I can get it to bin this way. I’ll let you know how this goes.