hic
hic copied to clipboard
nf-core
conda environment error
Hi, I have an error while trying to run the hic pipeline on the test data with the conda environment.
Looks like a python module is missing.
Thanks for your help
$ ./nextflow run nf-core/hic -profile test,conda
N E X T F L O W ~ version 21.04.3
Launching `nf-core/hic` [distracted_swanson] - revision: ac74763a91 [master]
------------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/hic v1.3.0
------------------------------------------------------
WARN: The `into` operator should be used to connect two or more target channels -- consider to replace it with `.set { fasta_for_index }`
Core Nextflow options
revision : master
runName : distracted_swanson
container : nfcore/hic:1.3.0
launchDir : /env/export/v_bigtmp/eb/test
workDir : /env/export/v_bigtmp/eb/test/work
projectDir : /home/bonnet/.nextflow/assets/nf-core/hic
userName : bonnet
profile : test,conda
configFiles : /home/bonnet/.nextflow/assets/nf-core/hic/nextflow.config
Input/output options
input_paths : [[SRR4292758_00, [https://github.com/nf-core/test-datasets/raw/hic/data/SRR4292758_00_R1.fastq.gz, https://github.com/nf-core/test-datasets/raw/hic/data/SRR4292758_00_R2.fastq.gz]]]
Reference genome options
fasta : https://github.com/nf-core/test-datasets/raw/hic/reference/W303_SGD_2015_JRIU00000000.fsa
Digestion Hi-C
restriction_site : A^AGCTT
ligation_site : AAGCTAGCTT
DNAse Hi-C
min_cis_dist : 0
Alignments
bwt2_opts_end2end : --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder
bwt2_opts_trimmed : --very-sensitive -L 20 --score-min L,-0.6,-0.2 --end-to-end --reorder
Valid Pairs Detection
max_insert_size : 600
min_insert_size : 100
max_restriction_fragment_size: 100000
min_restriction_fragment_size: 100
Contact maps
bin_size : 1000
ice_filter_high_count_perc : 0
Downstream Analysis
res_dist_decay : 1000
tads_caller : insulation,hicexplorer
res_tads : 1000
res_compartments : 1000
Generic options
max_multiqc_email_size : 25 MB
Max job request options
max_cpus : 2
max_memory : 4 GB
max_time : 1h
Institutional config options
config_profile_name : Hi-C test data from Schalbetter et al. (2017)
config_profile_description : Minimal test dataset to check pipeline function
------------------------------------------------------
Only displaying parameters that differ from defaults.
------------------------------------------------------
executor > local (29)
[c1/b39a04] process > get_software_versions [100%] 1 of 1 ✔
[9b/c38a4f] process > makeBowtie2Index (W303_SGD_2015_JRIU00000000) [100%] 1 of 1 ✔
[d5/16c011] process > makeChromSize (W303_SGD_2015_JRIU00000000.fsa) [100%] 1 of 1 ✔
[a6/f68e54] process > getRestrictionFragments (W303_SGD_2015_JRIU00000000.fsa A^AGCTT) [100%] 1 of 1 ✔
[33/2a727e] process > bowtie2_end_to_end (SRR4292758_00_R1) [100%] 2 of 2 ✔
[ea/c7188f] process > trim_reads (SRR4292758_00_R2) [100%] 2 of 2 ✔
[3e/3ca322] process > bowtie2_on_trimmed_reads (SRR4292758_00_R2) [100%] 2 of 2 ✔
[ce/d74ebe] process > bowtie2_merge_mapping_steps (SRR4292758_00_R2 = SRR4292758_00_R2.bam + SRR4292758_00_R2_unmap_trimmed.bam) [100%] 2 of 2 ✔
[bd/fd6221] process > combine_mates (SRR4292758_00 = SRR4292758_00_R1 + SRR4292758_00_R2) [100%] 1 of 1 ✔
[c9/c1e0bc] process > get_valid_interaction (SRR4292758_00) [100%] 1 of 1 ✔
[f5/2f1982] process > remove_duplicates (SRR4292758_00) [100%] 1 of 1 ✔
[3f/680f09] process > merge_stats (mRSstat) [100%] 4 of 4 ✔
[- ] process > build_contact_maps -
[- ] process > run_ice -
[1a/f1bc79] process > convert_to_pairs (SRR4292758_00) [100%] 1 of 1 ✔
[74/2a2b0e] process > cooler_raw (SRR4292758_00 - 1000) [100%] 1 of 1 ✔
[7e/a1b205] process > cooler_balance (SRR4292758_00 - 1000) [100%] 1 of 1 ✔
[98/37cb6f] process > cooler_zoomify (SRR4292758_00) [100%] 1 of 1 ✔
[76/f1f2bd] process > dist_decay (SRR4292758_00) [100%] 1 of 1 ✔
[33/859499] process > compartment_calling (SRR4292758_00 - 1000) [100%] 1 of 1, failed: 1 ✘
[80/ec5fcd] process > tads_hicexplorer (SRR4292758_00 - 1000) [100%] 1 of 1 ✔
