Error: ResolvePackageNotFound libgcc-ng, libstdcxx-ng, and isa-l #185
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Hello,
I have been trying to repeat a test run with a stable release 1.3.0. However, I encounter several errors regarding "package not found". Mostly, they are libgcc-ng, libstdcxx-ng, and isa-l. I kept installing these 3 packages but the problem still persists, i.e., unable to run the program. Could you please look into this problem and let me know how to fix it.
Also, if you suggest switching to Docker, could you please create another manual for the Docker platform? This would be great. Thank you very much.
Please see the following error messages for more details.
(nextflow) sttongjai@STTongjai:~$ nextflow run -r 1.3.0 hoelzer-lab/rnaflow -profile test,conda,local
N E X T F L O W ~ version 22.04.0
Launching
https://github.com/hoelzer-lab/rnaflow[condescending_torricelli] DSL2 - revision: e7d8a96 [1.3.0]Profile: test,conda,local
Current User: sttongjai
Nextflow-version: 22.04.0
Starting time: 2022-04-28T21:26:19.367523+07:00
Workdir location:
/home/sttongjai/work
Launchdir location:
/home/sttongjai
Permanent cache directory:
nextflow-autodownload-databases
Conda cache directory:
conda
Configuration files:
[/home/sttongjai/.nextflow/assets/hoelzer-lab/rnaflow/nextflow.config]
Cmd line:
nextflow run -r 1.3.0 hoelzer-lab/rnaflow -profile test,conda,local
Git info: https://github.com/hoelzer-lab/rnaflow - 1.3.0 [e7d8a96]
CPUs to use: 2, maximal CPUs to use: 4
WARNING: Output folder already exists. Results might be overwritten! You can adjust the output folder via [--output]
R N A F L O W : R N A - S E Q A S S E M B L Y & D I F F E R E N T I A L G E N E E X P R E S S I O N A N A L Y S I S
= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
Output path: results
Strandedness unstranded
Read mode: single-end
TPM threshold: 1
Comparisons: all
Nanopore mode: false
[- ] process > get_test_data:get_reduced_genome_test [ 0%] 0 of 1
executor > local (4)
executor > local (8)
executor > local (8)
executor > local (8)
[0c/17f6e6] process > get_test_data:get_reduced_genome_test [ 0%] 0 of 1
[c0/622b17] process > get_test_data:get_reduced_annotation_test [ 0%] 0 of 1
[38/e5d87c] process > download_sortmerna:sortmernaGet [ 0%] 0 of 1
[ef/c93e37] process > preprocess_illumina:fastqcPre (MAQCB_rep2) [ 0%] 0 of 4
[- ] process > preprocess_illumina:fastp -
[- ] process > preprocess_illumina:fastqcPost -
[- ] process > preprocess_illumina:extract_tar_bz2 -
executor > local (8)
[0c/17f6e6] process > get_test_data:get_reduced_genome_test [ 0%] 0 of 1
[c0/622b17] process > get_test_data:get_reduced_annotation_test [ 0%] 0 of 1
[38/e5d87c] process > download_sortmerna:sortmernaGet [ 0%] 0 of 1
[ef/c93e37] process > preprocess_illumina:fastqcPre (MAQCB_rep2) [ 0%] 0 of 4
[- ] process > preprocess_illumina:fastp -
[- ] process > preprocess_illumina:fastqcPost -
[- ] process > preprocess_illumina:extract_tar_bz2 -
[- ] process > preprocess_illumina:sortmerna -
[- ] process > preprocess_illumina:hisat2index -
[- ] process > preprocess_illumina:hisat2 -
[- ] process > preprocess_illumina:index_bam -
[- ] process > expression_reference_based:featurecounts -
[- ] process > expression_reference_based:format_annotation_gene_rows -
[- ] process > expression_reference_based:format_annotation -
[- ] process > expression_reference_based:tpm_filter -
[- ] process > expression_reference_based:deseq2 -
[e7/2563cd] process > expression_reference_based:multiqc_sample_names (1) [100%] 1 of 1 ✔
[- ] process > expression_reference_based:multiqc -
Creating env using conda: /home/sttongjai/.nextflow/assets/hoelzer-lab/rnaflow/envs/fastp.yaml [cache /home/sttongjai/conda/fastp-3e6e702456ac1f373ced1ed39b827af4]
Error executing process > 'preprocess_illumina:fastp (MAQCA_rep2)'
Caused by:
Failed to create Conda environment
command: conda env create --prefix /home/sttongjai/conda/fastp-3e6e702456ac1f373ced1ed39b827af4 --file /home/sttongjai/.nextflow/assets/hoelzer-lab/rnaflow/envs/fastp.yaml
status : 1
message:
ResolvePackageNotFound:
- libstdcxx-ng[version='>=9.4.0']
(nextflow) sttongjai@STTongjai:~$ conda install -c conda-forge libstdcxx-ng
Collecting package metadata (current_repodata.json): done
Solving environment: done
All requested packages already installed.
