vibansal / hapcut Goto Github PK

Hi,

I tried to run Hapcut on my data as recommended in the readme file but there was never an outputfile created.

Thanks,
Nath

Commands:
extractHAIRS --VCF consensus.vcf --bam raw.k4.R1R2.bam.sorted.bam --maxIS 600 > fragment
HAPCUT --fragments fragment --VCF consensus.vcf --output result.fa --maxiter 10 --maxmem 12000 --longreads 1 > hapcut.log

PS: I tried with and without file extension for the output file

Hi

I just run Hapcut and always get exit status 1，suggesting the jobs fails. But all the output seems to be fine. I checked the source code, and it seems that the program always return 1. Am I correct? And is there any specific reason for that?

Thanks,
Yunjiang

I am using extracHAIRS to get reads covering heterozygous SNPs. However, the SNPs seems to be ignored when two ends are overlapping. And the quality score for the base is not correct. In the attached example, the first read pairs are not reported even they cover the SNP, and the second read was reported but with the quality score < instead of D.

Commands

extractHAIRS --bam test.bam --VCF test.vcf --singlereads 1

BAM Files

7001113:798:HGCT5BCXY:1:2107:10688:87752 163 chr22 16056034 27 100M = 16056083 148 CACTCAGCCAGTTCACCCCACCCACATTCCACAGGCTGCTTTAGGCTTTAGGACAGTGGCAAACATGGCCTCTGCCATCCCGGTCTGTGAGCGCCCCTTC DDDDDIHIIIIIIIIIIIIIIIIIIIIIEHHIIIIHIIIIIIIIHHIIHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGHIIIH MD:Z:100 PG:Z:MarkDuplicates RG:Z:JY333 NM:i:0 AS:i:100 XS:i:100
7001113:798:HGCT5BCXY:1:2107:10688:87752 83 chr22 16056083 27 99M = 16056034 -148 AGGACAGTGGCAAACATGGCCTCTGCCATCCCGGTCTGTGAGCGCCCCTTCTTACACCAAGGTCAGTTGCTAACCAATGAGCTGCTGGGGGCCTCCTTC IIIIIIIIIIIIIIIIHIIIGIIIIHIIIHIIIIIIHIIIIGIIIIIIIGIIIHE1IIIIIIIIIIIIIIIIIIIIIIHIIIIIIIIIGIHEFD<0DD< MD:Z:99 PG:Z:MarkDuplicates RG:Z:JY333 NM:i:0 AS:i:99 XS:i:94
7001113:798:HGCT5BCXY:2:1213:5687:10232 163 chr22 16056108 27 98M = 16056333 325 CCATCCCGGTCTGTGAGCGCCCCTTCTTACACCAAGGTCAGTTGCTAACCAATGAGCTGCTGGGGGCCTCCTTCTCCCACTCCCACTGCACTGTGTCC 0<D@DEEHHCDCG<CGFHD<HHHHIIIHEHHIEH@DCHEEHHIIIIIIIE?HHIIFHIEHFH?GHDHEGHHIIHHIIIEHHHHG?HGHHHIIIEHHHH MD:Z:98 PG:Z:MarkDuplicates RG:Z:JY333 NM:i:0AS:i:98 XS:i:93

VCF File

chr22 16056126 . G A 198.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.519;DP=23;Dels=0.00;FS=1.848;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=32.97;MQ0=3;MQRankSum=-0.228;QD=8.64;ReadPosRankSum=-0.076;SOR=0.605;VQSLOD=1.97;culprit=FS GT:AD:DP:GQ:PL 0/1:13,10:23:99:227,0,219

Hello, I am running Hapcut and got empty fragment file. when I checked the log file, there are so many lines
"processed XXXXXX reads, useful fragments 0"
I tried running with test data and I do get output.
Can you please help.
Is there specific format for vcd file or output of mpielup will work.

Thanks and regards

Sandip

Hi,
I am finding several problem while trying to compile. firstly,

$ uname -a
Linux jimi.biocomputing.cl 3.10.0-123.20.1.el7.x86_64 #1 SMP Thu Jan 29 18:05:33 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux

Then, I got two error because the Makefile expect a folder hapcut-fosmid/with the files print_clusters.c and fosmidbam_hairs.c in it.

$ make hairs
gcc -D_GNU_SOURCE -Isamtools -g -O2 bamread.o hapfragments.o hashtable.o readfasta.o readvariant.o -o extractHAIRS extracthairs.c  -Lsamtools -lbam -lm -lz
extracthairs.c:50:92: error fatal: hapcut-fosmid/fosmidbam_hairs.c: Demasiados niveles de enlaces simbólicos
 #include "hapcut-fosmid/fosmidbam_hairs.c" // code for parsing fosmid pooled sequence data 
                                                                                            ^
compilación terminada.
make: *** [hairs] Error 1

and

$ make hairs
gcc -D_GNU_SOURCE -Isamtools -g -O2 bamread.o hapfragments.o hashtable.o readfasta.o readvariant.o -o extractHAIRS extracthairs.c  -Lsamtools -lbam -lm -lz
In file included from extracthairs.c:50:0:
hapcut-fosmid/fosmidbam_hairs.c:49:28: error fatal: print_clusters.c: No existe el fichero o el directorio
 #include "print_clusters.c"
                            ^
compilación terminada.
make: *** [hairs] Error 1

I created the folder and copied the files inside, then I got this error

$ make hairs
gcc -D_GNU_SOURCE -Isamtools -c bamread.c
gcc -D_GNU_SOURCE -c hashtable.c
gcc -D_GNU_SOURCE -c readvariant.c 
gcc -D_GNU_SOURCE -c readfasta.c
gcc -D_GNU_SOURCE -Isamtools -g -O2 bamread.o hapfragments.o hashtable.o readfasta.o readvariant.o -o extractHAIRS extracthairs.c  -Lsamtools -lbam -lm -lz
extracthairs.c: En la función ‘main’:
extracthairs.c:245:44: error: ‘PRIOR’ no se declaró aquí (primer uso en esta función)
   else if (strcmp(argv[i],"--prior") == 0) PRIOR = atoi(argv[i+1]); 
                                            ^
extracthairs.c:245:44: nota: cada identificador sin declarar se reporta sólo una vez para cada función en el que aparece
extracthairs.c:246:86: error: ‘COMPARE_PHASE’ no se declaró aquí (primer uso en esta función)
   else if (strcmp(argv[i],"--comparephase") == 0 || strcmp(argv[i],"--compare") ==0) COMPARE_PHASE = atoi(argv[i+1]); 
                                                                                      ^
make: *** [hairs] Error 1

I look forwards to using the software so any help will be much appreciated!

thanks in advance,