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Error in rep(no, length.out = len) : attempt to replicate an object of type 'language' #4

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lampinap opened this issue Nov 7, 2024 · 0 comments
Open

Error in rep(no, length.out = len) : attempt to replicate an object of type 'language' #4

lampinap opened this issue Nov 7, 2024 · 0 comments

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@lampinap
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lampinap commented Nov 7, 2024 •
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Here is the complete output of the .err filre resulting from the HPC slurm job submission. This is from a fresh install of the software. There is nothing other than the conda install steps in the .out file. Any help to debug would be greatly appreciated. I looks like the issue is in generating the output, which is an empty folder in this case. TIA

Loading required package: HiCExperiment
Consider using the `HiContacts` package to perform advanced genomic operations 
on `HiCExperiment` objects.

Read "Orchestrating Hi-C analysis with Bioconductor" online book to learn more:
https://js2264.github.io/OHCA/
HiCool :: Fetching bowtie genome index archive from regenie...
HiCool :: Unzipping bowtie2 genome index from refgenie...
trying URL 'https://github.com/conda-forge/miniforge/releases/download/24.3.0-0/Miniforge3-24.3.0-0-Linux-x86_64.sh'
Content type 'application/octet-stream' length 82796318 bytes (79.0 MB)
==================================================
downloaded 79.0 MB

+ /home/.cache/R/basilisk/1.18.0/0/bin/conda create --yes --prefix /home/.cache/R/basilisk/1.18.0/HiCool/1.6.0/env 'python=3.7.12' --quiet -c conda-forge -c bioconda --override-channels
+ /home/.cache/R/basilisk/1.18.0/0/bin/conda install --yes --prefix /home/.cache/R/basilisk/1.18.0/HiCool/1.6.0/env 'python=3.7.12' -c conda-forge -c bioconda --override-channels


==> WARNING: A newer version of conda exists. <==
    current version: 24.3.0
    latest version: 24.9.2

Please update conda by running

    $ conda update -n base -c conda-forge conda


+ /home/.cache/R/basilisk/1.18.0/0/bin/conda install --yes --prefix /home/.cache/R/basilisk/1.18.0/HiCool/1.6.0/env -c conda-forge -c bioconda 'python=3.7.12' 'python=3.7.12' 'bowtie2=2.5.0' 'samtools=1.16.1' 'hicstuff=3.1.5' 'chromosight=1.6.3' 'cooler=0.9.1' --override-channels


==> WARNING: A newer version of conda exists. <==
    current version: 24.3.0
    latest version: 24.9.2

Please update conda by running

    $ conda update -n base -c conda-forge conda


HiCool :: Initiating processing of fastq files [tmp folder: /scratch//2C7K6Z]...
HiCool :: Mapping fastq files...
[bam_sort_core] merging from 64 files and 64 in-memory blocks...
[E::idx_find_and_load] Could not retrieve index file for '/scratch//2C7K6Z/tmp/639e0fe6/temp_alignment.bam'
[bam_sort_core] merging from 0 files and 64 in-memory blocks...
[E::idx_find_and_load] Could not retrieve index file for '/scratch//2C7K6Z/tmp/639e0fe6/temp_alignment.bam'
[bam_sort_core] merging from 0 files and 64 in-memory blocks...
[E::idx_find_and_load] Could not retrieve index file for '/scratch//2C7K6Z/tmp/639e0fe6/temp_alignment.bam'
[bam_sort_core] merging from 0 files and 64 in-memory blocks...
[E::idx_find_and_load] Could not retrieve index file for '/scratch//2C7K6Z/tmp/639e0fe6/temp_alignment.bam'
[bam_sort_core] merging from 0 files and 64 in-memory blocks...
[E::idx_find_and_load] Could not retrieve index file for '/scratch//2C7K6Z/tmp/639e0fe6/temp_alignment.bam'
[bam_sort_core] merging from 0 files and 64 in-memory blocks...
[E::idx_find_and_load] Could not retrieve index file for '/scratch//2C7K6Z/tmp/639e0fe6/temp_alignment.bam'
[bam_sort_core] merging from 0 files and 64 in-memory blocks...
[E::idx_find_and_load] Could not retrieve index file for '/scratch//2C7K6Z/tmp/639e0fe6/temp_alignment.bam'
[bam_sort_core] merging from 0 files and 64 in-memory blocks...
[E::idx_find_and_load] Could not retrieve index file for '/scratch//2C7K6Z/tmp/639e0fe6/temp_alignment.bam'
[E::idx_find_and_load] Could not retrieve index file for '/scratch//2C7K6Z/tmp/639e0fe6/temp_alignment.bam'
[bam_sort_core] merging from 64 files and 64 in-memory blocks...
[E::idx_find_and_load] Could not retrieve index file for '/scratch//2C7K6Z/tmp/461ecffc/temp_alignment.bam'
[bam_sort_core] merging from 0 files and 64 in-memory blocks...
[E::idx_find_and_load] Could not retrieve index file for '/scratch//2C7K6Z/tmp/461ecffc/temp_alignment.bam'
[bam_sort_core] merging from 0 files and 64 in-memory blocks...
[E::idx_find_and_load] Could not retrieve index file for '/scratch//2C7K6Z/tmp/461ecffc/temp_alignment.bam'
[bam_sort_core] merging from 0 files and 64 in-memory blocks...
[E::idx_find_and_load] Could not retrieve index file for '/scratch//2C7K6Z/tmp/461ecffc/temp_alignment.bam'
[bam_sort_core] merging from 0 files and 64 in-memory blocks...
[E::idx_find_and_load] Could not retrieve index file for '/scratch//2C7K6Z/tmp/461ecffc/temp_alignment.bam'
[bam_sort_core] merging from 0 files and 64 in-memory blocks...
[E::idx_find_and_load] Could not retrieve index file for '/scratch//2C7K6Z/tmp/461ecffc/temp_alignment.bam'
[bam_sort_core] merging from 0 files and 64 in-memory blocks...
[E::idx_find_and_load] Could not retrieve index file for '/scratch//2C7K6Z/tmp/461ecffc/temp_alignment.bam'
[bam_sort_core] merging from 0 files and 64 in-memory blocks...
[E::idx_find_and_load] Could not retrieve index file for '/scratch//2C7K6Z/tmp/461ecffc/temp_alignment.bam'
[E::idx_find_and_load] Could not retrieve index file for '/scratch//2C7K6Z/tmp/461ecffc/temp_alignment.bam'
[E::idx_find_and_load] Could not retrieve index file for '/scratch//2C7K6Z/tmp/3_4698OSU_Z1630-Flt3_Hi-C_mm10^mapped-mm10^2C7K6Z.for.bam'
[E::idx_find_and_load] Could not retrieve index file for '/scratch//2C7K6Z/tmp/3_4698OSU_Z1630-Flt3_Hi-C_mm10^mapped-mm10^2C7K6Z.rev.bam'
INFO:cooler.create:Writing chunk 0: /scratch/2C7K6Z/tmp8yuoxbt6.multi.cool::0
INFO:cooler.create:Creating cooler at "/scratch/2C7K6Z/tmp8yuoxbt6.multi.cool::/0"
INFO:cooler.create:Writing chroms
INFO:cooler.create:Writing bins
INFO:cooler.create:Writing pixels
INFO:cooler.create:Writing indexes
INFO:cooler.create:Writing info
INFO:cooler.create:Writing chunk 1: /scratch/2C7K6Z/tmp8yuoxbt6.multi.cool::1
INFO:cooler.create:Creating cooler at "/scratch/2C7K6Z/tmp8yuoxbt6.multi.cool::/1"
INFO:cooler.create:Writing chroms
INFO:cooler.create:Writing bins
INFO:cooler.create:Writing pixels
INFO:cooler.create:Writing indexes
INFO:cooler.create:Writing info
INFO:cooler.create:Writing chunk 2: /scratch/2C7K6Z/tmp8yuoxbt6.multi.cool::2
INFO:cooler.create:Creating cooler at "/scratch/2C7K6Z/tmp8yuoxbt6.multi.cool::/2"
INFO:cooler.create:Writing chroms
INFO:cooler.create:Writing bins
INFO:cooler.create:Writing pixels
INFO:cooler.create:Writing indexes
INFO:cooler.create:Writing info
INFO:cooler.create:Writing chunk 3: /scratch/2C7K6Z/tmp8yuoxbt6.multi.cool::3
INFO:cooler.create:Creating cooler at "/scratch/2C7K6Z/tmp8yuoxbt6.multi.cool::/3"
INFO:cooler.create:Writing chroms
INFO:cooler.create:Writing bins
INFO:cooler.create:Writing pixels
INFO:cooler.create:Writing indexes
INFO:cooler.create:Writing info
INFO:cooler.create:Writing chunk 4: /scratch/2C7K6Z/tmp8yuoxbt6.multi.cool::4
INFO:cooler.create:Creating cooler at "/scratch/2C7K6Z/tmp8yuoxbt6.multi.cool::/4"
INFO:cooler.create:Writing chroms
INFO:cooler.create:Writing bins
INFO:cooler.create:Writing pixels
INFO:cooler.create:Writing indexes
INFO:cooler.create:Writing info
INFO:cooler.create:Writing chunk 5: /scratch/2C7K6Z/tmp8yuoxbt6.multi.cool::5
INFO:cooler.create:Creating cooler at "/scratch/2C7K6Z/tmp8yuoxbt6.multi.cool::/5"
INFO:cooler.create:Writing chroms
INFO:cooler.create:Writing bins
INFO:cooler.create:Writing pixels
INFO:cooler.create:Writing indexes
INFO:cooler.create:Writing info
INFO:cooler.create:Writing chunk 6: /scratch/2C7K6Z/tmp8yuoxbt6.multi.cool::6
INFO:cooler.create:Creating cooler at "/scratch/2C7K6Z/tmp8yuoxbt6.multi.cool::/6"
INFO:cooler.create:Writing chroms
INFO:cooler.create:Writing bins
INFO:cooler.create:Writing pixels
INFO:cooler.create:Writing indexes
INFO:cooler.create:Writing info
INFO:cooler.create:Writing chunk 7: /scratch/2C7K6Z/tmp8yuoxbt6.multi.cool::7
INFO:cooler.create:Creating cooler at "/scratch/2C7K6Z/tmp8yuoxbt6.multi.cool::/7"
INFO:cooler.create:Writing chroms
INFO:cooler.create:Writing bins
INFO:cooler.create:Writing pixels
INFO:cooler.create:Writing indexes
INFO:cooler.create:Writing info
INFO:cooler.create:Writing chunk 8: /scratch/2C7K6Z/tmp8yuoxbt6.multi.cool::8
INFO:cooler.create:Creating cooler at "/scratch/2C7K6Z/tmp8yuoxbt6.multi.cool::/8"
INFO:cooler.create:Writing chroms
INFO:cooler.create:Writing bins
INFO:cooler.create:Writing pixels
INFO:cooler.create:Writing indexes
INFO:cooler.create:Writing info
INFO:cooler.create:Writing chunk 9: /scratch/2C7K6Z/tmp8yuoxbt6.multi.cool::9
INFO:cooler.create:Creating cooler at "/scratch/2C7K6Z/tmp8yuoxbt6.multi.cool::/9"
INFO:cooler.create:Writing chroms
INFO:cooler.create:Writing bins
INFO:cooler.create:Writing pixels
INFO:cooler.create:Writing indexes
INFO:cooler.create:Writing info
