detected truncated fragment file

[guijie2015]

Hello,
I'm interested in trying out your program --because I'm working on testing phasing programs. However, I'm having some trouble running SpecHap.When I running programs, I get
"[SpecHap 2021:12:23 10:16:52]phasing haplotype for chr1"
"[SpecHap 2021:12:23 10:16:55]detected truncated fragment file, the truncated line is: 2 chr1:14506-14812:CGCAGTAGCGGTGGGAGG 0 -1 -1 4 0 6 0 0."
I don`t know how to solve this problem.If you can answer my question, I will be very grateful for you.

[panguangze]

Hello, I'm interested in trying out your program --because I'm working on testing phasing programs. However, I'm having some trouble running SpecHap.When I running programs, I get "[SpecHap 2021:12:23 10:16:52]phasing haplotype for chr1" "[SpecHap 2021:12:23 10:16:55]detected truncated fragment file, the truncated line is: 2 chr1:14506-14812:CGCAGTAGCGGTGGGAGG 0 -1 -1 4 0 6 0 0." I don`t know how to solve this problem.If you can answer my question, I will be very grateful for you.

What sequencing protocol of your data? And would you please show your Extrachair and SpecHap running command ?

[guijie2015]

Hello, I'm interested in trying out your program --because I'm working on testing phasing programs. However, I'm having some trouble running SpecHap.When I running programs, I get "[SpecHap 2021:12:23 10:16:52]phasing haplotype for chr1" "[SpecHap 2021:12:23 10:16:55]detected truncated fragment file, the truncated line is: 2 chr1:14506-14812:CGCAGTAGCGGTGGGAGG 0 -1 -1 4 0 6 0 0." I don`t know how to solve this problem.If you can answer my question, I will be very grateful for you.

What sequencing protocol of your data? And would you please show your Extrachair and SpecHap running command ?

Linked-read.
ExtractHAIRs --bam NA12878.sorted.bam /
--vcf NA12878.diploid_sorted.vcf.gz /
--PEonly 1 /
--out NA12878_linked_sorted.lst --10x 1
SpecHap --frag NA12878_linked_sorted.lst /
--frag_stat NA12878_sorted.bed.gz /
--vcf NA12878.diploid_sorted.vcf.gz /
--out NA12878_SpecHap.vcf /
--tenx 1
~

[panguangze]

Have you sorted the fragment file like sort -n -k6 in.lst > sorted.lst, since the ExtractHAIRs won't sort the fragment file.

[guijie2015]

Have you sorted the fragment file like sort -n -k6 in.lst > sorted.lst, since the ExtractHAIRs won't sort the fragment file.

yes ，I have done it.
sort -n -k6 NA12878_linked_sorted.lst > NA12878_linked_sorted.lst

[panguangze]

Have you sorted the fragment file like sort -n -k6 in.lst > sorted.lst, since the ExtractHAIRs won't sort the fragment file.

yes ，I have done it. sort -n -k6 NA12878_linked_sorted.lst > NA12878_linked_sorted.lst

I have checked that the ExtractHair in this repository is not the latest version, please use this one, https://github.com/panguangze/extractHairs.git (compile with CMake and only libhts needed). We will fix this error as soon as possible.

[evolgenomics]

Could you include the commit hash for the htslib it depends on for the included extractHairs repo? I used recursive updates to pull in the submodules but can't compile extractHairs successfully.

[evolgenomics]

I managed to get myself a VM for a clean compile. I can confirm that the frag.file is very different in format indeed:
Special ExtractHAIRs:
1 VH00745:4:AAATJ2MHV:2:1207:20617:18720 2 A03C43B01D60-1 -1 44 0 C 60 0 0.000000 1 VH00745:4:AAATJ2MHV:1:2509:48074:55597 2 A61C88B01D22-1 -1 47 1 C 60 0 0.000000 1 VH00745:4:AAATJ2MHV:2:1303:57466:4029 2 A71C05B01D13-1 -1 133 0 C 57 0 0.000000 1 VH00745:4:AAATJ2MHV:1:1510:11112:46056 2 A30C04B01D21-1 -1 181 0 C 38 0 0.000000 1 VH00745:4:AAATJ2MHV:2:1205:17587:44807 2 A14C31B01D16-1 -1 226 0 C 35 0 0.000000 1 VH00745:4:AAATJ2MHV:1:2312:25503:49691 2 A33C81B01D54-1 -1 237 1 C 60 0 0.000000 1 VH00745:4:AAATJ2MHV:2:1308:15391:42308 2 A22C06B01D09-1 -1 246 1 C 51 0 0.000000 1 VH00745:4:AAATJ2MHV:2:2603:30388:55370 2 A08C30B01D27-1 -1 248 0 C 39 0 0.000000
vs. standard ExtractHAIRs:
1 VH00745:4:AAATJ2MHV:2:1310:47051:15691 2 A96C31B01D80-1 -1 9 0 C 1 VH00745:4:AAATJ2MHV:2:1207:20617:18720 2 A03C43B01D60-1 -1 44 0 C 1 VH00745:4:AAATJ2MHV:2:2404:73409:38863 2 A93C82B01D11-1 -1 46 0 C 1 VH00745:4:AAATJ2MHV:1:2509:48074:55597 2 A61C88B01D22-1 -1 47 0 C 1 VH00745:4:AAATJ2MHV:2:1303:57466:4029 2 A71C05B01D13-1 -1 133 1 C 1 VH00745:4:AAATJ2MHV:1:1510:11112:46056 2 A30C04B01D21-1 -1 181 0 ; 1 VH00745:4:AAATJ2MHV:2:1205:17587:44807 2 A14C31B01D16-1 -1 226 0 C 1 VH00745:4:AAATJ2MHV:1:2312:25503:49691 2 A33C81B01D54-1 -1 237 00 CC 1 VH00745:4:AAATJ2MHV:1:2409:40651:37689 2 A48C38B01D73-1 -1 239 1 @ 1 VH00745:4:AAATJ2MHV:2:1308:15391:42308 2 A22C06B01D09-1 -1 246 1 C

