Concoct Error Could not retrieve index file

[howla1ke]

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]

The same issue is being faced by me, and can't figure out the reason @howla1ke .
A similar discussion is found here #307
Let's try this, if that helps us solve

[howla1ke]

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.