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./install all and ./run test fail #11

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clin888 opened this issue Jun 20, 2023 · 5 comments
Open

./install all and ./run test fail #11

clin888 opened this issue Jun 20, 2023 · 5 comments

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@clin888
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clin888 commented Jun 20, 2023

Hi Eric,

I am new to this software. Here are my log files. Please help.
Thanks

#.snakemake\log
Building DAG of jobs...
Using shell: /bin/bash
Provided cluster nodes: 100
Job stats:
job count min threads max threads

all 1 1 1
copy_splice_matrix_files 1 1 1
count_iris_predict_tasks 1 1 1
download_reference_file 2 1 1
iris_append_sjc 1 1 1
iris_epitope_post 1 1 1
iris_predict 1 1 1
iris_screen 1 1 1
iris_visual_summary 1 1 1
unzip_reference_file 2 1 1
write_param_file 1 1 1
total 13 1 1

Select jobs to execute...

[Mon Jun 19 16:52:29 2023]
localrule copy_splice_matrix_files:
input: /home/clin/IRIS/example/splicing_matrix/splicing_matrix.SE.cov10.NEPC_example.txt, /home/clin/IRIS/example/splicing_matrix/splicing_matrix.SE.cov10.NEPC_example.txt.idx
output: /home/clin/IRIS/IRIS_data/db/NEPC_test/splicing_matrix/splicing_matrix.SE.cov10.NEPC_test.txt, /home/clin/IRIS/IRIS_data/db/NEPC_test/splicing_matrix/splicing_matrix.SE.cov10.NEPC_test.txt.idx
jobid: 10
reason: Missing output files: /home/clin/IRIS/IRIS_data/db/NEPC_test/splicing_matrix/splicing_matrix.SE.cov10.NEPC_test.txt.idx, /home/clin/IRIS/IRIS_data/db/NEPC_test/splicing_matrix/splicing_matrix.SE.cov10.NEPC_test.txt
resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp

cp /home/clin/IRIS/example/splicing_matrix/splicing_matrix.SE.cov10.NEPC_example.txt /home/clin/IRIS/IRIS_data/db/NEPC_test/splicing_matrix/splicing_matrix.SE.cov10.NEPC_test.txt && cp /home/clin/IRIS/example/splicing_matrix/splicing_matrix.SE.cov10.NEPC_example.txt.idx /home/clin/IRIS/IRIS_data/db/NEPC_test/splicing_matrix/splicing_matrix.SE.cov10.NEPC_test.txt.idx

[Mon Jun 19 16:52:29 2023]
rule download_reference_file:
output: references/gencode.v26lift37.annotation.gtf.gz
log: references/download_reference_file_gencode.v26lift37.annotation.gtf.gz_log.out, references/download_reference_file_gencode.v26lift37.annotation.gtf.gz_log.err
jobid: 9
reason: Missing output files: references/gencode.v26lift37.annotation.gtf.gz
wildcards: file_name=gencode.v26lift37.annotation.gtf.gz
resources: mem_mb=4096, disk_mb=1000, tmpdir=, time_hours=12

curl -L 'ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_26/GRCh37_mapping/gencode.v26lift37.annotation.gtf.gz' -o references/gencode.v26lift37.annotation.gtf.gz 1> references/download_reference_file_gencode.v26lift37.annotation.gtf.gz_log.out 2> references/download_reference_file_gencode.v26lift37.annotation.gtf.gz_log.err
Submitted job 9 with external jobid '22798875'.

[Mon Jun 19 16:52:29 2023]
rule download_reference_file:
output: references/ucsc.hg19.fasta.gz
log: references/download_reference_file_ucsc.hg19.fasta.gz_log.out, references/download_reference_file_ucsc.hg19.fasta.gz_log.err
jobid: 6
reason: Missing output files: references/ucsc.hg19.fasta.gz
wildcards: file_name=ucsc.hg19.fasta.gz
resources: mem_mb=4096, disk_mb=1000, tmpdir=, time_hours=12

curl -L 'http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.fa.gz' -o references/ucsc.hg19.fasta.gz 1> references/download_reference_file_ucsc.hg19.fasta.gz_log.out 2> references/download_reference_file_ucsc.hg19.fasta.gz_log.err
Submitted job 6 with external jobid '22798876'.
[Mon Jun 19 16:52:30 2023]
Finished job 10.
1 of 13 steps (8%) done
Waiting at most 60 seconds for missing files.
[Mon Jun 19 16:52:59 2023]
Finished job 9.
2 of 13 steps (15%) done
Select jobs to execute...

