pyTask1 failed

[ybdong919]

executor > local (284)
[ae/f349d0] process > fastqc (5) [100%] 40 of 40 ✔
[f8/b021b6] process > trimmomatic (40) [100%] 40 of 40 ✔
[ac/02473f] process > bbtools (40) [100%] 40 of 40 ✔
[28/1c4344] process > fastqc2 (40) [100%] 40 of 40 ✔
[a5/03b5b4] process > multiqc (40) [100%] 40 of 40 ✔
[a3/ad6bdf] process > mash (40) [100%] 40 of 40 ✔
[af/c547f7] process > unicycler (27) [ 5%] 2 of 39
[09/170d52] process > quast (2) [100%] 2 of 2
[ff/f0ef6e] process > pyTask1 (2) [100%] 2 of 2, failed: 2
[- ] process > readssum -
[- ] process > pyTask2 -
[- ] process > prokka -
[- ] process > amrfinder -
[- ] process > mlst -
[- ] process > kraken -
[- ] process > pyTask3 -
[- ] process > pyTask4 -
[- ] process > plusAnalyses -
ERROR ~ Error executing process > 'pyTask1 (1)'

Caused by:
Process pyTask1 (1) terminated with an error exit status (1)

Command executed:

#!/usr/bin/env python3
import sys
import os
import subprocess
import argparse
import datetime
import fnmatch
import re
import pandas as pd

items = "/blue/bphl-florida/ntarigopula/data/pipeline_test/sanibel/20230912_jax_230605_PLN_WLK_AP_test_v2/output/JBI23000998A".strip().split("/")
#print(items[-1])
filepath1 = "/blue/bphl-florida/ntarigopula/data/pipeline_test/sanibel/20230912_jax_230605_PLN_WLK_AP_test_v2/output/JBI23000998A"+"/mash_output/"+items[-1]+"_distances_top10.tab"
with open(filepath1, 'r') as mash:
top_hit = mash.readline()
top_hit = str(top_hit)
cells = top_hit.split()
acell = cells[0]
subcells = re.split('-.-|subsp',acell)
subsubcells = subcells[1].split('')
genus = subsubcells[0]
species = subsubcells[1]
distance = cells[2]
accession = top_hit.split("-")[5]
#print(accession)

filepath2 = "/blue/bphl-florida/ntarigopula/data/pipeline_test/sanibel/20230912_jax_230605_PLN_WLK_AP_test_v2/output/JBI23000998A"+"/"+items[-1]+"_assembly/quast_results/report.tsv"
df = pd.read_table(filepath2, sep=" ")
assem = list(df.columns)[1]
#print(assem)
contigs = df[assem][12].astype(int)
long_contig = df[assem][13].astype(int)
n50 = df[assem][16].astype(int)
l50 = df[assem][18].astype(int)
genome = df[assem][14].astype(int)
gc = df[assem][15].astype(int)
#print(genome)

f = open("pyoutputs.txt", "w")
f.write(str(genus)+","+str(species)+","+str(distance)+","+str(accession)+","+str(assem)+","+str(contigs)+","+str(long_contig)+","+str(n50)+","+str(l50)+","+str(genome)+","+str(gc))
f.close

Command exit status:
1

Command output:
(empty)

Command error:
Traceback (most recent call last):
File ".command.sh", line 9, in
import pandas as pd
ModuleNotFoundError: No module named 'pandas'

[ybdong919]

pandas is not installed