v2.2.2 install error

[yipukangda]

I download latest zip file and unzipped. When I run install.sh, error as below show:

./install.sh: line 5: ./install.sh: No such file or directory
make: *** No targets specified and no makefile found.  Stop.
g++ -std=c++11 -o src/alignmentPiles.o -c src/alignmentPiles.cpp -Wall -O3 -std=c++11
g++ -std=c++11 -o src/alignmentWindows.o -c src/alignmentWindows.cpp -Wall -O3 -std=c++11
g++ -std=c++11 -o src/reverseComplement.o -c src/reverseComplement.cpp -Wall -O3 -std=c++11
g++ -std=c++11 -o src/utils.o -c src/utils.cpp -Wall -O3 -std=c++11
g++ -std=c++11 -o src/correctionAlignment.o -c src/correctionAlignment.cpp -Wall -O3 -std=c++11
In file included from src/correctionAlignment.cpp:2:0:
src/correctionAlignment.h:4:10: fatal error: ../BMEAN/utils.h: No such file or directory
 #include "../BMEAN/utils.h"
          ^~~~~~~~~~~~~~~~~~
compilation terminated.
Makefile:47: recipe for target 'correctionAlignment.o' failed
make: *** [correctionAlignment.o] Error 1

[morispi]

Hello,

The issue seems to come from the fact github doesn't include submodules in the archives in generates when created released. I added new archives containing those submodules.

Can you plesae download the CONSENT.tar.gz (135 MB archive) or the CONSENT.zip (134 MB archive) and try again please? I believe that should fix the issue.

Best, Pierre

[yipukangda]

@morispi Hi, I download 134M zip file and install with another problem /usr/bin/ld: cannot find -lspoa (Ubuntu 18.04.4 LTS (GNU/Linux 4.15.0-135-generic x86_64)), I can not find solution for this one on stackoverflow or anywhere else, so do you know how to solve it , thanks.

[morispi]

Seems like something else when wrong prior to the use of spoa. Can you unzip again, and copy/paste me the whole output when running ./install.sh please?

[yipukangda]

@morispi Hi, it seems with the version of ubuntu (no libspoa in ubuntu 18), so I change another device installed ubuntu 20 and install libspoa, no such error again.

[yipukangda]

@morispi Hi, I meet some problem with CONSENT-correct as issue (https://github.com/morispi/CONSENT/issues/4)

cmd:

./CONSENT-correct -j 10 --in ~/data/seq.fq --out ~/data/seq.corr.fa --type ONT

but the input contains no space in header,

and reads length is normal.

[morispi]

Hello,

Sorry for the late reply.

I'll have the same questions as on issue #4 :

1) Does CONSENT still corrects a few long reads, then crashes, or does it fails to perform correction at

2) Have you tried CONSENT on any other dataset? Any small dataset (at least 10x coverage) from any bacterial genome would do, that'd be just to know if the error appears whatever it is you attempt to correct.

Moreover, I see you're using a FASTQ file as input, and that it seems to be multiline. Does your FASTQ file also includes the lines of quality information? If it does not, that could also be the issue, since CONSENT is going to try to parse those quality lines, and will end up failing if they do not exist. If it does not contain quality information, try replacing the "@" with ">" in your input file, this may solve the issue.

Best, Pierre

[yipukangda]

@morispi hi, No corrected reads output, it just crashed and the input is fastq format with qual info lines,

I will try some smaller dataset after returning the lab.

Thanks

[jowodo]

Hi, I downloaded the 135MB tar.gz archive from the release page and got the same error:

g++ -std=c++11 -o bin/CONSENT-correction src/main.o src/utils.o src/correctionDBG.o src/correctionAlignment.o src/correctionMSA.o src/reverseComplement.o src/alignmentPiles.o src/alignmentWindows.o src/CONSENT-correction.o src/DBG.o BMEAN/bmean.o BMEAN/utils.o BMEAN/Complete-Striped-Smith-Waterman-Library/src/*.o -lpthread -LBMEAN/spoa/build/lib -lspoa
/usr/bin/ld: cannot find -lspoa

I'm on CentOS (Oracle Linux Server release 7.9) and couldn't find the library libspoa with yum search spoa and didn't find libspoa in the public conda repo. I found consent, though. When I tried the example data from CONSENT.tar.gz I got a similar error as in issue #23:

[Wed Feb 23 13:18:55 CET 2022] Correcting the long reads
/apps/consent/2.2.2/bin/CONSENT-correct: line 202: 15709 Illegal instruction     CONSENT-correction -a $tmpdir/"$alignments" -s "$minSupport" -S "$maxSupport" -l "$windowSize" -k "$merSize" -c "$commonKMers" -A "$minAnchors" -f "$solid" -m "$windowOverlap" -j "$nproc" -r "$reads" -M "$maxMSA" -p "$LRSCf" >> "$out"

where the Illegal instruction number is different every run.

SOLUTION: cmake version > 3.2 I found spoa on conda, and installed it and then linked the library:

# in CONSENT directory
./install.sh
./clean.sh
ln -s /apps/spoa/4.0.7/lib/libspoa.a BMEAN/spoa/build/lib/libspoa.a
./install.sh

I had to install and then clean before linking because otherwise the BMEAN/spoa/build direktory doesn't exist.