(nextflow) sttongjai@STTongjai:~$ nextflow run -r 1.3.0 hoelzer-lab/rnaflow -profile test,conda,local
N E X T F L O W ~ version 22.04.0
Launching
https://github.com/hoelzer-lab/rnaflow[prickly_leakey] DSL2 - revision: e7d8a96 [1.3.0]Profile: test,conda,local
Current User: sttongjai
Nextflow-version: 22.04.0
Starting time: 2022-04-28T21:27:10.269236+07:00
Workdir location:
/home/sttongjai/work
Launchdir location:
/home/sttongjai
Permanent cache directory:
nextflow-autodownload-databases
Conda cache directory:
conda
Configuration files:
[/home/sttongjai/.nextflow/assets/hoelzer-lab/rnaflow/nextflow.config]
Cmd line:
nextflow run -r 1.3.0 hoelzer-lab/rnaflow -profile test,conda,local
Git info: https://github.com/hoelzer-lab/rnaflow - 1.3.0 [e7d8a96]
CPUs to use: 2, maximal CPUs to use: 4
WARNING: Output folder already exists. Results might be overwritten! You can adjust the output folder via [--output]
R N A F L O W : R N A - S E Q A S S E M B L Y & D I F F E R E N T I A L G E N E E X P R E S S I O N A N A L Y S I S
= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
Output path: results
Strandedness unstranded
Read mode: single-end
TPM threshold: 1
Comparisons: all
Nanopore mode: false
[- ] process > get_test_data:get_reduced_genome_test -
executor > local (4)
executor > local (8)
executor > local (8)
executor > local (8)
executor > local (8)
[e6/901f21] process > get_test_data:get_reduced_genome_test [ 0%] 0 of 1
[4e/5bde82] process > get_test_data:get_reduced_annotation_test [ 0%] 0 of 1
[79/8dc456] process > download_sortmerna:sortmernaGet [ 0%] 0 of 1
[ba/e775da] process > preprocess_illumina:fastqcPre (MAQCB_rep1) [ 0%] 0 of 4
[- ] process > preprocess_illumina:fastp -
[- ] process > preprocess_illumina:fastqcPost -
[- ] process > preprocess_illumina:extract_tar_bz2 -
executor > local (8)
[e6/901f21] process > get_test_data:get_reduced_genome_test [ 0%] 0 of 1
[4e/5bde82] process > get_test_data:get_reduced_annotation_test [ 0%] 0 of 1
[79/8dc456] process > download_sortmerna:sortmernaGet [ 0%] 0 of 1
[ba/e775da] process > preprocess_illumina:fastqcPre (MAQCB_rep1) [ 0%] 0 of 4
[- ] process > preprocess_illumina:fastp -
[- ] process > preprocess_illumina:fastqcPost -
[- ] process > preprocess_illumina:extract_tar_bz2 -
[- ] process > preprocess_illumina:sortmerna -
[- ] process > preprocess_illumina:hisat2index -
[- ] process > preprocess_illumina:hisat2 -
[- ] process > preprocess_illumina:index_bam -
[- ] process > expression_reference_based:featurecounts -
[- ] process > expression_reference_based:format_annotation_gene_rows -
[- ] process > expression_reference_based:format_annotation -
[- ] process > expression_reference_based:tpm_filter -
[- ] process > expression_reference_based:deseq2 -
[51/234330] process > expression_reference_based:multiqc_sample_names (1) [100%] 1 of 1 ✔
[- ] process > expression_reference_based:multiqc -
Creating env using conda: /home/sttongjai/.nextflow/assets/hoelzer-lab/rnaflow/envs/fastp.yaml [cache /home/sttongjai/conda/fastp-3e6e702456ac1f373ced1ed39b827af4]