[d5/3959f7] process > tads_insulation (SRR4292758_00 - 1000) [100%] 1 of 1, failed: 1 ✘
[a3/21a9d8] process > multiqc [100%] 1 of 1 ✔
[e5/9db365] process > output_documentation [100%] 1 of 1 ✔
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/hic] Pipeline completed with errors-
Error executing process > 'tads_insulation (SRR4292758_00 - 1000)'
Caused by:
Process `tads_insulation (SRR4292758_00 - 1000)` terminated with an error exit status (1)
Command executed:
cooltools diamond-insulation --window-pixels SRR4292758_00_1000_norm.cool 15 25 50 > SRR4292758_00_insulation.tsv
Command exit status:
1
Command output:
(empty)
Command error:
Traceback (most recent call last):
File "/env/export/v_bigtmp/eb/test/work/conda/nf-core-hic-1.3.0-6b228b9d59279339a55b4a54b5df58de/bin/cooltools", line 5, in <module>
from cooltools.cli import cli
File "/env/export/v_bigtmp/eb/test/work/conda/nf-core-hic-1.3.0-6b228b9d59279339a55b4a54b5df58de/lib/python3.7/site-packages/cooltools/__init__.py", line 18, in <module>
from .lib import numutils, download_data, print_available_datasets, get_data_dir, download_file, get_md5sum
File "/env/export/v_bigtmp/eb/test/work/conda/nf-core-hic-1.3.0-6b228b9d59279339a55b4a54b5df58de/lib/python3.7/site-packages/cooltools/lib/numutils.py", line 8, in <module>
import numba
ModuleNotFoundError: No module named 'numba'
Work dir:
/env/export/v_bigtmp/eb/test/work/d5/3959f75f7d599155c053cca573ae37
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
Hi @erbon7 Thanks for reporting the issue. Indeed I can reproduce it, but I'm really surprise about it. I'll try to investigate and come back to you N
@erbon7
It seems that installing cooltools from bioconda instead of pip solves the issue.
I'll need to make additional test, to update the environment and make a new release ... which could take some times.
In the meantime, you can for instance, manually update your conda env as follow ;
conda activate work/conda/nf-core-hic-1.3.0-6b228b9d59279339a55b4a54b5df58de/
conda install -c bioconda cooltools
conda deactivate
Note that once your conda env is created (and corrected), you can set up a small config file for the conda cache dir to avoid regenerating the conda each time ...
$ cat conda.conf
conda {
cacheDir = my_conda_dir
}
$ nextflow run nf-core/hic -profile test,conda -c conda.conf
Indeed, with the patch the pipeline runs successfully. Thanks Nicolas for your fast response and for the tip.
@erbon7 It seems that installing
cooltoolsfrombiocondainstead ofpipsolves the issue. I'll need to make additional test, to update the environment and make a new release ... which could take some times.In the meantime, you can for instance, manually update your conda env as follow ;
conda activate work/conda/nf-core-hic-1.3.0-6b228b9d59279339a55b4a54b5df58de/ conda install -c bioconda cooltools conda deactivate
Hi, I got a similar error, but to install 'cooltools from 'bioconda' doesn't fix it. Any thoughts about it will be really appreciated.
Core Nextflow options revision : 1.3.0 runName : thirsty_lamarck container : nfcore/hic:1.3.0 launchDir : /media/b/Bigdata3/Chi/Ales_Cvekl/HiC_fastq workDir : /media/b/Bigdata3/Chi/Ales_Cvekl/HiC_fastq/work projectDir : /home/b/.nextflow/assets/nf-core/hic userName : b profile : test,conda configFiles : /home/b/.nextflow/assets/nf-core/hic/nextflow.config, /media/b/Bigdata3/Chi/Ales_Cvekl/HiC_fastq/conda_hic.conf
Error executing process > 'tads_insulation (SRR4292758_00 - 1000)'
Caused by: Process
tads_insulation (SRR4292758_00 - 1000)terminated with an error exit status (2)Command executed:
cooltools diamond-insulation --window-pixels SRR4292758_00_1000_norm.cool 15 25 50 > SRR4292758_00_insulation.tsv
Command exit status: 2
Command output: (empty)
Command error: Usage: cooltools [OPTIONS] COMMAND [ARGS]... Try 'cooltools -h' for help.
Error: No such command 'diamond-insulation'.
Work dir: /media/b/Bigdata3/Chi/Ales_Cvekl/HiC_fastq/work/4c/66d24e86e4b823228ce8865ec6305e
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