[Mon Jun 19 16:52:59 2023]
rule unzip_reference_file:
input: references/gencode.v26lift37.annotation.gtf.gz
output: references/gencode.v26lift37.annotation.gtf
log: references/unzip_reference_file_gencode.v26lift37.annotation.gtf_log.out, references/unzip_reference_file_gencode.v26lift37.annotation.gtf_log.err
jobid: 8
reason: Missing output files: references/gencode.v26lift37.annotation.gtf; Input files updated by another job: references/gencode.v26lift37.annotation.gtf.gz
wildcards: file_name=gencode.v26lift37.annotation.gtf
resources: mem_mb=4096, disk_mb=1000, tmpdir=, time_hours=12

gunzip -c references/gencode.v26lift37.annotation.gtf.gz 1> references/gencode.v26lift37.annotation.gtf 2> references/unzip_reference_file_gencode.v26lift37.annotation.gtf_log.err
Submitted job 8 with external jobid '22798927'.
Waiting at most 60 seconds for missing files.
[Mon Jun 19 16:53:29 2023]
Finished job 8.
3 of 13 steps (23%) done
[Mon Jun 19 16:53:31 2023]
Finished job 6.
4 of 13 steps (31%) done
Select jobs to execute...

[Mon Jun 19 16:53:31 2023]
rule unzip_reference_file:
input: references/ucsc.hg19.fasta.gz
output: references/ucsc.hg19.fasta
log: references/unzip_reference_file_ucsc.hg19.fasta_log.out, references/unzip_reference_file_ucsc.hg19.fasta_log.err
jobid: 5
reason: Missing output files: references/ucsc.hg19.fasta; Input files updated by another job: references/ucsc.hg19.fasta.gz
wildcards: file_name=ucsc.hg19.fasta
resources: mem_mb=4096, disk_mb=1810, tmpdir=, time_hours=12

gunzip -c references/ucsc.hg19.fasta.gz 1> references/ucsc.hg19.fasta 2> references/unzip_reference_file_ucsc.hg19.fasta_log.err
Submitted job 5 with external jobid '22798968'.
[Mon Jun 19 16:54:01 2023]
Finished job 5.
5 of 13 steps (38%) done
Select jobs to execute...

[Mon Jun 19 16:54:01 2023]
rule write_param_file:
input: references/ucsc.hg19.fasta
output: results/NEPC_test/screen.para
log: results/NEPC_test/write_param_file_log.out, results/NEPC_test/write_param_file_log.err
jobid: 4
reason: Missing output files: results/NEPC_test/screen.para; Input files updated by another job: references/ucsc.hg19.fasta
resources: mem_mb=4096, disk_mb=6103, tmpdir=, time_hours=12

/home/clin/IRIS/conda_wrapper /home/clin/IRIS/conda_env_3 python scripts/write_param_file.py --out-path results/NEPC_test/screen.para --group-name NEPC_test --iris-db /home/clin/IRIS/IRIS_data/db --psi-p-value-cutoffs ,,0.01 --sjc-p-value-cutoffs ,,0.000001 --delta-psi-cutoffs ,,0.05 --fold-change-cutoffs ,,1 --group-count-cutoffs ,,8 --reference-names-tissue-matched-normal '' --reference-names-tumor '' --reference-names-normal GTEx_Heart,GTEx_Blood,GTEx_Lung,GTEx_Liver,GTEx_Brain,GTEx_Nerve,GTEx_Muscle,GTEx_Spleen,GTEx_Thyroid,GTEx_Skin,GTEx_Kidney --comparison-mode group --statistical-test-type parametric --mapability-bigwig /home/clin/IRIS/IRIS_data/resources/mappability/wgEncodeCrgMapabilityAlign24mer.bigWig --reference-genome references/ucsc.hg19.fasta 1> results/NEPC_test/write_param_file_log.out 2> results/NEPC_test/write_param_file_log.err
Submitted job 4 with external jobid '22799008'.
[Mon Jun 19 16:54:11 2023]
Error in rule write_param_file:
jobid: 4
output: results/NEPC_test/screen.para
log: results/NEPC_test/write_param_file_log.out, results/NEPC_test/write_param_file_log.err (check log file(s) for error message)
shell:
/home/clin/IRIS/conda_wrapper /home/clin/IRIS/conda_env_3 python scripts/write_param_file.py --out-path results/NEPC_test/screen.para --group-name NEPC_test --iris-db /home/clin/IRIS/IRIS_data/db --psi-p-value-cutoffs ,,0.01 --sjc-p-value-cutoffs ,,0.000001 --delta-psi-cutoffs ,,0.05 --fold-change-cutoffs ,,1 --group-count-cutoffs ,,8 --reference-names-tissue-matched-normal '' --reference-names-tumor '' --reference-names-normal GTEx_Heart,GTEx_Blood,GTEx_Lung,GTEx_Liver,GTEx_Brain,GTEx_Nerve,GTEx_Muscle,GTEx_Spleen,GTEx_Thyroid,GTEx_Skin,GTEx_Kidney --comparison-mode group --statistical-test-type parametric --mapability-bigwig /home/clin/IRIS/IRIS_data/resources/mappability/wgEncodeCrgMapabilityAlign24mer.bigWig --reference-genome references/ucsc.hg19.fasta 1> results/NEPC_test/write_param_file_log.out 2> results/NEPC_test/write_param_file_log.err
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
cluster_jobid: 22799008

