rvaser / sift4g Goto Github PK
View Code? Open in Web Editor NEWSorting Intolerant From Tolerant For Genomes
License: GNU General Public License v3.0
Sorting Intolerant From Tolerant For Genomes
License: GNU General Public License v3.0
Dear rvaser;
I just tried to run the test_file[homo_sapiens_small] for building SIFT_db. Everthing was right until the populating databases state. There were warnings as:
Use of uninitialized value $siftscore in numeric ge (>=) at check_genes.pl line 53, <DB_IN> chunk 601612175.
Use of uninitialized value $siftscore in string ne at check_genes.pl line 53, <DB_IN> chunk 601612175.
Use of uninitialized value in string ne at check_genes.pl line 56, <DB_IN> chunk 601612175.
Use of uninitialized value in string ne at check_genes.pl line 56, <DB_IN> chunk 601612175
And there were .SIFTpredictions/.aligned.fasta in SIFT_predictions, 21.gz/MT.gz in GRCh38.83.
Do these warnings influence the results?(The warning message is full of screen and "all done" does not appear.)
When I stopped this command, it showed
File "check_SIFTDB.py", line 301, in
process_chr_file (infile, DNA_base_change_syn_nonsyn_counts, DNA_base_change_aa_pred, all_nonsyn_changes, dbSNP_predictions, novel_predictions, ref_predictions, aa_change_pred)
File "check_SIFTDB.py", line 202, in process_chr_file
for line in siftdb_fp.readlines():
File "/usr/lib/python3.8/codecs.py", line 319, in decode
def decode(self, input, final=False):
KeyboardInterrupt
I installed sift4g and SIFT4G_Create_Genomic_DB on ubuntu 20.04 with following packages:
Perl -- 5.30.0
DBI -- 1.643
BioPerl -- 1.7.8
LWP -- 6.67
Switch -- 2.17
Python 3.8.10
Best regards.
Hi,
I'm not sure why I run the sift4g with this error.
"terminate called after throwing an instance of 'std::regex_error'
what(): regex_error"
Could you please tell me?
Best wishes,
Liu
Hi Robert,
I am attempting to create a SIFT database by using Pauline's SIFT4G_Create_Genomic_DB method. I am working with a genome assembly and annotation from RefSeq (fasta: GCF_008728515.1_Panubis1.0_genomic.fna.gz, annotation: GCF_008728515.1_Panubis1.0_genomic.gtf.gz, both available at https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/008/728/515/GCF_008728515.1_Panubis1.0). A failure is occurring during the SIFT4G alignment step:
start siftsharp, getting the alignments
~/programs/sift/sift4g/bin/sift4g -d ~/programs/sift/SIFT_databases/uniref90.fasta -q ~/programs/sift/SIFT_databases/GCF_008728515.1_Panubis1.0/all_prot.fasta --subst ~/programs/sift/SIFT_databases/GCF_008728515.1_Panubis1.0/subst --out ~/programs/sift/SIFT_databases/GCF_008728515.1_Panubis1.0/SIFT_predictions --sub-results
** Checking query data and substitutions files **
** Searching database for candidate sequences **
** Aligning queries with candidate sequences **
Alignment score and position are not consensus.72.50/100.00% **
The error looks to be the same as pauline-ng/SIFT4G_Create_Genomic_DB#15, and is perhaps the same bug that you raised an issue for here: mkorpar/swsharp#1.
Have you found a work-around for this problem? Is it possible, for instance, to alter the GTF file to remove the sequence(s) triggering this error?
Thanks,
Jacqueline
P.S. I have successfully run the test examples for both sift4g and SIFT4G_Create_Genomic_DB, verifying that everything is installed correctly and apparently functional.
Hello Robert,
I used the genome fasta file , protein fasta files and genome annotation file to build the databas.Despite some warning, the database was set up successfully.SIFT numeric scores columns 10-12 have many rows say "NA".CHECK_GENES.LOG file columns 2-4 value very low.Through SIFT predicted ,I fonded that 85675 missense mutations in 42554 genes ,only 15777 sites was identified as NONSYNONYMOUS , 4141 sites was identified as DELETERIOUS and 1160 sites was identified as TOLERATED . I don't know the reason why many missense mutation sites can't be dentified.
