fischer-hub
commented
2 years ago Hey @sttongjai !
What system are you working on?
Installing the packages manually might not work because they wont necessarily be accessible when the fastp conda environment is active. They would have to be installed into the environment, which seems to fail in your case. It seems to me some packages are not available for your system. If that is the case and you are working on a local machine anyway, I suggest using Docker or Singularity and then running the pipeline with -profile test,singularity,local or -profile test,docker,local. That way you don't have to take care of the packages being installed correctly.
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: e7d8a96067 [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 [e7d8a9606743ce26557a3ff212a7ec6b695b4833]
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:
(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: e7d8a96067 [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 [e7d8a9606743ce26557a3ff212a7ec6b695b4833]
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:
(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:
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: e7d8a96067 [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 [e7d8a9606743ce26557a3ff212a7ec6b695b4833]
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:
(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:
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: e7d8a96067 [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 [e7d8a9606743ce26557a3ff212a7ec6b695b4833]
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:
(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:
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: e7d8a96067 [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 [e7d8a9606743ce26557a3ff212a7ec6b695b4833]
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:
(nextflow) sttongjai@STTongjai:~$