Issue regarding 'nextflow run evotools/nf-LO'

[Heather1999]

Hello, thank you for developing this tool, I tried to run the following code :
nextflow run evotools/nf-LO --source /home/sealight1999/references/GRCH38/GRCh38_no_alt.fna --target /home/sealight1999/references/CHM13/ chm13v2.0_1.fa --aligner minimap2 –outdir /home/sealight1999/references -profile local
But encountered following warnings:
[c3/9fda46] NOTE: Process PREPROC:tgt2bit (tgt2Bit) terminated with an error exit status (127) -- Execution is retried (1)
[ae/47e4dc] NOTE: Process PREPROC:splitsrc (splitsrc) terminated with an error exit status (127) -- Execution is retried (1)
[e7/fdb913] NOTE: Process PREPROC:src2bit (src2Bit) terminated with an error exit status (127) -- Execution is retried (1)
[fd/3eadf0] NOTE: Process PREPROC:splittgt (splittgt) terminated with an error exit status (127) -- Execution is retried (1)
[03/acbfe7] NOTE: Process PREPROC:tgt2bit (tgt2Bit) terminated with an error exit status (127) -- Execution is retried (2)
[8e/ecf45f] NOTE: Process PREPROC:splitsrc (splitsrc) terminated with an error exit status (127) -- Execution is retried (2)
[22/e11aa5] NOTE: Process PREPROC:src2bit (src2Bit) terminated with an error exit status (127) -- Execution is retried (2)
[62/97c512] NOTE: Process PREPROC:splittgt (splittgt) terminated with an error exit status (127) -- Execution is retried (2)
[83/bd21fa] NOTE: Process PREPROC:tgt2bit (tgt2Bit) terminated with an error exit status (127) -- Error is ignored
[3f/930365] NOTE: Process PREPROC:splitsrc (splitsrc) terminated with an error exit status (127) -- Error is ignored
[9e/fdca06] NOTE: Process PREPROC:src2bit (src2Bit) terminated with an error exit status (127) -- Error is ignored
[77/94ba10] NOTE: Process PREPROC:splittgt (splittgt) terminated with an error exit status (127) -- Error is ignored
WARN: Graphviz is required to render the execution DAG in the given format -- See http://www.graphviz.org for more info.

What could be wrong? Thank you!

[Heather1999]

Plus when I run assets/install.py, it did not seem successful.. the following are the bottom-most output:

utils.c:33:10: fatal error: zlib.h: No such file or directory
33 | #include <zlib.h>
| ^~~~~~~~
compilation terminated.
make[1]: *** [makefile:9: utils.o] Error 1
make[1]: Leaving directory '/home/sealight1999/app/nextflow/nf-LO/assets/bin/GSAlign_src/src/BWT_Index'
make: *** [makefile:13: bwt_index] Error 2
install.sh: line 99: pip2: command not found
--2024-03-03 19:30:24-- https://github.com/lh3/minimap2/releases/download/v2.17/minimap2-2.17_x64-linux.tar.bz2
Resolving github.com (github.com)... 20.27.177.113
Connecting to github.com (github.com)|20.27.177.113|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://objects.githubusercontent.com/github-production-release-asset-2e65be/97612481/fafde000-6ec7-11e9-8f99-513f7e53bc2c?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAVCODYLSA53PQK4ZA%2F20240303%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20240303T113025Z&X-Amz-Expires=300&X-Amz-Signature=b168d2871a3ae8a79b86b7ed0cfa39a0db835d6972c2293e25a1409ca166535b&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=97612481&response-content-disposition=attachment%3B%20filename%3Dminimap2-2.17_x64-linux.tar.bz2&response-content-type=application%2Foctet-stream [following]
--2024-03-03 19:30:25-- https://objects.githubusercontent.com/github-production-release-asset-2e65be/97612481/fafde000-6ec7-11e9-8f99-513f7e53bc2c?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAVCODYLSA53PQK4ZA%2F20240303%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20240303T113025Z&X-Amz-Expires=300&X-Amz-Signature=b168d2871a3ae8a79b86b7ed0cfa39a0db835d6972c2293e25a1409ca166535b&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=97612481&response-content-disposition=attachment%3B%20filename%3Dminimap2-2.17_x64-linux.tar.bz2&response-content-type=application%2Foctet-stream
Resolving objects.githubusercontent.com (objects.githubusercontent.com)... 185.199.108.133, 185.199.111.133, 185.199.110.133, ...
Connecting to objects.githubusercontent.com (objects.githubusercontent.com)|185.199.108.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 2100809 (2.0M) [application/octet-stream]
Saving to: ‘minimap2-2.17_x64-linux.tar.bz2’

minimap2-2.17_x64-linux.tar.bz2 100%[===========================================================================================>] 2.00M 10.4MB/s in 0.2s