Error executing process > 'preprocess_illumina:fastp (MAQCA_rep1)'
Caused by:
Failed to create Conda environment
command: conda env create --prefix /home/sttongjai/conda/fastp-3e6e702456ac1f373ced1ed39b827af4 --file /home/sttongjai/.nextflow/assets/hoelzer-lab/rnaflow/envs/fastp.yaml
status : 1
message:
ResolvePackageNotFound:
- libstdcxx-ng[version='>=9.4.0']
(nextflow) sttongjai@STTongjai:~$ conda install -c conda-forge/label/gcc7 libstdcxx-ng
Collecting package metadata (current_repodata.json): done
Solving environment: done
Package Plan
environment location: /home/sttongjai/miniconda3/envs/nextflow
added / updated specs:
- libstdcxx-ng
The following packages will be SUPERSEDED by a higher-priority channel:
ca-certificates conda-forge::ca-certificates-2021.10.~ --> conda-forge/label/gcc7::ca-certificates-2018.10.15-ha4d7672_0
Proceed ([y]/n)? y
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(nextflow) sttongjai@STTongjai:~$ nextflow run -r 1.3.0 hoelzer-lab/rnaflow -profile test,conda,local
N E X T F L O W ~ version 22.04.0
Launching
https://github.com/hoelzer-lab/rnaflow[sick_torvalds] DSL2 - revision: e7d8a96 [1.3.0]Profile: test,conda,local
Current User: sttongjai
Nextflow-version: 22.04.0
Starting time: 2022-04-28T21:28:48.129787+07:00
Workdir location:
/home/sttongjai/work
Launchdir location:
/home/sttongjai
Permanent cache directory:
nextflow-autodownload-databases
Conda cache directory:
conda
Configuration files:
[/home/sttongjai/.nextflow/assets/hoelzer-lab/rnaflow/nextflow.config]
Cmd line:
nextflow run -r 1.3.0 hoelzer-lab/rnaflow -profile test,conda,local
Git info: https://github.com/hoelzer-lab/rnaflow - 1.3.0 [e7d8a96]
CPUs to use: 2, maximal CPUs to use: 4
WARNING: Output folder already exists. Results might be overwritten! You can adjust the output folder via [--output]
R N A F L O W : R N A - S E Q A S S E M B L Y & D I F F E R E N T I A L G E N E E X P R E S S I O N A N A L Y S I S
= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
Output path: results
Strandedness unstranded
Read mode: single-end
TPM threshold: 1
Comparisons: all
Nanopore mode: false
[- ] process > get_test_data:get_reduced_genome_test -
executor > local (1)
executor > local (8)
executor > local (8)
executor > local (8)
executor > local (8)
[9a/4cd2db] process > get_test_data:get_reduced_genome_test [ 0%] 0 of 1
[ce/9c37c5] process > get_test_data:get_reduced_annotation_test [ 0%] 0 of 1
[ae/df15a4] process > download_sortmerna:sortmernaGet [ 0%] 0 of 1
[70/a1653f] process > preprocess_illumina:fastqcPre (MAQCB_rep2) [ 0%] 0 of 4
[- ] process > preprocess_illumina:fastp -
[- ] process > preprocess_illumina:fastqcPost -
[- ] process > preprocess_illumina:extract_tar_bz2 -
executor > local (8)
[- ] process > get_test_data:get_reduced_genome_test -
[ce/9c37c5] process > get_test_data:get_reduced_annotation_test [ 0%] 0 of 1
[- ] process > download_sortmerna:sortmernaGet -
[53/25cd94] process > preprocess_illumina:fastqcPre (MAQCA_rep1) [ 0%] 0 of 2