[panguangze]

Could you include the commit hash for the htslib it depends on for the included extractHairs repo? I used recursive updates to pull in the submodules but can't compile extractHairs successfully.
https://github.com/panguangze/extractHairs.git This repo can be built with htslib-1.5.1(tested on my computer)

[panguangze]

I managed to get myself a VM for a clean compile. I can confirm that the frag.file is very different in format indeed: Special ExtractHAIRs: 1 VH00745:4:AAATJ2MHV:2:1207:20617:18720 2 A03C43B01D60-1 -1 44 0 C 60 0 0.000000 1 VH00745:4:AAATJ2MHV:1:2509:48074:55597 2 A61C88B01D22-1 -1 47 1 C 60 0 0.000000 1 VH00745:4:AAATJ2MHV:2:1303:57466:4029 2 A71C05B01D13-1 -1 133 0 C 57 0 0.000000 1 VH00745:4:AAATJ2MHV:1:1510:11112:46056 2 A30C04B01D21-1 -1 181 0 C 38 0 0.000000 1 VH00745:4:AAATJ2MHV:2:1205:17587:44807 2 A14C31B01D16-1 -1 226 0 C 35 0 0.000000 1 VH00745:4:AAATJ2MHV:1:2312:25503:49691 2 A33C81B01D54-1 -1 237 1 C 60 0 0.000000 1 VH00745:4:AAATJ2MHV:2:1308:15391:42308 2 A22C06B01D09-1 -1 246 1 C 51 0 0.000000 1 VH00745:4:AAATJ2MHV:2:2603:30388:55370 2 A08C30B01D27-1 -1 248 0 C 39 0 0.000000 vs. standard ExtractHAIRs: 1 VH00745:4:AAATJ2MHV:2:1310:47051:15691 2 A96C31B01D80-1 -1 9 0 C 1 VH00745:4:AAATJ2MHV:2:1207:20617:18720 2 A03C43B01D60-1 -1 44 0 C 1 VH00745:4:AAATJ2MHV:2:2404:73409:38863 2 A93C82B01D11-1 -1 46 0 C 1 VH00745:4:AAATJ2MHV:1:2509:48074:55597 2 A61C88B01D22-1 -1 47 0 C 1 VH00745:4:AAATJ2MHV:2:1303:57466:4029 2 A71C05B01D13-1 -1 133 1 C 1 VH00745:4:AAATJ2MHV:1:1510:11112:46056 2 A30C04B01D21-1 -1 181 0 ; 1 VH00745:4:AAATJ2MHV:2:1205:17587:44807 2 A14C31B01D16-1 -1 226 0 C 1 VH00745:4:AAATJ2MHV:1:2312:25503:49691 2 A33C81B01D54-1 -1 237 00 CC 1 VH00745:4:AAATJ2MHV:1:2409:40651:37689 2 A48C38B01D73-1 -1 239 1 @ 1 VH00745:4:AAATJ2MHV:2:1308:15391:42308 2 A22C06B01D09-1 -1 246 1 C

Yes, We made some changes to the standard ExtractHair for the downstream SpecHap phasing.

[panguangze]

Could you include the commit hash for the htslib it depends on for the included extractHairs repo? I used recursive updates to pull in the submodules but can't compile extractHairs successfully.
https://github.com/panguangze/extractHairs.git This repo can be built with htslib-1.5.1(tested on my computer with linux OS). what is your operating system platform? Linux , Win or Mac?

[panguangze]

If still unavailable,please send me the build error

[evolgenomics]

I'm on an GNU Linux LTS 20.0.
BTW, I found that for me your commit hash refers to the release 1.6, but there's a function call: "bcf_hdf_format" that was needed after the release:

/usr/local/SpecHap/vcf_io.cpp:115:5: error: ‘bcf_hdr_format’ was not declared in this scope
     bcf_hdr_format(header, 0, &kstring);
     ^~~~~~~~~~~~~~
/usr/local/SpecHap/vcf_io.cpp:115:5: note: suggested alternative: ‘bcf_hrec_format’
     bcf_hdr_format(header, 0, &kstring);
     ^~~~~~~~~~~~~~
     bcf_hrec_format
.
.
.
CMakeFiles/SpecHap.dir/build.make:302: recipe for target 'CMakeFiles/SpecHap.dir/vcf_io.cpp.o' failed
make[2]: *** [CMakeFiles/SpecHap.dir/vcf_io.cpp.o] Error 1
CMakeFiles/Makefile2:104: recipe for target 'CMakeFiles/SpecHap.dir/all' failed
make[1]: *** [CMakeFiles/SpecHap.dir/all] Error 2
Makefile:129: recipe for target 'all' failed
make: *** [all] Error 2

You might want to update your README.md instruction with the htslib and samtools commits.

I resolved the issue with the htslib 1.9/samtools 1.9 releases (later releases introduced an API, which again breaks the build, I think).

I wasn't able to get it done in the local context. That's why in the example above I went on an VM running an Ubuntu 18.04.5 LTS (GNU/Linux 5.4.89 x86_64) kernel.