And here is my file and command lines:
gene-annotation-src:
D.gtf.gz 6.27MB
D.pep.all.fa.gz 10.0MB
less -S D.gtf.gz
pseudo-chr0 EVM transcript 61149 61566 . - . transcript_id "D15542.t1"; gene_id "D15542"
pseudo-chr0 EVM exon 61149 61417 . - . transcript_id "D15542.t1"; gene_id "D15542";
pseudo-chr0 EVM exon 61485 61566 . - . transcript_id "D15542.t1"; gene_id "D15542";
pseudo-chr0 EVM CDS 61149 61417 . - 2 transcript_id "D15542.t1"; gene_id "D15542";
pseudo-chr0 EVM CDS 61485 61566 . - 0 transcript_id "D15542.t1"; gene_id "D15542";
less -S D.pep.all.fa.gz
protein|D19569.t1 ID=D19569.t1|Parent=D19569|Name=
MSGPGYMDHVFKANANSNSNPPCESKKMDPATKIGATSTTNTCPLPSPKIFANSELLTTSTEAAVTIPVNTKTSDAKSCQSVTNYGRVTGNSTRSDSLESSSAPLKPHTGGDVRWDAINSVCSKDSPLGLSHFRLLKRLGYGDIGSVYLVELRGTNTYFAMKVMDRGS
protein|D19568.t1 ID=D19568.t1|Parent=D19568|Name=
MLLQNWSFSGGLLSHSLLLHSRNPSNIISSALFPRRKAKAATTFLCLRLGIDEIAEIAHNKVLIAAVVSAAIGQLSKPFTSAILYGNKNNFDFRAAFQAGGFPSTHSSAVVATATSLGLERGFSDTIFGLAVVYAGLIMYDAQGVRREVGTHAKALNSVLLKNQLNSI
protein|D19566.t1 ID=D19566.t1|Parent=D19566|Name=
MVSPLLLQIPINTTSNGVTSAKANTNYPLPSPPVTSQSRELEEAEVEADDEVVGNGVLNQNVLSEDEYIRIFPRGIGPKPTEFKCEASRETPVVIMNHINLVEILMDLVEILMDVGSK*
chr-src:
reference.fa.gz 305MB
less -S reference.fa.gz
pseudo-chr0
TGGACTGACTGGACTGGGAAAATTTGTATTGTATTGGAGTATTGGATTGTTCTGGGAGTATTGACTTGTATTGTACATGTAAAGTATGAAAAGCTTGTAAAAGGACAAAACCTGGTCCCACATGGGGTGAAGTTTAAGTCGTCCTTTGAAAGATAGGATAGTCCTTAT.....
......
.....
.....
pseudo-chr9
TTATATATTAATATATAATAATAAATAATGAGAAATAAAATACCAAAAATACTATAATTACCTAGAACACCTAAAAATACCTAAACTTAATCAAAACTTATTTTTATGGATTTTTAAGGATTTTCTAAAGAGTAAAAACTAATTAACACTAAAAATACCAAAAAAATA....
....
scaffold808_size847463_ERROPOS700000
ATGATCTTCCAAAACTTGGAAAACCATCTTCAAGTGTTTGTGGACCATGTCAGCTAGGAAAGCAAATTAAGAGTCCTCACAAGAAGTCAAAATTCATTCACACCTCTCGTGTCTTAGAGTTGATTAATATGGATCTCATGGGTCCAATGAGAACAGAAAGCGTAGGGG.....
.....
Configuration File :
D.txt
GENETIC_CODE_TABLE=1
GENETIC_CODE_TABLENAME=Standard
MITO_GENETIC_CODE_TABLE=11
MITO_GENETIC_CODE_TABLENAME=Bacterial, Archaeal and Plant PlastidPARENT_DIR=/loc/d01/user009/D/third_build_sift
ORG=D
ORG_VERSION=D_v1
DBSNP_VCF_FILE=
#Running SIFT 4G
SIFT4G_PATH=/loc/d01/user009/software/sift4g/bin/sift4g
PROTEIN_DB=/loc/d01/user009/D/uniref90.fasta
COMPUTER=GIS-KATNISS
#Sub-directories, don't need to change
GENE_DOWNLOAD_DEST=gene-annotation-src
CHR_DOWNLOAD_DEST=chr-src
LOGFILE=Log.txt
ZLOGFILE=Log2.txt
FASTA_DIR=fasta
SUBST_DIR=subst
ALIGN_DIR=SIFT_alignments
SIFT_SCORE_DIR=SIFT_predictions
SINGLE_REC_BY_CHR_DIR=singleRecords
SINGLE_REC_WITH_SIFTSCORE_DIR=singleRecords_with_scores
VDBSNP_DIR=dbSNP
#Doesn't need to change
FASTA_LOG=fasta.log
INVALID_LOG=invalid.log
PEPTIDE_LOG=peptide.log
ENS_PATTERN=ENS
SINGLE_RECORD_PATTERN=:change:_aa1valid_dbsnp.singleRecord
perl make-SIFT-db-all.pl -config D.txt
sift4g -t 48 -d ./uniref90.fasta -q /loc/d01/user009/D/third_build_sift/all_prot.fasta --subst /loc/d01/user009/D/third_build_sift/su
bst --out/loc/d01/user009/D/third_build_sift/SIFT_predictions --sub-results
Use of uninitialized value $fasta_subseq in concatenation (.) or string at generate-fasta-subst-files-BIOPERL.pl line 446, <IN_TX> line 20913.
