FileNotFoundError: [Errno 2] No such file or directory: 'makeblastdb'

[wdecoster]

I right now don't have the time to investigate this further but I already wanted to report the error.

It's perhaps a dependency that needs to be installed?

[M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 1066443 reads
Traceback (most recent call last):
  File "advntr.py", line 60, in <module>
    run_advntr()
  File "advntr.py", line 49, in run_advntr
    genotype(args, genotype_parser)
  File "/home/wdecoster/bin/adVNTR/src/advntr_commands.py", line 73, in genotype
    genome_analyzier.find_repeat_counts_from_alignment_file(input_file)
  File "/home/wdecoster/bin/adVNTR/src/genome_analyzer.py", line 71, in find_repeat_counts_from_alignment_file
    vntr_reads = self.get_vntr_filtered_reads_map(unmapped_reads_file)
  File "/home/wdecoster/bin/adVNTR/src/profiler.py", line 8, in wrapper
    retval = func(*args, **kwargs)
  File "/home/wdecoster/bin/adVNTR/src/genome_analyzer.py", line 33, in get_vntr_filtered_reads_map
    read_ids = self.vntr_finder[vid].filter_reads_with_keyword_matching(self.working_dir, read_file, illumina)
  File "/home/wdecoster/bin/adVNTR/src/profiler.py", line 8, in wrapper
    retval = func(*args, **kwargs)
  File "/home/wdecoster/bin/adVNTR/src/vntr_finder.py", line 88, in filter_reads_with_keyword_matching
    empty_db = make_blast_database(read_file, blast_db_name)
  File "/home/wdecoster/bin/adVNTR/src/blast_wrapper.py", line 13, in make_blast_database
    call(['makeblastdb'] + make_db_args)
  File "/home/wdecoster/anaconda3/lib/python3.6/subprocess.py", line 267, in call
    with Popen(*popenargs, **kwargs) as p:
  File "/home/wdecoster/anaconda3/lib/python3.6/subprocess.py", line 707, in __init__
    restore_signals, start_new_session)
  File "/home/wdecoster/anaconda3/lib/python3.6/subprocess.py", line 1333, in _execute_child
    raise child_exception_type(errno_num, err_msg)
FileNotFoundError: [Errno 2] No such file or directory: 'makeblastdb'

Cheers, Wouter

[mehrdadbakhtiari]

Hi Wouter,

Is ncbi-blast (version 2.2.29 or above) installed? It seems that the program cannot find makeblastdb, which is one the blast's scripts. Let me know if makeblastdb is available in the path but the problem exists.

Best, Mehrdad

[wdecoster]

Uh I missed point 3 in the dependencies :-)

In addition, ncbi-blast version 2.2.29 or above is required

I happily installed dependencies but missed this one. So this is not an issue. Sorry!