Comments (3)
RenzoTale88
commented on July 29, 2024
Hi @Fuyt27, thank you for using nf-LO!
Are you installing the environment before running nf-LO, or are you letting nf-LO to install the environment by itself?
If you are using the first approac, I would suggest to:
- Install the environment
- Find the installation path to the environment with
conda info --envs - Pass the path to the environment using
--with-conda /PATH/TO/MY/ANACONDA/ENV/
If you are using the second solution (what i would recommend), I would suggest to go through the mamba route described (here)[https://nf-lo.readthedocs.io/en/latest/install.html#mamba] (install mamba in your anaconda base environment, then use the --mamba flag).
I hope this helps.
Andrea
from nf-lo.
Fuyt27
commented on July 29, 2024
I used the second solution and use --mamba but still failed. Here is my script:
nextflow run /gpfsdata/home/zhangpj/CH/tools/nf-LO/main.nf --source ./Macaca_fascicularis.Macaca_fascicularis_6.0.dna.toplevel.fa.gz --target ./Homo_sapiens.GRCh38.dna.toplevel.fa.gz --distance near --aligner lastz --outdir ./liftover_genome1_genome2 --no_netsynt --mamba -profile conda
and the error info is
N E X T F L O W ~ version 21.10.6
Launching /gpfsdata/home/zhangpj/CH/tools/nf-LO/main.nf [big_torricelli] - revision: 0226af5ff9
======================================
__ _ ____
/ | | | / __ \
_ __ | | ______ | | | | | |
| '_ | | || | | | | | |
| | | | | | || || |
|| ||| |____/
Nextflow LiftOver v 1.7.0
======================================
source : ./Macaca_fascicularis.Macaca_fascicularis_6.0.dna.toplevel.fa.gz
target : ./Homo_sapiens.GRCh38.dna.toplevel.fa.gz
aligner : lastz
distance : near
custom align : false
custom chain : false
source chunk : 20000000
source overlap : 0
target chunk : 10000000
target overlap : 100000
output folder : ./liftover_genome1_genome2
liftover name : liftover
annot : false
annot type : false
liftover meth. : liftover
igenomes_base : s3://ngi-igenomes/igenomes/
igenomes_ignore : false
mamba : true
no_maf : false
skip netsynt : true
max cpu : 55
max mem : 29 GB
max rt : 240.h
Using CrossMap
[- ] process > PREPROC:src2bit -
[- ] process > PREPROC:tgt2bit -
[- ] process > PREPROC:splitsrc -
[- ] process > PREPROC:groupsrc -
[- ] process > PREPROC:splittgt -
[- ] process > PREPROC:grouptgt -
[- ] process > PREPROC:pairs -
[- ] process > ALIGNER:lastz -
[- ] process > ALIGNER:axtChain -
[- ] process > ALIGNER:chainMerge -
[- ] process > ALIGNER:chainNet -
[- ] process > ALIGNER:chainsubset -
[- ] process > ALIGNER:chain2maf -
[- ] process > ALIGNER:name_maf_seq -
[- ] process > ALIGNER:mafstats -
[- ] process > PREPROC:src2bit -
[- ] process > PREPROC:tgt2bit -
[- ] process > PREPROC:splitsrc -
[- ] process > PREPROC:groupsrc -
[- ] process > PREPROC:splittgt -
[- ] process > PREPROC:grouptgt -
[- ] process > PREPROC:pairs -
[- ] process > ALIGNER:lastz -
[- ] process > ALIGNER:axtChain -
[- ] process > ALIGNER:chainMerge -
[- ] process > ALIGNER:chainNet -
[- ] process > ALIGNER:chainsubset -
[- ] process > ALIGNER:chain2maf -
[- ] process > ALIGNER:name_maf_seq -
[- ] process > ALIGNER:mafstats -
Creating env using mamba: /gpfsdata/home/zhangpj/CH/tools/nf-LO/assets/environment.yml [cache /gpfsdata/home/zhangpj/CH/monkey/work/conda/nf-LO-94c4346dca8beb9d44e946b84885c100]
