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pauline-ng / SIFT4G_Create_Genomic_DB

Create genomic databases with SIFT predictions. Input is an organism's genomic DNA (.fa) file and the gene annotation file (.gtf). Output will be a database that can be used with SIFT4G_Annotator.jar to annotate VCF files.
GNU General Public License v3.0
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problem for constructing the database of test data #46

Closed yinhongwei4079 closed 3 years ago

yinhongwei4079 commented 3 years ago

@pauline-ng Hi, we want to build database for pig. Firstly, we download the PROTEIN_DB from https://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref90/uniref90.fasta.gz, we run human_samll_test. But we can't get the database. here is the output of our progress

converting gene format to use-able input done converting gene format making single records file done making single records template making noncoding records file done making noncoding records make the fasta sequences done making the fasta sequences start siftsharp, getting the alignments /vol3/agis/likui_group/yinhongwei/software/miniconda/bin/sift4g -d /vol3/agis/likui_group/yinhongwei/pig/uniprot/uniref90.fasta -q ./test_files/homo_sapiens_small/all_prot.fasta --subst ./test_files/homo_sapiens_small/subst --out ./test_files/homo_sapiens_small/SIFT_predictions --sub-results

we check the dir of subst, it had results of transcipt and it show likes head ENST00000342101.subst M1V M1L M1L M1T M1K M1R M1I M1I M1I M1M when we checked the dir of SIFT_predictions, it was empty. i didn't know what is the problem and could you give us some guidlines ?

pauline-ng commented 3 years ago

Hi,

Can you tell me what's the output when you run this command directly?

/vol3/agis/likui_group/yinhongwei/software/miniconda/bin/sift4g -d /vol3/agis/likui_group/yinhongwei/pig/uniprot/uniref90.fasta -q ./test_files/homo_sapiens_small/all_prot.fasta --subst ./test_files/homo_sapiens_small/subst --out ./test_files/homo_sapiens_small/SIFT_predictions --sub-results

yinhongwei4079 commented 3 years ago

@pauline-ng we run this command directly, it shows /opt/gridview//pbs/dispatcher/mom_priv/jobs/6614448.admin.SC: line 2: 21876 Illegal instruction (core dumped) /vol3/agis/likui_group/yinhongwei/software/miniconda/bin/sift4g -d /vol3/agis/likui_group/yinhongwei/pig/uniprot/uniref90.fasta -q ./test_files/homo_sapiens_small/all_prot.fasta --subst ./test_files/homo_sapiens_small/subst --out ./test_files/homo_sapiens_small/SIFT_predictions --sub-results could you tell me what is the problem?

pauline-ng commented 3 years ago

@rvaser - can you help Yin Hong Wei with this "core dumped" message from sift4g?

rvaser commented 3 years ago

Hello, did you compile the sift4g code on the same machine you run it? What is your OS? Can you please run cat /proc/cpuinfo | grep "avx" and paste the output here? Illegal instruction could mean that the compiled SIMD instructions are not supported on your machine.

Best regards, Robert

yinhongwei4079 commented 3 years ago

@rvaser we install the sift4g with miniconda. we run the code of cat /proc/cpuinfo | grep "avx". here is its output . flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good xtopology nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm ida arat epb xsaveopt pln pts dts tpr_shadow vnmi flexpriority ept vpid fsgsbase smep erms

rvaser commented 3 years ago

Can you try and compile from source on your machine? Might be that the bioconda executable was compiled with AVX2 which is not supported on your machine. Run the following:

git clone --recursive https://github.com/rvaser/sift4g.git sift4g
cd sift4g
make
yinhongwei4079 commented 3 years ago

@rvaser @pauline-ng thanks