Argument "" isn't numeric in numeric eq (==) at generate-fasta-subst-files-BIOPERL.pl line 465, <IN_TX> line 21729.
Use of uninitialized value $mutated_aa in string eq at generate-fasta-subst-files-BIOPERL.pl line 894.
Use of uninitialized value $aa2 in string eq at generate-fasta-subst-files-BIOPERL.pl line 621.
Argument "" isn't numeric in addition (+) at generate-fasta-subst-files-BIOPERL.pl line 866.
Use of uninitialized value $coord in concatenation (.) or string at generate-fasta-subst-files-BIOPERL.pl line 918.
Use of uninitialized value $exon_num in concatenation (.) or string at generate-fasta-subst-files-BIOPERL.pl line 918.
....
** Selecting alignments with median threshold: 2.75 **
** Generating SIFT predictions with sequence identity: 100.00% **
CHECK_GENES.LOG file:
Chr Genes with SIFT Scores Pos with SIFT scores Pos with Confident Scores
pseudo-chr0 10 (227/2287) 14 (637725/4718761) 2(11664/637725)
pseudo-chr1 26 (1338/5214) 35 (4911882/13886195) 12(595766/4911882)
pseudo-chr10 24 (664/2724) 34 (2309132/6785718) 17(384198/2309132)
pseudo-chr11 24 (576/2441) 32 (1872042/5869154) 14(266614/1872042)
.....
My directory:
4.0K ./SIFT_alignments
3.8G ./SIFT_predictions
1.2G ./subst
83G ./singleRecords
220K ./singleRecords_with_scores
306M ./chr-src
4.0K ./dbSNP
37M ./gene-annotation-src
220M ./fasta
2.3G ./D_v1
4.0K ./tmp
91G .
I would be thankful for all the help.
Best regards,
Enter
Hello,
I got the following error when building a library using sift4g and sift4g can bring predictions. But still many errors in log file
`Use of uninitialized value $aa in string eq at make-single-records-BIOPERL.pl line 274.
Use of uninitialized value $aa in concatenation (.) or string at make-single-records-BIOPERL.pl line 280.
Use of uninitialized value $aa in string eq at make-single-records-BIOPERL.pl line 274.
Use of uninitialized value $aa in concatenation (.) or string at make-single-records-BIOPERL.pl line 280.
Use of uninitialized value $orig_aa in string eq at make-single-records-BIOPERL.pl line 551.
Use of uninitialized value $mutated_aa in string eq at make-single-records-BIOPERL.pl line 551.
Use of uninitialized value $orig_aa in string eq at make-single-records-BIOPERL.pl line 551.
Use of uninitialized value $mutated_aa in string eq at make-single-records-BIOPERL.pl line 551.
Use of uninitialized value $orig_aa in string eq at make-single-records-BIOPERL.pl line 551.
Use of uninitialized value $mutated_aa in string eq at make-single-records-BIOPERL.pl line 551.
Use of uninitialized value $orig_aa in string eq at make-single-records-BIOPERL.pl line 551.
Use of uninitialized value $mutated_aa in string eq at make-single-records-BIOPERL.pl line 551.
Use of uninitialized value in concatenation (.) or string at make-single-records-BIOPERL.pl line 305.
Use of uninitialized value in concatenation (.) or string at make-single-records-BIOPERL.pl line 305.
Use of uninitialized value in concatenation (.) or string at make-single-records-BIOPERL.pl line 305.