executor > local (3)
[3b/f18bcf] process > PREPROC:src2bit (src2Bit) [ 0%] 0 of 1
[f5/51329b] process > PREPROC:tgt2bit (tgt2Bit) [ 0%] 0 of 1
[- ] process > PREPROC:splitsrc [ 0%] 0 of 1
[- ] process > PREPROC:groupsrc -
[ff/ddc258] process > PREPROC:splittgt (splittgt) [ 0%] 0 of 1
[- ] process > PREPROC:grouptgt -
[- ] process > PREPROC:pairs -
[- ] process > ALIGNER:lastz -
[- ] process > ALIGNER:axtChain -
[- ] process > ALIGNER:chainMerge -
[- ] process > ALIGNER:chainNet -
[- ] process > ALIGNER:chainsubset -
[- ] process > ALIGNER:chain2maf -
[- ] process > ALIGNER:name_maf_seq -
[- ] process > ALIGNER:mafstats -
executor > local (4)
[3b/f18bcf] process > PREPROC:src2bit (src2Bit) [ 0%] 0 of 1
[f5/51329b] process > PREPROC:tgt2bit (tgt2Bit) [ 0%] 0 of 1
[d4/fa0b63] process > PREPROC:splitsrc (splitsrc) [ 0%] 0 of 1
[- ] process > PREPROC:groupsrc -
[ff/ddc258] process > PREPROC:splittgt (splittgt) [ 0%] 0 of 1
[- ] process > PREPROC:grouptgt -
[- ] process > PREPROC:pairs -
[- ] process > ALIGNER:lastz -
[- ] process > ALIGNER:axtChain -
[- ] process > ALIGNER:chainMerge -
[- ] process > ALIGNER:chainNet -
[- ] process > ALIGNER:chainsubset -
[- ] process > ALIGNER:chain2maf -
[- ] process > ALIGNER:name_maf_seq -
[- ] process > ALIGNER:mafstats -
executor > local (4)
[3b/f18bcf] process > PREPROC:src2bit (src2Bit) [ 0%] 0 of 1
[f5/51329b] process > PREPROC:tgt2bit (tgt2Bit) [ 0%] 0 of 1
[d4/fa0b63] process > PREPROC:splitsrc (splitsrc) [ 0%] 0 of 1
[- ] process > PREPROC:groupsrc -
[ff/ddc258] process > PREPROC:splittgt (splittgt) [ 50%] 1 of 2, failed: 1, r...
[- ] process > PREPROC:grouptgt -
[- ] process > PREPROC:pairs -
[- ] process > ALIGNER:lastz -
[- ] process > ALIGNER:axtChain -
[- ] process > ALIGNER:chainMerge -
[- ] process > ALIGNER:chainNet -
[- ] process > ALIGNER:chainsubset -
[- ] process > ALIGNER:chain2maf -
[- ] process > ALIGNER:name_maf_seq -
[- ] process > ALIGNER:mafstats -
[ff/ddc258] NOTE: Process PREPROC:splittgt (splittgt) terminated with an error exit status (255) -- Execution is retried (1)
executor > local (6)
[3b/f18bcf] process > PREPROC:src2bit (src2Bit) [ 0%] 0 of 1
[87/449559] process > PREPROC:tgt2bit (tgt2Bit) [ 50%] 1 of 2, failed: 1, r...
[d4/fa0b63] process > PREPROC:splitsrc (splitsrc) [ 0%] 0 of 1
[- ] process > PREPROC:groupsrc -
[fb/708994] process > PREPROC:splittgt (splittgt) [ 50%] 1 of 2, failed: 1, r...
[- ] process > PREPROC:grouptgt -
[- ] process > PREPROC:pairs -
[- ] process > ALIGNER:lastz -
[- ] process > ALIGNER:axtChain -
[- ] process > ALIGNER:chainMerge -
[- ] process > ALIGNER:chainNet -
[- ] process > ALIGNER:chainsubset -
[- ] process > ALIGNER:chain2maf -
[- ] process > ALIGNER:name_maf_seq -
[- ] process > ALIGNER:mafstats -
[ff/ddc258] NOTE: Process PREPROC:splittgt (splittgt) terminated with an error exit status (255) -- Execution is retried (1)
[f5/51329b] NOTE: Process PREPROC:tgt2bit (tgt2Bit) terminated with an error exit status (255) -- Execution is retried (1)
executor > local (7)
[3b/f18bcf] process > PREPROC:src2bit (src2Bit) [ 0%] 0 of 1
[87/449559] process > PREPROC:tgt2bit (tgt2Bit) [ 50%] 1 of 2, failed: 1, r...