Error executing rule write_param_file on cluster (jobid: 4, external: 22799008, jobscript: /home/clin/IRIS/.snakemake/tmp.7v6mkgax/snakejob.write_param_file.4.sh). For error details see the cluster log and the log files of the involved rule(s).
Trying to restart job 4.
Select jobs to execute...

[Mon Jun 19 16:54:11 2023]
rule write_param_file:
input: references/ucsc.hg19.fasta
output: results/NEPC_test/screen.para
log: results/NEPC_test/write_param_file_log.out, results/NEPC_test/write_param_file_log.err
jobid: 4
reason: Missing output files: results/NEPC_test/screen.para; Input files updated by another job: references/ucsc.hg19.fasta
resources: mem_mb=4096, disk_mb=6103, tmpdir=, time_hours=12

/home/clin/IRIS/conda_wrapper /home/clin/IRIS/conda_env_3 python scripts/write_param_file.py --out-path results/NEPC_test/screen.para --group-name NEPC_test --iris-db /home/clin/IRIS/IRIS_data/db --psi-p-value-cutoffs ,,0.01 --sjc-p-value-cutoffs ,,0.000001 --delta-psi-cutoffs ,,0.05 --fold-change-cutoffs ,,1 --group-count-cutoffs ,,8 --reference-names-tissue-matched-normal '' --reference-names-tumor '' --reference-names-normal GTEx_Heart,GTEx_Blood,GTEx_Lung,GTEx_Liver,GTEx_Brain,GTEx_Nerve,GTEx_Muscle,GTEx_Spleen,GTEx_Thyroid,GTEx_Skin,GTEx_Kidney --comparison-mode group --statistical-test-type parametric --mapability-bigwig /home/clin/IRIS/IRIS_data/resources/mappability/wgEncodeCrgMapabilityAlign24mer.bigWig --reference-genome references/ucsc.hg19.fasta 1> results/NEPC_test/write_param_file_log.out 2> results/NEPC_test/write_param_file_log.err
Submitted job 4 with external jobid '22799023'.
[Mon Jun 19 16:54:22 2023]
Error in rule write_param_file:
jobid: 4
output: results/NEPC_test/screen.para
log: results/NEPC_test/write_param_file_log.out, results/NEPC_test/write_param_file_log.err (check log file(s) for error message)
shell:
/home/clin/IRIS/conda_wrapper /home/clin/IRIS/conda_env_3 python scripts/write_param_file.py --out-path results/NEPC_test/screen.para --group-name NEPC_test --iris-db /home/clin/IRIS/IRIS_data/db --psi-p-value-cutoffs ,,0.01 --sjc-p-value-cutoffs ,,0.000001 --delta-psi-cutoffs ,,0.05 --fold-change-cutoffs ,,1 --group-count-cutoffs ,,8 --reference-names-tissue-matched-normal '' --reference-names-tumor '' --reference-names-normal GTEx_Heart,GTEx_Blood,GTEx_Lung,GTEx_Liver,GTEx_Brain,GTEx_Nerve,GTEx_Muscle,GTEx_Spleen,GTEx_Thyroid,GTEx_Skin,GTEx_Kidney --comparison-mode group --statistical-test-type parametric --mapability-bigwig /home/clin/IRIS/IRIS_data/resources/mappability/wgEncodeCrgMapabilityAlign24mer.bigWig --reference-genome references/ucsc.hg19.fasta 1> results/NEPC_test/write_param_file_log.out 2> results/NEPC_test/write_param_file_log.err
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
cluster_jobid: 22799023

