No such file or directory error

[jeremysutherland]

Script

db="ncbi_nt/ncbi_nt"
kma -ipe A16_S5_3_F22_S139_R1_001.atria.fastq.gz A16_S5_3_F22_S139_R2_001.atria.fastq.gz -o A16_S5_3_F22_S139_out_kma -t_db $db -t 20 -1t1 -mem_mode -and -apm f

List files

(ccmetagen) [jus1990@p-sc-2393 ccmetagen]$ ls
A16_S5_3_F22_S139_out_kma.aln
A16_S5_3_F22_S139_out_kma.fsa
A16_S5_3_F22_S139_R1_001.atria.fastq.gz
A16_S5_3_F22_S139_R2_001.atria.fastq.gz
merged.tab
syn.tab
taxdump.tar.gz
A16_S5_3_F22_S139_out_kma.frag.gz
A16_S5_3_F22_S139_out_kma.res
ncbi_nt
taxa.tab

run CCMetagen.py

(ccmetagen) [jus1990@p-sc-2393 ccmetagen]$ CCMetagen.py -i A16_S5_3_F22_S139_out_kma -o results

Reading file A16_S5_3_F22_S139_out_kma

Traceback (most recent call last):
File "/storage/home/jus1990/work/miniconda3/envs/ccmetagen/bin/CCMetagen.py", line 211, in
df = pd.read_csv(f, sep='\t', index_col=0, encoding='latin1')
File "/storage/home/jus1990/work/miniconda3/envs/ccmetagen/lib/python3.6/site-packages/pandas/io/parsers.py", line 688, in read_csv
return _read(filepath_or_buffer, kwds)
File "/storage/home/jus1990/work/miniconda3/envs/ccmetagen/lib/python3.6/site-packages/pandas/io/parsers.py", line 454, in _read
parser = TextFileReader(fp_or_buf, **kwds)
File "/storage/home/jus1990/work/miniconda3/envs/ccmetagen/lib/python3.6/site-packages/pandas/io/parsers.py", line 948, in init
self._make_engine(self.engine)
File "/storage/home/jus1990/work/miniconda3/envs/ccmetagen/lib/python3.6/site-packages/pandas/io/parsers.py", line 1180, in _make_engine
self._engine = CParserWrapper(self.f, **self.options)
File "/storage/home/jus1990/work/miniconda3/envs/ccmetagen/lib/python3.6/site-packages/pandas/io/parsers.py", line 1993, in init
src = open(src, "rb")
FileNotFoundError: [Errno 2] No such file or directory: 'A16_S5_3_F22_S139_out_kma' <<<<<<<<<<<<<<<<<<<<<

[vrmarcelino]

I think the .res is missing. Try: CCMetagen.py -i A16_S5_3_F22_S139_out_kma.res -o results

[jeremysutherland]

Thanks that did the trick. But I ran into a different issue:

(ccmetagen) [jus1990@p-sc-2360 ccmetagen]$ CCMetagen.py -i A16_S5_3_F22_S139_out_kma.res -o results

Reading file A16_S5_3_F22_S139_out_kma.res


Traceback (most recent call last):
  File "/storage/home/jus1990/work/miniconda3/envs/ccmetagen/bin/CCMetagen.py", line 274, in <module>
    df = fParseKMA.populate_w_tax(df, ref_database, st, gt, ft, ot, ct, pt)
  File "/storage/home/jus1990/work/miniconda3/envs/ccmetagen/lib/python3.6/site-packages/ccmetagen/fParseKMA.py", line 104, in populate_w_tax
    match_info = fNCBItax.lineage_extractor(match_info.TaxId, match_info, taxfile)
  File "/storage/home/jus1990/work/miniconda3/envs/ccmetagen/lib/python3.6/site-packages/ccmetagen/fNCBItax.py", line 24, in lineage_extractor
    lineage = ncbi.get_lineage(query_taxid)
  File "/storage/home/jus1990/work/miniconda3/envs/ccmetagen/lib/python3.6/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 238, in get_lineage
    raise ValueError("%s taxid not found" %taxid)
ValueError: 3878 taxid not found

[vrmarcelino]

You probably need to update your local ETE3 database, which contains the taxids and lineage information:

python
from ete3 import NCBITaxa
ncbi = NCBITaxa()
ncbi.update_taxonomy_database()
quit()