[d4/fa0b63] process > PREPROC:splitsrc (splitsrc) [ 0%] 0 of 1
[- ] process > PREPROC:groupsrc -
[f1/8b4686] process > PREPROC:splittgt (splittgt) [ 66%] 2 of 3, failed: 2, r...
[- ] process > PREPROC:grouptgt -
[- ] process > PREPROC:pairs -
[- ] process > ALIGNER:lastz -
[- ] process > ALIGNER:axtChain -
[- ] process > ALIGNER:chainMerge -
[- ] process > ALIGNER:chainNet -
[- ] process > ALIGNER:chainsubset -
[- ] process > ALIGNER:chain2maf -
[- ] process > ALIGNER:name_maf_seq -
[- ] process > ALIGNER:mafstats -
[ff/ddc258] NOTE: Process PREPROC:splittgt (splittgt) terminated with an error exit status (255) -- Execution is retried (1)
[f5/51329b] NOTE: Process PREPROC:tgt2bit (tgt2Bit) terminated with an error exit status (255) -- Execution is retried (1)
[fb/708994] NOTE: Process PREPROC:splittgt (splittgt) terminated with an error exit status (255) -- Execution is retried (2)
executor > local (8)
[3b/f18bcf] process > PREPROC:src2bit (src2Bit) [ 0%] 0 of 1
[ee/57bb5d] process > PREPROC:tgt2bit (tgt2Bit) [ 66%] 2 of 3, failed: 2, r...
[d4/fa0b63] process > PREPROC:splitsrc (splitsrc) [ 0%] 0 of 1
[- ] process > PREPROC:groupsrc -
[f1/8b4686] process > PREPROC:splittgt (splittgt) [ 66%] 2 of 3, failed: 2, r...
[- ] process > PREPROC:grouptgt -
[- ] process > PREPROC:pairs -
[- ] process > ALIGNER:lastz -
[- ] process > ALIGNER:axtChain -
[- ] process > ALIGNER:chainMerge -
[- ] process > ALIGNER:chainNet -
[- ] process > ALIGNER:chainsubset -
[- ] process > ALIGNER:chain2maf -
[- ] process > ALIGNER:name_maf_seq -
[- ] process > ALIGNER:mafstats -
[ff/ddc258] NOTE: Process PREPROC:splittgt (splittgt) terminated with an error exit status (255) -- Execution is retried (1)
[f5/51329b] NOTE: Process PREPROC:tgt2bit (tgt2Bit) terminated with an error exit status (255) -- Execution is retried (1)
[fb/708994] NOTE: Process PREPROC:splittgt (splittgt) terminated with an error exit status (255) -- Execution is retried (2)
[87/449559] NOTE: Process PREPROC:tgt2bit (tgt2Bit) terminated with an error exit status (255) -- Execution is retried (2)
executor > local (8)
[3b/f18bcf] process > PREPROC:src2bit (src2Bit) [ 0%] 0 of 1
[ee/57bb5d] process > PREPROC:tgt2bit (tgt2Bit) [100%] 3 of 3, failed: 3, r...
[d4/fa0b63] process > PREPROC:splitsrc (splitsrc) [ 0%] 0 of 1
[- ] process > PREPROC:groupsrc -
[f1/8b4686] process > PREPROC:splittgt (splittgt) [100%] 3 of 3, failed: 3, r...
