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Traceback issues #3

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oeco28 opened this issue Nov 22, 2019 · 0 comments
Open

Traceback issues #3

oeco28 opened this issue Nov 22, 2019 · 0 comments

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@oeco28
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oeco28 commented Nov 22, 2019

Hi!
I am trying the general pathways analysis with my data and I get a callback() error that I am having a hard time interpreting.
I prepared the reference:
$paladin prepare -r1

And then map read data to the uniprot reference:

$paladin align -t 4 -o paladin1 uniprot_sprot.fasta.gz 4_CAAGCT_S38_L007_R1_001.fastq.gz

I get paladin1.sam and paladin1_uniprot.tsv as output files

I was curious about using the plugin to esimate pathways
and I tried running:

$/data/cornejo/projects/programs/paladin-plugins/paladin-plugins.py @@pathways -i paladin1_uniprot.tsv -q 20 -s Firmicutes -p ec00521

and

$paladin-plugins.py @@pathways -i paladin1_uniprot.tsv -q 20 -l 2

I am having the issue that I get a callback() error. See below. But I am not sure about how to interpret it..

Populating taxonomic lineage data...
Traceback (most recent call last):
File "/data/cornejo/projects/programs/paladin-plugins/paladin-plugins.py", line 118, in
core.main.exec_pipeline(pipeline)
File "/data/cornejo/projects/programs/paladin-plugins/core/main.py", line 350, in exec_pipeline
dependency.callback_init()
File "/data/cornejo/projects/programs/paladin-plugins/plugins/taxonomy.py", line 78, in taxonomy_init
populate_database()
File "/data/cornejo/projects/programs/paladin-plugins/plugins/taxonomy.py", line 146, in populate_database
DataStore.get_entry("taxonomy").insert_rows("lineage", [(fields[1], fields[8])])
File "/data/cornejo/projects/programs/paladin-plugins/core/datastore.py", line 75, in insert_rows
cursor.executemany("INSERT INTO {0} VALUES ({1})".format(name, param_tokens), data)
sqlite3.OperationalError: disk I/O error

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