Error executing rule write_param_file on cluster (jobid: 4, external: 22799023, jobscript: /home/clin/IRIS/.snakemake/tmp.7v6mkgax/snakejob.write_param_file.4.sh). For error details see the cluster log and the log files of the involved rule(s).
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2023-06-19T165228.360928.snakemake.log

#install_log
Package libgcc conflicts for:
r-base==3.4.1 -> libgcc
seaborn==0.9.0 -> scipy[version='>=0.15.2'] -> libgcc
seq2hla==2.2 -> bowtie==1.1.2 -> libgcc
statsmodels==0.10.2 -> scipy[version='>=0.14'] -> libgcc

Package _openmp_mutex conflicts for:
r-base==3.4.1 -> libgcc-ng[version='>=4.9'] -> _openmp_mutex[version='>=4.5']
rmats==4.1.2 -> libgcc-ng[version='>=10.3.0'] -> _openmp_mutex
star==2.7.10b -> libgcc-ng[version='>=12'] -> _openmp_mutex[version='>=4.5']
python=2.7 -> libgcc-ng[version='>=7.3.0'] -> _openmp_mutex[version='>=4.5']
rmats==4.1.2 -> _openmp_mutex[version='>=4.5']
scipy==1.2.0 -> libgcc-ng[version='>=7.3.0'] -> _openmp_mutex[version='|>=4.5',build=_llvm]
pysam==0.15.4 -> libgcc-ng[version='>=7.3.0'] -> _openmp_mutex[version='>=4.5']
seq2hla==2.2 -> r-base -> _openmp_mutex
bedtools==2.29.0 -> libgcc-ng[version='>=7.3.0'] -> _openmp_mutex[version='>=4.5']
pybigwig==0.3.13 -> libgcc-ng[version='>=7.3.0'] -> _openmp_mutex[version='>=4.5']
numpy==1.16.5 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='|>=4.5',build=_llvm]
statsmodels==0.10.2 -> libgcc-ng[version='>=7.3.0'] -> _openmp_mutex[version='>=4.5']

Package xz conflicts for:
r-base==3.4.1 -> cairo[version='>=1.14.12,<2.0.0a0'] -> xz[version='5.0.|>=5.2.10,<6.0a0|>=5.2.3,<6.0a0|>=5.2.4,<6.0a0|>=5.2.6,<6.0a0|>=5.2.6,<5.3.0a0|>=5.2.5,<5.3.0a0|>=5.2.4,<5.3.0a0|>=5.2.5,<6.0a0|>=5.2.8,<6.0a0']
bedtools==2.29.0 -> xz[version='>=5.2.4,<5.3.0a0']
r-base==3.4.1 -> xz[version='5.2.|>=5.2.3,<5.3.0a0']
rmats==4.1.2 -> python[version='>=3.9,<3.10.0a0'] -> xz[version='5.2.|>=5.2.10,<6.0a0|>=5.2.5,<5.3.0a0|>=5.2.6,<6.0a0|>=5.4.2,<6.0a0|>=5.2.8,<6.0a0|>=5.2.5,<6.0a0|>=5.2.4,<5.3.0a0|>=5.2.4,<6.0a0|>=5.2.6,<5.3.0a0|>=5.2.3,<5.3.0a0|>=5.2.3,<6.0a0']
pysam==0.15.4 -> python[version='>=3.6,<3.7.0a0'] -> xz[version='5.2.|>=5.2.3,<5.3.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0|>=5.2.3,<6.0a0|>=5.2.10,<6.0a0|>=5.2.6,<6.0a0']
statsmodels==0.10.2 -> python[version='>=3.6,<3.7.0a0'] -> xz[version='5.2.|>=5.2.3,<5.3.0a0|>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0|>=5.2.3,<6.0a0|>=5.2.6,<6.0a0|>=5.4.2,<6.0a0|>=5.2.10,<6.0a0']
star==2.7.10b -> htslib[version='>=1.17,<1.18.0a0'] -> xz[version='>=5.2.6,<5.3.0a0|>=5.2.6,<6.0a0']
seaborn==0.9.0 -> python -> xz[version='5.0.|5.2.|>=5.2.3,<5.3.0a0|>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0|>=5.2.6,<5.3.0a0|>=5.2.6,<6.0a0|>=5.4.2,<6.0a0|>=5.2.10,<6.0a0|>=5.2.8,<6.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0|>=5.2.3,<6.0a0']
pysam==0.15.4 -> xz[version='>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0']
scipy==1.2.0 -> python[version='>=3.7,<3.8.0a0'] -> xz[version='5.2.|>=5.2.10,<6.0a0|>=5.2.3,<5.3.0a0|>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0|>=5.2.6,<6.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0|>=5.2.3,<6.0a0']
numpy==1.16.5 -> python[version='>=3.7,<3.8.0a0'] -> xz[version='5.2.|>=5.2.10,<6.0a0|>=5.2.3,<5.3.0a0|>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0|>=5.2.6,<6.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0|>=5.4.2,<6.0a0|>=5.2.3,<6.0a0']
cufflinks==2.2.1 -> python[version='>=3.5,<3.6.0a0'] -> xz[version='5.0.|5.2.|>=5.2.3,<5.3.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0|>=5.2.3,<6.0a0|>=5.2.5,<5.3.0a0|>=5.2.4,<5.3.0a0']
seq2hla==2.2 -> r-base -> xz[version='5.2.|>=5.2.3,<5.3.0a0|>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0|>=5.2.6,<6.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0|>=5.2.3,<6.0a0']
pybigwig==0.3.13 -> python[version='>=3.6,<3.7.0a0'] -> xz[version='5.0.|5.2.|>=5.2.3,<5.3.0a0|>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0|>=5.2.3,<6.0a0|>=5.2.10,<6.0a0|>=5.2.6,<6.0a0']

Package intel-openmp conflicts for:
seaborn==0.9.0 -> scipy[version='>=0.15.2'] -> intel-openmp[version='>=2021.4.0,<2022.0a0|>=2023.1.0,<2024.0a0']
statsmodels==0.10.2 -> scipy[version='>=0.14'] -> intel-openmp[version='>=2021.4.0,<2022.0a0|>=2023.1.0,<2024.0a0']
numpy==1.16.5 -> mkl[version='>=2019.4,<2021.0a0'] -> intel-openmp
scipy==1.2.0 -> mkl[version='>=2019.1,<2021.0a0'] -> intel-openmp

Package llvm-openmp conflicts for:
numpy==1.16.5 -> mkl[version='>=2019.4,<2021.0a0'] -> llvm-openmp[version='>=10.0.0|>=11.0.0|>=9.0.1|>=16.0.5|>=14.0.4|>=13.0.1|>=12.0.1|>=11.1.0|>=11.0.1|>=16.0.1|>=10.0.1']
rmats==4.1.2 -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1']
scipy==1.2.0 -> blas=[build=openblas] -> llvm-openmp[version='>=10.0.0|>=11.0.0|>=11.0.1|>=11.1.0|>=12.0.1|>=13.0.1|>=14.0.4|>=16.0.5|>=9.0.1|>=16.0.1|>=10.0.1']

Package readline conflicts for:
python=2.7 -> sqlite[version='>=3.30.1,<4.0a0'] -> readline[version='>=8.1,<9.0a0|>=8.1.2,<9.0a0|>=8.2,<9.0a0']
python=2.7 -> readline[version='6.2.|7.0|7.0.|>=7.0,<8.0a0|>=8.0,<9.0a0|7.*']

Package liblapacke conflicts for:
numpy==1.16.5 -> blas=[build=openblas] -> liblapacke[version='3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.9.0|3.9.0|3.9.0|3.9.0',build='0_openblas|8_openblas|12_openblas|13_openblas|15_openblas|16_openblas|17_openblas|10_openblas|11_linux64_openblas|12_linux64_openblas|14_linux64_openblas|15_linux64_openblas|16_linux64_openblas|17_linux64_openblas|13_linux64_openblas|9_openblas|8_openblas|7_openblas|6_openblas|5_openblas|14_openblas|11_openblas|10_openblas|9_openblas|7_openblas|6_openblas|5_openblas|4_openblas|3_openblas|2_openblas']
scipy==1.2.0 -> blas=[build=openblas] -> liblapacke[version='3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.9.0|3.9.0|3.9.0|3.9.0',build='0_openblas|8_openblas|12_openblas|13_openblas|15_openblas|16_openblas|17_openblas|10_openblas|11_linux64_openblas|12_linux64_openblas|14_linux64_openblas|15_linux64_openblas|16_linux64_openblas|17_linux64_openblas|13_linux64_openblas|9_openblas|8_openblas|7_openblas|6_openblas|5_openblas|14_openblas|11_openblas|10_openblas|9_openblas|7_openblas|6_openblas|5_openblas|4_openblas|3_openblas|2_openblas']