[- ] process > PREPROC:grouptgt -
[- ] process > PREPROC:pairs -
[- ] process > ALIGNER:lastz -
[- ] process > ALIGNER:axtChain -
[- ] process > ALIGNER:chainMerge -
[- ] process > ALIGNER:chainNet -
[- ] process > ALIGNER:chainsubset -
[- ] process > ALIGNER:chain2maf -
[- ] process > ALIGNER:name_maf_seq -
[- ] process > ALIGNER:mafstats -
[ff/ddc258] NOTE: Process PREPROC:splittgt (splittgt) terminated with an error exit status (255) -- Execution is retried (1)
[f5/51329b] NOTE: Process PREPROC:tgt2bit (tgt2Bit) terminated with an error exit status (255) -- Execution is retried (1)
[fb/708994] NOTE: Process PREPROC:splittgt (splittgt) terminated with an error exit status (255) -- Execution is retried (2)
[87/449559] NOTE: Process PREPROC:tgt2bit (tgt2Bit) terminated with an error exit status (255) -- Execution is retried (2)
[f1/8b4686] NOTE: Process PREPROC:splittgt (splittgt) terminated with an error exit status (255) -- Error is ignored
[ee/57bb5d] NOTE: Process PREPROC:tgt2bit (tgt2Bit) terminated with an error exit status (255) -- Error is ignored
executor > local (9)
[3b/f18bcf] process > PREPROC:src2bit (src2Bit) [ 0%] 0 of 1
[ee/57bb5d] process > PREPROC:tgt2bit (tgt2Bit) [100%] 3 of 3, failed: 3, r...
[d4/fa0b63] process > PREPROC:splitsrc (splitsrc) [100%] 1 of 1 ✔
[e7/3ce25a] process > PREPROC:groupsrc (groupsrc) [ 0%] 0 of 1
[f1/8b4686] process > PREPROC:splittgt (splittgt) [100%] 3 of 3, failed: 3, r...
[- ] process > PREPROC:grouptgt -
[- ] process > PREPROC:pairs -
[- ] process > ALIGNER:lastz -
[- ] process > ALIGNER:axtChain -
[- ] process > ALIGNER:chainMerge -
[- ] process > ALIGNER:chainNet -
[- ] process > ALIGNER:chainsubset -
[- ] process > ALIGNER:chain2maf -
[- ] process > ALIGNER:name_maf_seq -
[- ] process > ALIGNER:mafstats -
[ff/ddc258] NOTE: Process PREPROC:splittgt (splittgt) terminated with an error exit status (255) -- Execution is retried (1)
[f5/51329b] NOTE: Process PREPROC:tgt2bit (tgt2Bit) terminated with an error exit status (255) -- Execution is retried (1)
[fb/708994] NOTE: Process PREPROC:splittgt (splittgt) terminated with an error exit status (255) -- Execution is retried (2)
[87/449559] NOTE: Process PREPROC:tgt2bit (tgt2Bit) terminated with an error exit status (255) -- Execution is retried (2)
[f1/8b4686] NOTE: Process PREPROC:splittgt (splittgt) terminated with an error exit status (255) -- Error is ignored
[ee/57bb5d] NOTE: Process PREPROC:tgt2bit (tgt2Bit) terminated with an error exit status (255) -- Error is ignored
executor > local (9)
[3b/f18bcf] process > PREPROC:src2bit (src2Bit) [ 0%] 0 of 1
[ee/57bb5d] process > PREPROC:tgt2bit (tgt2Bit) [100%] 3 of 3, failed: 3, r...
[d4/fa0b63] process > PREPROC:splitsrc (splitsrc) [100%] 1 of 1 ✔
[e7/3ce25a] process > PREPROC:groupsrc (groupsrc) [100%] 1 of 1 ✔
[f1/8b4686] process > PREPROC:splittgt (splittgt) [100%] 3 of 3, failed: 3, r...