[- ] process > preprocess_illumina:fastp -
[- ] process > preprocess_illumina:fastqcPost -
[- ] process > preprocess_illumina:extract_tar_bz2 -
[- ] process > preprocess_illumina:sortmerna -
[- ] process > preprocess_illumina:hisat2index -
[- ] process > preprocess_illumina:hisat2 -
[- ] process > preprocess_illumina:index_bam -
[- ] process > expression_reference_based:featurecounts -
[- ] process > expression_reference_based:format_annotation_gene_rows -
[- ] process > expression_reference_based:format_annotation -
[- ] process > expression_reference_based:tpm_filter -
[- ] process > expression_reference_based:deseq2 -
[7d/daf1e7] process > expression_reference_based:multiqc_sample_names (1) [100%] 1 of 1 ✔
[- ] process > expression_reference_based:multiqc -
Creating env using conda: /home/sttongjai/.nextflow/assets/hoelzer-lab/rnaflow/envs/fastp.yaml [cache /home/sttongjai/conda/fastp-3e6e702456ac1f373ced1ed39b827af4]
Error executing process > 'preprocess_illumina:fastp (MAQCB_rep1)'
Caused by:
Failed to create Conda environment
command: conda env create --prefix /home/sttongjai/conda/fastp-3e6e702456ac1f373ced1ed39b827af4 --file /home/sttongjai/.nextflow/assets/hoelzer-lab/rnaflow/envs/fastp.yaml
status : 1
message:
ResolvePackageNotFound:
- libstdcxx-ng[version='>=9.4.0']
(nextflow) sttongjai@STTongjai:~$ conda install -c conda-forge/label/cf202003 libstdcxx-ng
Collecting package metadata (current_repodata.json): done
Solving environment: done
Package Plan
environment location: /home/sttongjai/miniconda3/envs/nextflow
added / updated specs:
- libstdcxx-ng
The following packages will be UPDATED:
ca-certificates conda-forge/label/gcc7::ca-certificat~ --> conda-forge/label/cf202003::ca-certificates-2019.11.28-hecc5488_0
Proceed ([y]/n)? y
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(nextflow) sttongjai@STTongjai:~$ nextflow run -r 1.3.0 hoelzer-lab/rnaflow -profile test,conda,local
N E X T F L O W ~ version 22.04.0
Launching
https://github.com/hoelzer-lab/rnaflow[distraught_stonebraker] DSL2 - revision: e7d8a96 [1.3.0]Profile: test,conda,local
Current User: sttongjai
Nextflow-version: 22.04.0
Starting time: 2022-04-28T21:32:26.622408+07:00
Workdir location:
/home/sttongjai/work
Launchdir location:
/home/sttongjai
Permanent cache directory:
nextflow-autodownload-databases
Conda cache directory:
conda
Configuration files:
[/home/sttongjai/.nextflow/assets/hoelzer-lab/rnaflow/nextflow.config]
Cmd line:
nextflow run -r 1.3.0 hoelzer-lab/rnaflow -profile test,conda,local
Git info: https://github.com/hoelzer-lab/rnaflow - 1.3.0 [e7d8a96]
CPUs to use: 2, maximal CPUs to use: 4
WARNING: Output folder already exists. Results might be overwritten! You can adjust the output folder via [--output]
R N A F L O W : R N A - S E Q A S S E M B L Y & D I F F E R E N T I A L G E N E E X P R E S S I O N A N A L Y S I S
= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
Output path: results
Strandedness unstranded
Read mode: single-end
TPM threshold: 1
Comparisons: all
Nanopore mode: false
