Kate Floer
01/22/2025, 4:35 PMnextflow run nf-core/hic -profile test,conda --outdir /home/floer/nf_test executor > local (7)
[47/557dd9] NFCORE_HIC:HIC:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv) [100%] 1 of 1 ✔
[bc/3b6050] NFCORE_HIC:HIC:PREPARE_GENOME:BOWTIE2_BUILD (W303_SGD_2015_JRIU00000000.fsa) [100%] 1 of 1 ✔
[f4/a8e314] NFCORE_HIC:HIC:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (W303_SGD_2015_JRIU00000000.fsa) [100%] 1 of 1 ✔
[2a/cafb8d] NFCORE_HIC:HIC:PREPARE_GENOME:GET_RESTRICTION_FRAGMENTS (A^AGCTT) [100%] 1 of 1 ✔
[a6/cba38e] NFCORE_HIC:HIC:FASTQC (SRR4292758) [100%] 1 of 1 ✔
[- ] NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN -
[- ] NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:TRIM_READS -
[- ] NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN_TRIMMED -
[- ] NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:MERGE_BOWTIE2 -
[- ] NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:COMBINE_MATES -
[- ] NFCORE_HIC:HIC:HICPRO:GET_VALID_INTERACTION -
[- ] NFCORE_HIC:HIC:HICPRO:MERGE_VALID_INTERACTION -
[- ] NFCORE_HIC:HIC:HICPRO:MERGE_STATS -
[- ] NFCORE_HIC:HIC:HICPRO:HICPRO2PAIRS -
[cc/0c1892] NFCORE_HIC:HIC:COOLER:COOLER_MAKEBINS (null}) [100%] 2 of 2, failed: 2 ✘
[- ] NFCORE_HIC:HIC:COOLER:COOLER_CLOAD -
[- ] NFCORE_HIC:HIC:COOLER:COOLER_BALANCE -
[- ] NFCORE_HIC:HIC:COOLER:COOLER_ZOOMIFY -
[- ] NFCORE_HIC:HIC:COOLER:COOLER_DUMP -
[- ] NFCORE_HIC:HIC:COOLER:SPLIT_COOLER_DUMP -
[- ] NFCORE_HIC:HIC:HIC_PLOT_DIST_VS_COUNTS -
[- ] NFCORE_HIC:HIC:COMPARTMENTS:COOLTOOLS_EIGSCIS -
[- ] NFCORE_HIC:HIC:TADS:COOLTOOLS_INSULATION -
[- ] NFCORE_HIC:HIC:TADS:HIC_FIND_TADS -
[- ] NFCORE_HIC:HIC:CUSTOM_DUMPSOFTWAREVERSIONS -
[- ] NFCORE_HIC:HIC:MULTIQC -
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Error executing process > 'NFCORE_HIC:HIC:COOLER:COOLER_MAKEBINS (null})'
Caused by:
Process `NFCORE_HIC:HIC:COOLER:COOLER_MAKEBINS (null})` terminated with an error exit status (1)
Command executed:
cooler makebins \
\
W303_SGD_2015_JRIU00000000.fsa.sizes \
2000 > cooler_bins_2000.bed
cat <<-END_VERSIONS > versions.yml
"NFCORE_HIC:HIC:COOLER:COOLER_MAKEBINS":
cooler: $(cooler --version 2>&1 | sed 's/cooler, version //')
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
Traceback (most recent call last):
File "/home/floer/work/conda/env-cd84d045ac8cca6d16b389fcdb8d93bc/bin/cooler", line 6, in <module>
from cooler.cli import cli
File "/home/floer/work/conda/env-cd84d045ac8cca6d16b389fcdb8d93bc/lib/python3.11/site-packages/cooler/__init__.py", line 14, in <module>
from .api import Cooler, annotate
File "/home/floer/work/conda/env-cd84d045ac8cca6d16b389fcdb8d93bc/lib/python3.11/site-packages/cooler/api.py", line 13, in <module>
from .core import (
File "/home/floer/work/conda/env-cd84d045ac8cca6d16b389fcdb8d93bc/lib/python3.11/site-packages/cooler/core.py", line 3, in <module>
from pandas.api.types import is_categorical
ImportError: cannot import name 'is_categorical' from 'pandas.api.types' (/home/floer/work/conda/env-cd84d045ac8cca6d16b389fcdb8d93bc/lib/python3.11/site-packages/pandas/api/types/__init__.py)
Work dir:
/home/floer/work/0f/27c3e96b6a4de722b1cdd73e386a1a
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
-- Check '.nextflow.log' file for detailsSimon Pearce
01/27/2025, 10:44 AM