2024-03-03 19:30:26 (10.4 MB/s) - ‘minimap2-2.17_x64-linux.tar.bz2’ saved [2100809/2100809]

minimap2-2.17_x64-linux/
minimap2-2.17_x64-linux/minimap2
minimap2-2.17_x64-linux/NEWS.md
minimap2-2.17_x64-linux/k8
minimap2-2.17_x64-linux/LICENSE.txt
minimap2-2.17_x64-linux/cookbook.md
minimap2-2.17_x64-linux/README-js.md
minimap2-2.17_x64-linux/minimap2.1
minimap2-2.17_x64-linux/paftools.js
minimap2-2.17_x64-linux/README.md
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 18.1M 100 18.1M 0 0 4993k 0 0:00:03 0:00:03 --:--:-- 4994k
Cloning into 'sonLib'...
remote: Enumerating objects: 6309, done.
remote: Counting objects: 100% (64/64), done.
remote: Compressing objects: 100% (47/47), done.
remote: Total 6309 (delta 28), reused 40 (delta 16), pack-reused 6245
Receiving objects: 100% (6309/6309), 17.46 MiB | 8.55 MiB/s, done.
Resolving deltas: 100% (4036/4036), done.
cd externalTools && make all
make[1]: Entering directory '/home/sealight1999/app/nextflow/nf-LO/assets/bin/GSAlign_src/sonLib/externalTools'
cd cutest && make all
make[2]: Entering directory '/home/sealight1999/app/nextflow/nf-LO/assets/bin/GSAlign_src/sonLib/externalTools/cutest'
/home/sealight1999/miniconda3/bin/x86_64-conda_cos6-linux-gnu-gcc -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c
make[2]: /home/sealight1999/miniconda3/bin/x86_64-conda_cos6-linux-gnu-gcc: Command not found
make[2]: *** [Makefile:12: ../../lib/cuTest.a] Error 127
make[2]: Leaving directory '/home/sealight1999/app/nextflow/nf-LO/assets/bin/GSAlign_src/sonLib/externalTools/cutest'
make[1]: *** [Makefile:11: cutestM] Error 2
make[1]: Leaving directory '/home/sealight1999/app/nextflow/nf-LO/assets/bin/GSAlign_src/sonLib/externalTools'
make: *** [Makefile:15: externalToolsP] Error 2
Cloning into 'pinchesAndCacti'...
remote: Enumerating objects: 893, done.
remote: Counting objects: 100% (81/81), done.
remote: Compressing objects: 100% (54/54), done.
remote: Total 893 (delta 38), reused 60 (delta 24), pack-reused 812
Receiving objects: 100% (893/893), 371.53 KiB | 2.90 MiB/s, done.
Resolving deltas: 100% (529/529), done.
include.mk:8: ../sonLib/include.mk: No such file or directory
make: *** No rule to make target '../sonLib/include.mk'. Stop.
Cloning into 'mafTools'...
remote: Enumerating objects: 5489, done.
remote: Counting objects: 100% (22/22), done.
remote: Compressing objects: 100% (19/19), done.
remote: Total 5489 (delta 6), reused 9 (delta 3), pack-reused 5467
Receiving objects: 100% (5489/5489), 4.30 MiB | 7.80 MiB/s, done.
Resolving deltas: 100% (2887/2887), done.
Makefile:16: Because dependency ../sonLib is missing mafComparator, mafTransitiveClosure, mafStats, mafToFastaStitcher, mafPairCoverage, mafCoverage will not be built / tested / cleaned. See README.md for information about dependencies.
cd lib && make all
make[1]: Entering directory '/home/sealight1999/app/nextflow/nf-LO/assets/bin/GSAlign_src/sonLib/pinchesAndCacti/mafTools/lib'
gcc -O3 -c -std=c99 -O3 -Wextra -Wall -Werror -pedantic -I ../external/ -I ../inc/ common.c -o common.o.tmp
mv common.o.tmp common.o
gcc -O3 -c -std=c99 -O3 -Wextra -Wall -Werror -pedantic -I ../external/ -I ../inc/ sharedMaf.c -o sharedMaf.o.tmp -lm
mv sharedMaf.o.tmp sharedMaf.o
gcc -c -std=c99 -O3 -Wextra -Wall -Werror -pedantic -I ../external/ -I ../inc/ ../external/CuTest.c
ar rc CuTest.a CuTest.o
ranlib CuTest.a
rm -f CuTest.o
mv CuTest.a ../external/CuTest.a
make[1]: Leaving directory '/home/sealight1999/app/nextflow/nf-LO/assets/bin/GSAlign_src/sonLib/pinchesAndCacti/mafTools/lib'
cd mafValidator && make all
make[1]: Entering directory '/home/sealight1999/app/nextflow/nf-LO/assets/bin/GSAlign_src/sonLib/pinchesAndCacti/mafTools/mafValidator'
cp src/mafValidator.py ../bin/mafValidator.py.tmp
chmod +x ../bin/mafValidator.py.tmp
mv ../bin/mafValidator.py.tmp ../bin/mafValidator.py
make[1]: Leaving directory '/home/sealight1999/app/nextflow/nf-LO/assets/bin/GSAlign_src/sonLib/pinchesAndCacti/mafTools/mafValidator'
cd mafPositionFinder && make all
make[1]: Entering directory '/home/sealight1999/app/nextflow/nf-LO/assets/bin/GSAlign_src/sonLib/pinchesAndCacti/mafTools/mafPositionFinder'
/home/sealight1999/miniconda3/bin/x86_64-conda_cos6-linux-gnu-gcc -c -o src/buildVersion.o src/buildVersion.c
/bin/bash: /home/sealight1999/miniconda3/bin/x86_64-conda_cos6-linux-gnu-gcc: No such file or directory
make[1]: *** [: src/buildVersion.o] Error 127
make[1]: Leaving directory '/home/sealight1999/app/nextflow/nf-LO/assets/bin/GSAlign_src/sonLib/pinchesAndCacti/mafTools/mafPositionFinder'
make: *** [Makefile:41: mafPositionFinder.all] Error 2
chmod: cannot access './bin/*': No such file or directory

[RenzoTale88]

Hi @Heather1999, error 127 is due to the workflow not finding the required dependencies. I'd suggest to either:

1. create a docker/singularity container with the required dependencies, as described here
2. install anaconda on the system, and then run the workflow with -profile conda