executor > local (1)
executor > local (8)
executor > local (8)
executor > local (8)
executor > local (8)
[8e/60f490] process > get_test_data:get_reduced_genome_test [ 0%] 0 of 1
[5b/293977] process > get_test_data:get_reduced_annotation_test [ 0%] 0 of 1
[5a/589950] process > download_sortmerna:sortmernaGet [ 0%] 0 of 1
[63/8620c9] process > preprocess_illumina:fastqcPre (MAQCB_rep1) [ 0%] 0 of 4
[- ] process > preprocess_illumina:fastp -
[- ] process > preprocess_illumina:fastqcPost -
[- ] process > preprocess_illumina:extract_tar_bz2 -
executor > local (8)
[- ] process > get_test_data:get_reduced_genome_test -
[- ] process > get_test_data:get_reduced_annotation_test -
[- ] process > download_sortmerna:sortmernaGet -
[63/8620c9] process > preprocess_illumina:fastqcPre (MAQCB_rep1) [ 0%] 0 of 4
[- ] process > preprocess_illumina:fastp -
[- ] process > preprocess_illumina:fastqcPost -
[- ] process > preprocess_illumina:extract_tar_bz2 -
[- ] process > preprocess_illumina:sortmerna -
[- ] process > preprocess_illumina:hisat2index -
[- ] process > preprocess_illumina:hisat2 -
[- ] process > preprocess_illumina:index_bam -
[- ] process > expression_reference_based:featurecounts -
[- ] process > expression_reference_based:format_annotation_gene_rows -
[- ] process > expression_reference_based:format_annotation -
[- ] process > expression_reference_based:tpm_filter -
[- ] process > expression_reference_based:deseq2 -
[8c/94bbd9] process > expression_reference_based:multiqc_sample_names (1) [100%] 1 of 1 ✔
[- ] process > expression_reference_based:multiqc -
Creating env using conda: /home/sttongjai/.nextflow/assets/hoelzer-lab/rnaflow/envs/fastp.yaml [cache /home/sttongjai/conda/fastp-3e6e702456ac1f373ced1ed39b827af4]
Error executing process > 'preprocess_illumina:fastp (MAQCB_rep2)'
Caused by:
Failed to create Conda environment
command: conda env create --prefix /home/sttongjai/conda/fastp-3e6e702456ac1f373ced1ed39b827af4 --file /home/sttongjai/.nextflow/assets/hoelzer-lab/rnaflow/envs/fastp.yaml
status : 1
message:
ResolvePackageNotFound:
- isa-l
(nextflow) sttongjai@STTongjai:~$ conda install -c conda-forge isa-l
Collecting package metadata (current_repodata.json): done
Solving environment: done
Package Plan
environment location: /home/sttongjai/miniconda3/envs/nextflow
added / updated specs:
- isa-l
The following packages will be UPDATED:
ca-certificates conda-forge/label/cf202003::ca-certif~ --> conda-forge::ca-certificates-2021.10.8-ha878542_0
Proceed ([y]/n)? y
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(nextflow) sttongjai@STTongjai:~$ nextflow run -r 1.3.0 hoelzer-lab/rnaflow -profile test,conda,local
N E X T F L O W ~ version 22.04.0
Launching
https://github.com/hoelzer-lab/rnaflow[sharp_nobel] DSL2 - revision: e7d8a96 [1.3.0]Profile: test,conda,local
Current User: sttongjai
Nextflow-version: 22.04.0
Starting time: 2022-04-28T21:33:50.834568+07:00
Workdir location:
/home/sttongjai/work
Launchdir location:
/home/sttongjai
Permanent cache directory:
