FrostFlow13
commented
1 year ago I'd like to second this - I just tried to install Hairsplitter today as well (I've been struggling to find a program that can accurately split the haplotypes of a collapsed diploid genome, and the description of Hairsplitter sounded perfect for our needs), and I also had the same error (I believe, at least):
[ 48%] Building CXX object CMakeFiles/filter_variants.dir/filter_variants.cpp.o
/users/PAS1802/woodruff207/Hairsplitter/src/filter_variants.cpp:12:10: fatal error: clipp.h: No such file or directory
12 | #include "clipp.h" //library to build command line interfaces
| ^~~~~~~~~
compilation terminated.
make[2]: *** [CMakeFiles/filter_variants.dir/filter_variants.cpp.o] Error 1
make[1]: *** [CMakeFiles/filter_variants.dir/all] Error 2
make: *** [all] Error 2Again, I'm very excited to try out Hairsplitter, it just seems like there's one file missing (clipp.h), maybe?
EDIT1
I found clipp.h from another branch of Hairsplitter and incorporated it - that seems to have bypassed the issue with running "make". However, I have now hit a new issue:
sh: /users/PAS1802/woodruff207/Hairsplitter/src/build/fa2gfa: No such file or directory
/users/PAS1802/woodruff207/Hairsplitter/hairsplitter.py -f ../1_demul_adtrim/BC15.fastq -i 1376-haploid.fasta -x ont -o ../8_hairsplitter -t 28
HairSplitter v1.3.1 (github.com/RolandFaure/HairSplitter). Last update: 2023-08-10
******************
* *
* Hairsplitter *
* Welcome! *
* *
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ERROR: Conversion from fasta to gfa failed while running the command:
/users/PAS1802/woodruff207/Hairsplitter/src/build/fa2gfa 1376-haploid.fasta > ../8_hairsplitter/tmp/assembly.gfaIt seems like there's no "build" directory in the /src/ directory, which I've confirmed by poking around the directories (it also appears that it might be also missing from GitHub itself?).
EDIT2
I got it a bit farther once again! This time, I made a new build directory inside /src/, ran "cmake .. -DCMAKE[...]", then ran "make" inside the build directory and it appeared to build it just fine. However, it now appears to error out on stage 5 from what I can tell:
- Loading all reads from ../1_demul_adtrim/BC15.fastq in memory
- Loading all contigs from ../8_hairsplitter/tmp/cleaned_assembly.gfa in memory
- Loading alignments of the reads on the contigs from ../8_hairsplitter/tmp/reads_on_asm.sam
- Calling variants on each contig using basic pileup
terminate called after throwing an instance of 'std::invalid_argument'
what(): stoi
/users/PAS1802/woodruff207/Hairsplitter/hairsplitter.py -f ../1_demul_adtrim/BC15.fastq -i 1376-haploid.fasta -x ont -o ../8_hairsplitter -t 28
HairSplitter v1.3.1 (github.com/RolandFaure/HairSplitter). Last update: 2023-08-10
******************
* *
* Hairsplitter *
* Welcome! *
* *
******************
===== STAGE 1: Cleaning graph of small contigs that are unconnected parts of haplotypes [ 2023-08-10 15:35:08.559528 ]
When the assemblers manage to locally phase the haplotypes, they sometimes assemble the alternative haplotype as a separate contig, unconnected in the gfa graph. This affects negatively the performance of Hairsplitter. Let's delete these contigs
- Mapping the assembly against itself
Running: /users/PAS1802/woodruff207/Hairsplitter/src/build/clean_graph ../8_hairsplitter/tmp/assembly.gfa ../8_hairsplitter/tmp/cleaned_assembly.gfa ../8_hairsplitter ../8_hairsplitter/hairsplitter.log 28 minimap2
- Eliminated small unconnected contigs that align on other contigs
===== STAGE 2: Aligning reads on the reference [ 2023-08-10 15:35:10.486125 ]
- Converting the assembly in fasta format
- Aligning the reads on the assembly
