ga_merge_fasta.py not on docker image
Closed this issue · 6 comments
MetaPro.py dies with
/mydata/testout/GA_BWA/data/jobs/contigs_0_chocophlan_h3_chunk_bwa_pp not found. kill the pipe. restart this stage
This appears to be due to a missing script:
2021-11-04 19:20:53.449761 GA BWA merge leftover reads contigs_0 python3: can't open file '/pipeline/Scripts/ga_merge_fasta.py': [Errno 2] No such file or directory
Process Process-1:
Traceback (most recent call last):
File "/usr/lib/python3.6/multiprocessing/process.py", line 258, in _bootstrap
self.run()
File "/usr/lib/python3.6/multiprocessing/process.py", line 93, in run
self._target(*self._args, **self._kwargs)
File "/pipeline/MetaPro_commands.py", line 118, in create_and_launch
sp.check_output(["sh", shell_script_full_path])#, stderr = sp.STDOUT)
File "/usr/lib/python3.6/subprocess.py", line 356, in check_output
**kwargs).stdout
File "/usr/lib/python3.6/subprocess.py", line 438, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['sh', '/mydata/testout/GA_BWA/BWA_pp_contigs_0_chocophlan_h3_chunk.sh']' returned non-zero exit status 2.
And indeed:
>ls /pipeline/Scripts/ga*
/pipeline/Scripts/ga_BLAT_generic_v2.py
/pipeline/Scripts/ga_BWA_generic_v2.py
/pipeline/Scripts/ga_Diamond_generic_v2.py
/pipeline/Scripts/ga_Final_merge_v4.py
that's a goof on my end.
thanks! please pull the latest develop image
I did, but now I get a new error
Traceback (most recent call last):
File "/pipeline/MetaPro.py", line 2731, in <module>
main(config_file, pair_1, pair_2, single, contig, output_folder, num_threads, args_pack, tutorial_mode)
File "/pipeline/MetaPro.py", line 802, in main
command_list = commands.create_BWA_pp_command_v2(GA_BWA_label, assemble_contigs_label, ref_tag, ref_path, full_sample_path, marker_file)
File "/pipeline/MetaPro_commands.py", line 2181, in create_BWA_pp_command_v2
if("chunk" in ref_file):
NameError: name 'ref_file' is not defined
Which is true, ref_file is not passed to this function:
def create_BWA_pp_command_v2(self, stage_name, dependency_stage_name, ref_tag, ref_path, query_file, marker_file):
sample_root_name = os.path.basename(query_file)
sample_root_name = os.path.splitext(sample_root_name)[0]
#meant to be called on the split-file version. PP script will not merge gene maps.
subfolder = os.path.join(self.Output_Path, stage_name)
data_folder = os.path.join(subfolder, "data")
bwa_folder = os.path.join(data_folder, "1_bwa")
split_folder = os.path.join(data_folder, "0_read_split")
pp_folder = os.path.join(data_folder, "2_bwa_pp")
final_folder = os.path.join(subfolder, "final_results")
dep_loc = os.path.join(self.Output_Path, dependency_stage_name, "final_results")
jobs_folder = os.path.join(data_folder, "jobs")
self.make_folder(subfolder)
self.make_folder(data_folder)
self.make_folder(bwa_folder)
self.make_folder(final_folder)
self.make_folder(jobs_folder)
self.make_folder(pp_folder)
reads_in = query_file
bwa_in = os.path.join(bwa_folder, sample_root_name + "_" + ref_tag + ".sam")
reads_out = ""
if("chunk" in ref_file):
whoops, used the wrong varname.
Please try now. (supossed to have been ref_path, to sense if the version of chocophlan is the smaller, whole-version, or the new, bigger, updated version that had to be chunked in order to fit on our hardware)
Same problem. The docker image is an hour old, so I did get the new one.
Can you do an actual test run yourself? Saves me some debugging.
should be ok now. it was 1 locations of the wrong var, to allow for back-compatibility of chocophlan.
patched ages ago.