nextflow-autodownload-databases
Conda cache directory:
conda
Configuration files:
[/home/sttongjai/.nextflow/assets/hoelzer-lab/rnaflow/nextflow.config]
Cmd line:
nextflow run -r 1.3.0 hoelzer-lab/rnaflow -profile test,conda,local
Git info: https://github.com/hoelzer-lab/rnaflow - 1.3.0 [e7d8a96]
CPUs to use: 2, maximal CPUs to use: 4
WARNING: Output folder already exists. Results might be overwritten! You can adjust the output folder via [--output]
R N A F L O W : R N A - S E Q A S S E M B L Y & D I F F E R E N T I A L G E N E E X P R E S S I O N A N A L Y S I S
= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
Output path: results
Strandedness unstranded
Read mode: single-end
TPM threshold: 1
Comparisons: all
Nanopore mode: false
[- ] process > get_test_data:get_reduced_genome_test -
executor > local (3)
executor > local (8)
executor > local (8)
executor > local (8)
executor > local (8)
[58/d141f9] process > get_test_data:get_reduced_genome_test [ 0%] 0 of 1
[f0/341a73] process > get_test_data:get_reduced_annotation_test [ 0%] 0 of 1
[0d/0cf4bb] process > download_sortmerna:sortmernaGet [ 0%] 0 of 1
[99/f1b0dc] process > preprocess_illumina:fastqcPre (MAQCA_rep2) [ 0%] 0 of 4
[- ] process > preprocess_illumina:fastp -
[- ] process > preprocess_illumina:fastqcPost -
[- ] process > preprocess_illumina:extract_tar_bz2 -
executor > local (8)
[58/d141f9] process > get_test_data:get_reduced_genome_test [ 0%] 0 of 1
[f0/341a73] process > get_test_data:get_reduced_annotation_test [ 0%] 0 of 1
[0d/0cf4bb] process > download_sortmerna:sortmernaGet [ 0%] 0 of 1
[99/f1b0dc] process > preprocess_illumina:fastqcPre (MAQCA_rep2) [ 0%] 0 of 4
[- ] process > preprocess_illumina:fastp -
[- ] process > preprocess_illumina:fastqcPost -
[- ] process > preprocess_illumina:extract_tar_bz2 -
[- ] process > preprocess_illumina:sortmerna -
[- ] process > preprocess_illumina:hisat2index -
[- ] process > preprocess_illumina:hisat2 -
[- ] process > preprocess_illumina:index_bam -
[- ] process > expression_reference_based:featurecounts -
[- ] process > expression_reference_based:format_annotation_gene_rows -
[- ] process > expression_reference_based:format_annotation -
[- ] process > expression_reference_based:tpm_filter -
[- ] process > expression_reference_based:deseq2 -
[44/27e583] process > expression_reference_based:multiqc_sample_names (1) [100%] 1 of 1 ✔
[- ] process > expression_reference_based:multiqc -
Creating env using conda: /home/sttongjai/.nextflow/assets/hoelzer-lab/rnaflow/envs/fastp.yaml [cache /home/sttongjai/conda/fastp-3e6e702456ac1f373ced1ed39b827af4]
Error executing process > 'preprocess_illumina:fastp (MAQCB_rep1)'
Caused by:
Failed to create Conda environment
command: conda env create --prefix /home/sttongjai/conda/fastp-3e6e702456ac1f373ced1ed39b827af4 --file /home/sttongjai/.nextflow/assets/hoelzer-lab/rnaflow/envs/fastp.yaml
status : 1
message:
ResolvePackageNotFound:
- isa-l
(nextflow) sttongjai@STTongjai:~$
The text was updated successfully, but these errors were encountered: