search

jandrewrfarrell / RUFUS

RUFUS k-mer based genomic variant detection
51 stars 13 forks source link

Trouble building from source #18

Closed moldach closed 3 years ago

moldach commented 3 years ago

I'm working on a Linux based HPC working with private data hence the environment is restrictive (no internet connection); therefore packages must be built from source.

Following the installation instructions I do not see a bin folder within RUFUS-master?

$ git clone https://github.com/jandrewrfarrell/RUFUS.git
$ cd RUFUS
$ ls
-rw-r--r-- 1 moldach mtgraovac   614 Jan 15 13:50 CMakeLists.txt
drwxr-xr-x 3 moldach mtgraovac  4096 Jan 15 13:50 externals
-rw-r--r-- 1 moldach mtgraovac  6192 Jan 15 13:50 README.md
drwxr-xr-x 4 moldach mtgraovac  4096 Jan 15 13:50 resources
-rwxr-xr-x 1 moldach mtgraovac 37532 Jan 15 13:50 runRufus.sh
drwxr-xr-x 3 moldach mtgraovac  4096 Jan 15 13:50 scripts
drwxr-xr-x 5 moldach mtgraovac  4096 Jan 15 13:50 src
drwxr-xr-x 2 moldach mtgraovac  4096 Jan 15 13:50 testRun

Therefore I just tried cmake from the RUFUS-master directory

$ which gcc
/usr/bin/gcc
$ which g++
/usr/bin/g++
$ cmake .
-- The C compiler identification is GNU 8.3.1
-- The CXX compiler identification is GNU 8.3.1
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
TEST: ENV{CPLUS_INCLUDE_PATH}
TEST: ENV{CPLUS_INCLUDE_PATH}
TEST: ENV{CPLUS_INCLUDE_PATH}
-- Configuring done
-- Generating done
-- Build files have been written to: /project/M-mtgraovac182840/tools/RUFUS-master

It looks to have installed properly although when I submit the following I get an error looking to be an issue with jellyfish? which I thought was bundled internally with RUFUS?

$ /project/M-mtgraovac182840/tools/RUFUS-master/runRufus.sh \
        --ref /project/M-mtgraovac182840/indexes/GRCh37/Homo_sapiens.GRCh37.dna.toplevel.fa \
        --kmersize 25 \
        --threads 10 \
        --subject MTG_human_genomics_pipeline-master/alignment/bwa/proband_bwaMEM_sort_dedupped.bam \
        --controls MTG_human_genomics_pipeline-master/alignment/bwa/dad_bwaMEM_sort_dedupped.bam \
        --controls MTG_human_genomics_pipeline-master/alignment/bwa/mom_bwaMEM_sort_dedupped.bam

$ bash run-rufus.sh
/project/M-mtgraovac182840/matthew/tool-testing
marc
Fri Jan 15 14:15:59 MST 2021
checking for samtools
/project/M-mtgraovac182840/tools/samtools-1.3.1/bin/samtools
samtools found
_arg_fastqA =
_arg_fastqB =
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
Final reference path being used is /project/M-mtgraovac182840/indexes/GRCh37/Homo_sapiens.GRCh37.dna.toplevel.fa
Final bwa reference path being used is /project/M-mtgraovac182840/indexes/GRCh37/Homo_sapiens.GRCh37.dna.topleve                                                                                                                    l.fa
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
proband extension is bam
you provided the proband cram file MTG_human_genomics_pipeline-master/alignment/bwa/proband_bwaMEM_sort_dedupped                                                                                                                    .bam
parent file name is dad_bwaMEM_sort_dedupped.bam
parent file extension name is bam
You provided the control bam file MTG_human_genomics_pipeline-master/alignment/bwa/dad_bwaMEM_sort_dedupped.bam
parent file name is mom_bwaMEM_sort_dedupped.bam
parent file extension name is bam
You provided the control bam file MTG_human_genomics_pipeline-master/alignment/bwa/mom_bwaMEM_sort_dedupped.bam
~~~~~~~~~~~~ printing out paramater values used in script ~~~~~~~~~~~~~~~~
value of ProbandGenerator proband_bwaMEM_sort_dedupped.bam.generator
Value of ParentGenerators:
 dad_bwaMEM_sort_dedupped.bam.generator
 mom_bwaMEM_sort_dedupped.bam.generator
Value of K is: 25
Value of Threads is: 10
value of ref is: /project/M-mtgraovac182840/indexes/GRCh37/Homo_sapiens.GRCh37.dna.toplevel.fa
value of min is:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Did not provide refHash
$_arg_min is empty
_arg_min is
MutantMinCov is
parent is  dad_bwaMEM_sort_dedupped.bam.generator
parent is  mom_bwaMEM_sort_dedupped.bam.generator
Running jellyfish for dad_bwaMEM_sort_dedupped.bam.generator
/usr/bin/time: cannot run /project/M-mtgraovac182840/tools/RUFUS-master/scripts/..//bin/externals/jellyfish/src/                                                                                                                    jellyfish_project/bin/jellyfish: No such file or directory
Command exited with non-zero status 127
        Command being timed: "/project/M-mtgraovac182840/tools/RUFUS-master/scripts/..//bin/externals/jellyfish/                                                                                                                    src/jellyfish_project/bin/jellyfish count --disk -m 25 -L 2 -s 8G -t 8 -o dad_bwaMEM_sort_dedupped.bam.generator                                                                                                                    .Jhash -C dad_bwaMEM_sort_dedupped.bam.generator.fq"
        User time (seconds): 0.00
        System time (seconds): 0.00
        Percent of CPU this job got: 42%
        Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.00
        Average shared text size (kbytes): 0
        Average unshared data size (kbytes): 0
        Average stack size (kbytes): 0
        Average total size (kbytes): 0
        Maximum resident set size (kbytes): 940
        Average resident set size (kbytes): 0
        Major (requiring I/O) page faults: 0
        Minor (reclaiming a frame) page faults: 24
        Voluntary context switches: 3
        Involuntary context switches: 0
        Swaps: 0
        File system inputs: 0
        File system outputs: 0
        Socket messages sent: 0
moldach commented 3 years ago

Closing this issue now as I realize it's the same (similar?) issue as #19