Package statsmodels conflicts for:
statsmodels==0.10.2
seaborn==0.9.0 -> statsmodels[version='>=0.5.0']

Package libgcc-ng conflicts for:
python=2.7 -> openssl[version='>=1.1.1a,<1.1.2a'] -> libgcc-ng[version='>=10.3.0|>=12|>=9.4.0|>=9.3.0|>=7.5.0']
python=2.7 -> libgcc-ng[version='>=11.2.0|>=4.9|>=7.3.0|>=7.2.0']

Package zlib conflicts for:
python=2.7 -> sqlite[version='>=3.30.1,<4.0a0'] -> zlib[version='>=1.2.12,<1.3.0a0|>=1.2.13,<2.0a0']
python=2.7 -> zlib[version='1.2.|1.2.11|1.2.11.|>=1.2.11,<1.3.0a0|1.2.8|>=1.2.13,<1.3.0a0']

Package libstdcxx-ng conflicts for:
python=2.7 -> ncurses[version='>=6.1,<7.0.0a0'] -> libstdcxx-ng[version='>=11.2.0|>=7.5.0|>=9.4.0']
python=2.7 -> libstdcxx-ng[version='>=4.9|>=7.3.0|>=7.2.0']

Package star conflicts for:
rmats==4.1.2 -> star[version='>=2.5']
star==2.7.10b

Package ncurses conflicts for:
python=2.7 -> readline[version='>=8.0,<9.0a0'] -> ncurses[version='5.9|>=6.2,<7.0.0a0|>=6.4,<7.0a0']
python=2.7 -> ncurses[version='5.9.|>=6.1,<7.0.0a0|>=6.3,<7.0a0|>=6.2,<7.0a0|>=6.1,<7.0a0|>=6.0,<7.0a0|6.0.']The following specifications were found to be incompatible with your system:

  • feature:/linux-64::__glibc==2.27=0
  • feature:|@/linux-64::__glibc==2.27=0
  • bedtools==2.29.0 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
  • numpy==1.16.5 -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
  • pybigwig==0.3.13 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
  • pysam==0.15.4 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
  • r-base==3.4.1 -> libgcc-ng[version='>=4.9'] -> __glibc[version='>=2.17']
  • rmats==4.1.2 -> libgfortran-ng -> __glibc[version='>=2.17']
  • scipy==1.2.0 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
  • statsmodels==0.10.2 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']

Your installed version is: 2.27

Note that strict channel priority may have removed packages required for satisfiability.
@EricKutschera
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The workflow looks like it failed on: rule write_param_file which is the first rule that tried to use the conda environment. There should be an error message in one of the log files for that job: results/NEPC_test/write_param_file_log.out or results/NEPC_test/write_param_file_log.err

The install log shows that the conda install failed to find compatible packages. It has this line:
Note that strict channel priority may have removed packages required for satisfiability.

You could try running conda config --show-sources to see if any of your config files are forcing strict channel priority

@clin888
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clin888 commented Jun 21, 2023

Hi Eric,

Thank you for your response. Do I need to alter the strict order?

conda config --show-sources
==> /home/.condarc <==
channel_priority: strict
channels:

  • conda-forge
  • bioconda
  • defaults

@clin888
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clin888 commented Jun 21, 2023

Hi Eric,

The output from write_param_file_log.err is
write_param_file.py: error: /home/IRIS/IRIS_data/resources/mappability/wgEncodeCrgMapabilityAlign24mer.bigWig does not exist

Thanks

@EricKutschera
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I was able to run the install without setting channel_priority: and without setting any channels:. You could try (temporarily) removing those lines from your config and rerunning the install

The file resources/mappability/wgEncodeCrgMapabilityAlign24mer.bigWig can be downloaded with these instructions https://github.com/Xinglab/IRIS/tree/v2.0.1#12-download-iris-db

@clin888
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clin888 commented Jun 28, 2023

Thank you, Eric

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