- Running minimap with command line:
minimap2 ../8_hairsplitter/tmp/cleaned_assembly.fasta ../1_demul_adtrim/BC15.fastq -x map-ont -a --secondary=no -t 28 > ../8_hairsplitter/tmp/reads_on_asm.sam 2> ../8_hairsplitter/tmp/logminimap.txt
The log of minimap2 can be found at ../8_hairsplitter/tmp/logminimap.txt
===== STAGE 3: Calling variants [ 2023-08-10 15:38:05.211768 ]
Running: /users/PAS1802/woodruff207/Hairsplitter/src/build/call_variants ../8_hairsplitter/tmp/cleaned_assembly.gfa ../1_demul_adtrim/BC15.fastq ../8_hairsplitter/tmp/reads_on_asm.sam 28 ../8_hairsplitter/tmp ../8_hairsplitter/tmp/error_rate.txt 0 ../8_hairsplitter/tmp/variants.col ../8_hairsplitter/tmp/variants.vcf
===== STAGE 4: Filtering variants [ 2023-08-10 15:59:38.048162 ]
- Filtering variants
Running: /users/PAS1802/woodruff207/Hairsplitter/src/build/filter_variants ../8_hairsplitter/tmp/variants.col 0.0154948 28 0 ../8_hairsplitter/tmp/filtered_variants.col ../8_hairsplitter/tmp/variants.vcf ../8_hairsplitter/tmp/variants_filtered.vcf
===== STAGE 5: Separating reads by haplotype of origin [ 2023-08-10 16:34:13.356621 ]
- Separating reads by haplotype of origin
Running: /users/PAS1802/woodruff207/Hairsplitter/src/build/separate_reads ../8_hairsplitter/tmp/filtered_variants.col 28 0.0154948 0 ../8_hairsplitter/tmp/reads_haplo.gro
ERROR: separate_reads failed. Was trying to run: /users/PAS1802/woodruff207/Hairsplitter/src/build/separate_reads ../8_hairsplitter/tmp/filtered_variants.col 28 0.0154948 0 ../8_hairsplitter/tmp/reads_haplo.groI'm not entirely sure why it threw and error this time - digging more into that. It looks like the important part is:
terminate called after throwing an instance of 'std::invalid_argument'
what(): stoior
===== STAGE 5: Separating reads by haplotype of origin [ 2023-08-10 16:34:13.356621 ]
- Separating reads by haplotype of origin
Running: /users/PAS1802/woodruff207/Hairsplitter/src/build/separate_reads ../8_hairsplitter/tmp/filtered_variants.col 28 0.0154948 0 ../8_hairsplitter/tmp/reads_haplo.gro
ERROR: separate_reads failed. Was trying to run: /users/PAS1802/woodruff207/Hairsplitter/src/build/separate_reads ../8_hairsplitter/tmp/filtered_variants.col 28 0.0154948 0 ../8_hairsplitter/tmp/reads_haplo.grobut I'm not sure how to go about solving this issue. Inside the file "separate_reads.cpp", lines 86 and 115 mention "std::stoi", but I don't personally know enough about that type of code to tell what might be happening.
Just in case it's important, here are all of the file names and sizes inside my output directory:
file dependancies_log.txt 0 Bytes 8/10/2023 3:35:06 PM
file assembly.fa 13.9 MB 8/10/2023 3:35:08 PM
file trash.txt 246 Bytes 8/10/2023 3:35:08 PM
file assembly.gfa 13.9 MB 8/10/2023 3:35:08 PM
file minimap2.log 707 Bytes 8/10/2023 3:35:10 PM
file assembly_against_itself.sam 13.9 MB 8/10/2023 3:35:10 PM
file cleaned_assembly.fasta 13.9 MB 8/10/2023 3:35:10 PM
file cleaned_assembly.gfa 13.9 MB 8/10/2023 3:35:10 PM
file reads_on_asm.sam 13.7 GB 8/10/2023 3:38:05 PM
file logminimap.txt 1.46 KB 8/10/2023 3:38:05 PM
file variants.col 98.4 GB 8/10/2023 3:59:31 PM
file variants.vcf 12.2 MB 8/10/2023 3:59:31 PM
file error_rate.txt 10 Bytes 8/10/2023 3:59:34 PM
file filtered_variants.col 53.1 GB 8/10/2023 4:34:12 PM
file variants_filtered.vcf 146 Bytes 8/10/2023 4:34:12 PM
file reads_haplo.gro 0 Bytes 8/10/2023 4:34:13 PM
RolandFaure
Hello,
I tried cloning and installing as described in the documentation but failed to install
Then I tried running cmake and make from the src/ subdirectory:
Indeed I tried to locate this file but could not:
Any help would be appreciated
Thanks Alex