INFO:cooler.create:Writing chunk 10: /scratch/2C7K6Z/tmp8yuoxbt6.multi.cool::10
INFO:cooler.create:Creating cooler at "/scratch/2C7K6Z/tmp8yuoxbt6.multi.cool::/10"
INFO:cooler.create:Writing chroms
INFO:cooler.create:Writing bins
INFO:cooler.create:Writing pixels
INFO:cooler.create:Writing indexes
INFO:cooler.create:Writing info
INFO:cooler.create:Writing chunk 11: /scratch/2C7K6Z/tmp8yuoxbt6.multi.cool::11
INFO:cooler.create:Creating cooler at "/scratch/2C7K6Z/tmp8yuoxbt6.multi.cool::/11"
INFO:cooler.create:Writing chroms
INFO:cooler.create:Writing bins
INFO:cooler.create:Writing pixels
INFO:cooler.create:Writing indexes
INFO:cooler.create:Writing info
INFO:cooler.create:Writing chunk 12: /scratch/2C7K6Z/tmp8yuoxbt6.multi.cool::12
INFO:cooler.create:Creating cooler at "/scratch/2C7K6Z/tmp8yuoxbt6.multi.cool::/12"
INFO:cooler.create:Writing chroms
INFO:cooler.create:Writing bins
INFO:cooler.create:Writing pixels
INFO:cooler.create:Writing indexes
INFO:cooler.create:Writing info
INFO:cooler.create:Merging into /scratch//2C7K6Z/3_4698OSU_Z1630-Flt3_Hi-C_mm10^mapped-mm10^2C7K6Z.cool
INFO:cooler.create:Creating cooler at "/scratch//2C7K6Z/3_4698OSU_Z1630-Flt3_Hi-C_mm10^mapped-mm10^2C7K6Z.cool::/"
INFO:cooler.create:Writing chroms
INFO:cooler.create:Writing bins
INFO:cooler.create:Writing pixels
INFO:cooler.reduce:nnzs: [14840377, 14758404, 14828599, 14825253, 14822395, 14817752, 14811206, 14798260, 14778154, 14791768, 14793333, 14754347, 13770361]
INFO:cooler.reduce:current: [14840377, 159623, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
INFO:cooler.reduce:current: [14840377, 14755648, 403962, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
INFO:cooler.reduce:current: [14840377, 14755648, 14828599, 575359, 0, 0, 0, 0, 0, 0, 0, 0, 0]
INFO:cooler.reduce:current: [14840377, 14755648, 14828599, 14825253, 750093, 0, 0, 0, 0, 0, 0, 0, 0]
INFO:cooler.reduce:current: [14840377, 14755648, 14828599, 14825253, 14820839, 929250, 0, 0, 0, 0, 0, 0, 0]
INFO:cooler.reduce:current: [14840377, 14755648, 14828599, 14825253, 14820839, 14817752, 1111489, 0, 0, 0, 0, 0, 0]
INFO:cooler.reduce:current: [14840377, 14755648, 14828599, 14825253, 14820839, 14817752, 14811206, 1300270, 0, 0, 0, 0, 0]
INFO:cooler.reduce:current: [14840377, 14755648, 14828599, 14825253, 14820839, 14817752, 14811206, 14798260, 1501979, 0, 0, 0, 0]
INFO:cooler.reduce:current: [14840377, 14755648, 14828599, 14825253, 14820839, 14817752, 14811206, 14798260, 14778154, 1723819, 0, 0, 0]
INFO:cooler.reduce:current: [14840377, 14755648, 14828599, 14825253, 14820839, 14817752, 14811206, 14798260, 14778154, 14791768, 1932041, 0, 0]
INFO:cooler.reduce:current: [14840377, 14755648, 14828599, 14825253, 14820839, 14817752, 14811206, 14798260, 14778154, 14791768, 14793333, 2138697, 0]
INFO:cooler.reduce:current: [14840377, 14755648, 14828599, 14825253, 14820839, 14817752, 14811206, 14798260, 14778154, 14791768, 14793333, 14754347, 2384333]
INFO:cooler.reduce:current: [14840377, 14758404, 14828599, 14825253, 14822395, 14817752, 14811206, 14798260, 14778154, 14791768, 14793333, 14754347, 13770361]
INFO:cooler.create:Writing indexes
INFO:cooler.create:Writing info
Error in rep(no, length.out = len) : 
  attempt to replicate an object of type 'language'
Calls: HiCool -> <Anonymous> -> fun -> ifelse -> ifelse -> ifelse
Execution halted
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