conda info -e
should show you your environments
ddocent_env /home/dongmin/.conda/envs/ddocent_env
base * /home/dongmin/miniconda3
cocacola_env /home/dongmin/miniconda3/envs/cocacola_env
concoct_env /home/dongmin/miniconda3/envs/concoct_env
ddocent_env /home/dongmin/miniconda3/envs/ddocent_env
gimme /home/dongmin/miniconda3/envs/gimme
qiime2-2018.6 /home/dongmin/miniconda3/envs/qiime2-2018.6
Hello there,
I ran a de novo assembly of metagenomics ngs data with MEGAHIT and afterwards I followed the CONCOCT tutorial. When running
concoct_coverage_table.py final.contigs_10K.bed ~/*sorted.bam > coverage_table.tsv
I get an error message for each line in the bed file:
...
Errors in BED line 'k141_25554 0 324 k141_25554.0'
Errors in BED line 'k141_25555 0 377 k141_25555.0'
Errors in BED line 'k141_25556 0 380 k141_25556.0'
Errors in BED line 'k141_25557 0 623 k141_25557.0'
Errors in BED line 'k141_25558 0 350 k141_25558.0'
Errors in BED line 'k141_25559 0 301 k141_25559.0'
...
I only have one sample. Maybe that is causing an exception?
Any help would be appreciated. Thank you.
@alneberg I got it running in my normal enviroment. I had to switch to python 3, install scikit-learn with pip and now it is currently running (I can see the samtools process).
It is one sample containing an unknown number of bacterial species (most likely also undescribed ones). So I can skip concoct for my analysis?
concoct --composition_file contigs_10K.fa --coverage_file coverage_table.tsv -b concoct_output
with the following errors: Traceback (most recent call last):INFO:root:Will call vbgmm with parameters:
... step (see log example in this issue: BinPro/CONCOCT#238 ) ?
Hi, I'm running into the "Errors in BED line..." problem when running concoct_coverage_table.py (first few lines and the final error message pasted below). Same result when I try running samtools bedcov. I'm working with a new conda installation of concoct and have tried your suggestions to other posters above, but with no change in the output so far. Any idea what else could be causing this or what else I could try? Any help would be much appreciated!
Errors in BED line 'k127_592283 0 315 k127_592283.concoct_part_0'
Errors in BED line 'k127_643785 0 329 k127_643785.concoct_part_0'
Errors in BED line 'k127_283271 0 304 k127_283271.concoct_part_0'
Errors in BED line 'k127_669536 0 363 k127_669536.concoct_part_0'
Errors in BED line 'k127_746789 0 329 k127_746789.concoct_part_0'
Errors in BED line 'k127_206016 0 1047 k127_206016.concoct_part_0'
...
Traceback (most recent call last):
File "/n/home00/lmward/.conda/envs/concoct_env2/bin/concoct_coverage_table.py", line 91, in <module>
generate_input_table(args.bedfile, args.bamfiles, samplenames=samplenames)
File "/n/home00/lmward/.conda/envs/concoct_env2/bin/concoct_coverage_table.py", line 61, in generate_input_table
df = pd.read_table(fh, header=None)
File "/n/home00/lmward/.conda/envs/concoct_env2/lib/python3.7/site-packages/pandas/io/parsers.py", line 676, in parser_f
return _read(filepath_or_buffer, kwds)
File "/n/home00/lmward/.conda/envs/concoct_env2/lib/python3.7/site-packages/pandas/io/parsers.py", line 448, in _read
parser = TextFileReader(fp_or_buf, kwds)
File "/n/home00/lmward/.conda/envs/concoct_env2/lib/python3.7/site-packages/pandas/io/parsers.py", line 880, in init
self._make_engine(self.engine)
File "/n/home00/lmward/.conda/envs/concoct_env2/lib/python3.7/site-packages/pandas/io/parsers.py", line 1114, in _make_engine
self._engine = CParserWrapper(self.f, self.options)
File "/n/home00/lmward/.conda/envs/concoct_env2/lib/python3.7/site-packages/pandas/io/parsers.py", line 1891, in init
self._reader = parsers.TextReader(src, **kwds)
File "pandas/_libs/parsers.pyx", line 532, in pandas._libs.parsers.TextReader.cinit
pandas.errors.EmptyDataError: No columns to parse from file