[- ] process > PREPROC:grouptgt -
[- ] process > PREPROC:pairs -
[- ] process > ALIGNER:lastz -
[- ] process > ALIGNER:axtChain -
[- ] process > ALIGNER:chainMerge -
[- ] process > ALIGNER:chainNet -
[- ] process > ALIGNER:chainsubset -
[- ] process > ALIGNER:chain2maf -
[- ] process > ALIGNER:name_maf_seq -
[- ] process > ALIGNER:mafstats -
[fb/708994] NOTE: Process PREPROC:splittgt (splittgt) terminated with an error exit status (255) -- Execution is retried (2)
[87/449559] NOTE: Process PREPROC:tgt2bit (tgt2Bit) terminated with an error exit status (255) -- Execution is retried (2)
[f1/8b4686] NOTE: Process PREPROC:splittgt (splittgt) terminated with an error exit status (255) -- Error is ignored
[ee/57bb5d] NOTE: Process PREPROC:tgt2bit (tgt2Bit) terminated with an error exit status (255) -- Error is ignored
executor > local (9)
[3b/f18bcf] process > PREPROC:src2bit (src2Bit) [100%] 1 of 1 ✔
[ee/57bb5d] process > PREPROC:tgt2bit (tgt2Bit) [100%] 3 of 3, failed: 3, r...
[d4/fa0b63] process > PREPROC:splitsrc (splitsrc) [100%] 1 of 1 ✔
[e7/3ce25a] process > PREPROC:groupsrc (groupsrc) [100%] 1 of 1 ✔
[f1/8b4686] process > PREPROC:splittgt (splittgt) [100%] 3 of 3, failed: 3, r...
[- ] process > PREPROC:grouptgt -
[- ] process > PREPROC:pairs -
[- ] process > ALIGNER:lastz -
[- ] process > ALIGNER:axtChain -
[- ] process > ALIGNER:chainMerge -
[- ] process > ALIGNER:chainNet -
[- ] process > ALIGNER:chainsubset -
[- ] process > ALIGNER:chain2maf -
[- ] process > ALIGNER:name_maf_seq -
[- ] process > ALIGNER:mafstats -
executor > local (9)
[3b/f18bcf] process > PREPROC:src2bit (src2Bit) [100%] 1 of 1 ✔
[ee/57bb5d] process > PREPROC:tgt2bit (tgt2Bit) [100%] 3 of 3, failed: 3, r...
[d4/fa0b63] process > PREPROC:splitsrc (splitsrc) [100%] 1 of 1 ✔
[e7/3ce25a] process > PREPROC:groupsrc (groupsrc) [100%] 1 of 1 ✔
[f1/8b4686] process > PREPROC:splittgt (splittgt) [100%] 3 of 3, failed: 3, r...
[- ] process > PREPROC:grouptgt -
[- ] process > PREPROC:pairs -
[- ] process > ALIGNER:lastz -
[- ] process > ALIGNER:axtChain -
[- ] process > ALIGNER:chainMerge -
[- ] process > ALIGNER:chainNet -
[- ] process > ALIGNER:chainsubset -
[- ] process > ALIGNER:chain2maf -
[- ] process > ALIGNER:name_maf_seq -
[- ] process > ALIGNER:mafstats -
Completed at: 20-Oct-2022 13:39:08
Duration : 9m 17s
CPU hours : (a few seconds)
Succeeded : 3
Ignored : 2
Failed : 6
from nf-lo.
Fuyt27
commented on July 29, 2024
It seems that i succeed in running this pipiline by using docker!! Thanks anyway and your tool is very helpful for me
from nf-lo.
Related Issues (20)
- Process requirement exceed available CPUs -- req: 2; avail: 1 HOT 9
- Failed in ALIGNER:lastz HOT 1
- ALIGNER:chainMerge (chainmerge) FAILED HOT 7
- error exit status (255) HOT 4
- liftover failed with cross map HOT 7
- having trouble installing nf-lo manually HOT 1
- minimap2: Stdin is empty HOT 16
- cannot build singularity/docker images with the current continuumio/miniconda3 image
- grouptgt error HOT 1
- Too large of a bash script for slurm in chainMerge HOT 3
- Issue about Annotation HOT 2
- A problem while using nf-LO HOT 1
- Issue regarding 'nextflow run evotools/nf-LO' HOT 2
- Process `ALIGNER:chainMerge (chainmerge)` terminated with an error exit status (1) -- Execution is retried (1) HOT 19
- The current r-environment.yml never resolves HOT 7
- Minimap2 and gsalign using too few cpus HOT 2
- pipeline commands HOT 1
- environment.yml error even while running via docker HOT 6
- How to merge chain file from different chromosome HOT 2
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from nf-lo.