Comments (10)
Hi, I am just about to release a patch for 3.2.1, could you try when released?
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Just echo-ing this -- I got the exact same error running the nf-core/cutandrun v3.2-g506a325 version of the pipeline on Nextflow 23.04.3 in Slurm/HPC setting.
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Sure, I actually just had some C&R data come off the sequencer on Friday so I planned to run the pipeline this week anyways. I'll follow up in the next few days.
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I came up with
--- a/bin/calc_frag_hist.py
+++ b/bin/calc_frag_hist.py
@@ -57,6 +57,9 @@ print("Calclate fragment histogram")
frag_path = os.path.abspath(args.frag_path)
frag_hist = None
+group_short = None
+rep_short = None
+
# Create list of deeptools raw fragment files
dt_frag_list = glob.glob(frag_path)
dt_frag_list.sort()
but happily receive other instructions to test.
from cutandrun.
After addressing variable visibility, the error changes to
ERROR ~ Error executing process > 'NFCORE_CUTANDRUN:CUTANDRUN:FRAG_LEN_HIST'
Caused by:
Process `NFCORE_CUTANDRUN:CUTANDRUN:FRAG_LEN_HIST` terminated with an error exit status (1)
Command executed:
calc_frag_hist.py \
--frag_path "*len.txt" \
--output frag_len_hist.txt
if [ -f "frag_len_hist.txt" ]; then
cat frag_len_header.txt frag_len_hist.txt > frag_len_mqc.yml
fi
cat <<-END_VERSIONS > versions.yml
"NFCORE_CUTANDRUN:CUTANDRUN:FRAG_LEN_HIST":
python: $(python --version | grep -E -o "([0-9]{1,}\.)+[0-9]{1,}")
numpy: $(python -c 'import numpy; print(numpy.__version__)')
pandas: $(python -c 'import pandas; print(pandas.__version__)')
seaborn: $(python -c 'import seaborn; print(seaborn.__version__)')
END_VERSIONS
Command exit status:
1
Command output:
Calclate fragment histogram
Command error:
Calclate fragment histogram
Traceback (most recent call last):
File "/home/sm718/.nextflow/assets/nf-core/cutandrun/bin/calc_frag_hist.py", line 117, in <module>
frag_hist["group"] = group_short
TypeError: 'NoneType' object does not support item assignment
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No one else is reporting these errors, this is strange!
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I just send batch job to our cluster with v3.2.1, let's see what happens here.
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Cannot find revision 3.2.1
-- Make sure that it exists in the remote repository https://github.com/nf-core/cutandrun
Can I call this with explicit -r 3.2.1? Or is it still just 3.2?
from cutandrun.
3.2.1 is out. nextflow pull cutandrun
just performed the update for me. Still running :-/
My initial reflex was that this could be a Python-version issue wrt variable scoping when these are implicitly defined in the loop - but I tested this and this is not the case. That said, Python is 3.7 for me.
From how I interpret this, this only makes sense if the loop is never entered, i.e. if
list(range(len(dt_frag_list)))
is empty.
Does that make any sense?
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I have rerun 3.2.1 and it first failed with the same error, then added
--- a/bin/calc_frag_hist.py
+++ b/bin/calc_frag_hist.py
@@ -25,6 +25,7 @@
# Author: @chris-cheshire
import os
+import sys
import glob
import argparse
@@ -61,6 +62,8 @@ frag_hist = None
dt_frag_list = glob.glob(frag_path)
dt_frag_list.sort()
+print("I: Iterating over "+str(len(dt_frag_list))+" files with fragments from derived from glob search '"+frag_path+"' - this number should not be 0, the argument was '"+args.frag_path+"', all executed in '"+os.getcwd()+"'")
+
for i in list(range(len(dt_frag_list))):
# Create dataframe from csv file for each file and save to a list of data frames
dt_frag_i = pd.read_csv(dt_frag_list[i], sep="\t", header=None, names=["Size", "Occurrences"])
and "-resume"-ed , corrected Python errors in my debug line :-) and resumed again. And then it worked. I found that the peak lists were not all cached when resumed - some files had still to be run. Would that be a potential explanation for the error? For a clearer error message, would you consider adding an extra debug message or even an early exit when the semantics are disturbed, like a glob not returning any results? Would you prefer me preparing a PR for that?
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