Use of uninitialized value in concatenation (.) or string at make-single-records-BIOPERL.pl line 305.
Use of uninitialized value in concatenation (.) or string at make-single-records-BIOPERL.pl line 305.
Use of uninitialized value in concatenation (.) or string at make-single-records-BIOPERL.pl line 305.
Use of uninitialized value in concatenation (.) or string at make-single-records-BIOPERL.pl line 305.
Use of uninitialized value in concatenation (.) or string at make-single-records-BIOPERL.pl line 305.
done making single records template
making noncoding records file
done making noncoding records
make the fasta sequences
Use of uninitialized value $mutated_aa in string eq at generate-fasta-subst-files-BIOPERL.pl line 894.
Use of uninitialized value $mutated_aa in string eq at generate-fasta-subst-files-BIOPERL.pl line 894.
Use of uninitialized value $mutated_aa in string eq at generate-fasta-subst-files-BIOPERL.pl line 894.
Use of uninitialized value $aa2 in string eq at generate-fasta-subst-files-BIOPERL.pl line 621.
Use of uninitialized value $aa2 in string eq at generate-fasta-subst-files-BIOPERL.pl line 621.
Use of uninitialized value $aa2 in string ne at generate-fasta-subst-files-BIOPERL.pl line 626.
Use of uninitialized value $aa2 in string eq at generate-fasta-subst-files-BIOPERL.pl line 621.
Use of uninitialized value $aa2 in string eq at generate-fasta-subst-files-BIOPERL.pl line 621.
Use of uninitialized value $aa2 in string ne at generate-fasta-subst-files-BIOPERL.pl line 626.
Use of uninitialized value $aa2 in string eq at generate-fasta-subst-files-BIOPERL.pl line 621.
Use of uninitialized value $aa2 in string eq at generate-fasta-subst-files-BIOPERL.pl line 621.
Use of uninitialized value $aa2 in string ne at generate-fasta-subst-files-BIOPERL.pl line 626.
done making the fasta sequences
start siftsharp, getting the alignments
/home/huangzr/sift4g/bin/sift4g -d /disk1/huangzr/nr/nr -q /vloume01/huangzr/database/sift/nr/hongyan/all_prot.fasta --subst /vloume01/huangzr/database/sift/nr/hongyan/subst --out /vloume01/huangzr/database/sift/nr/hongyan/SIFT_predictions --sub-results
** Checking query data and substitutions files **
Any suggestions?
Thanks,
rey
We are attempting to built a SIFT database (https://sift.bii.a-star.edu.sg/sift4g/SIFT4G_codes.html) using the sift4g algorithm on our Linux supercomputing cluster. However, we have hit the following difficult-to-parse error once it reaches what appears to be the sift4g portion of database building. Could you please advise us on the best way forward? Let us know what additional information you need.
done making the fasta sequences
start siftsharp, getting the alignments
/home/staff/chiroTester/tools/SIFT/sift4g/bin/sift4g -d /home/staff/chiroTester/ref_files/uniref90.fasta.gz -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
** Checking query data and substitutions files **
** Searching database for candidate sequences **
[ERROR:src/chain.c:70]: invalid chain data
Hi,
I have a question on test_data. When i compile the sift4g on my ubuntu and test on test_data.
the command "./bin/sift4g -q ./test_files/query.fasta --subst ./test_files/ -d ./test_files/sample_protein_database.fa" always showed
** Checking query data and substitutions files **
terminate called after throwing an instance of 'std::regex_error'
what(): regex_error
Aborted (core dumped)
But the command "./bin/sift4g -q ./test_files/query.fasta -d ./test_files/sample_protein_database.fa" seems work.
Could you help me?
I talked with @pauline-ng ,because I tried to build a database using SIFT4G_Create_Genomic_DB. The same error seems happend again.
Bests,
Nan
Hello,
I am trying to run sift4G with my own database. I have checked the chromosome names of the vcf matched the database. But no result at all. No error, either. Could you please give me any suggestions to fix it?
Below is an example of my VCF file.
1 103 . C T 45.17 PASS .
1 112 . C T 40.13 PASS .
1 405 . C T 209 PASS .
1 670 . G A 77 PASS .
This is what I got when I ran sift4G
Started Running .......
Running in Multitranscripts mode
Chromosome WithSIFT4GAnnotations WithoutSIFT4GAnnotations Progress
1 0 0 Completed : 1/1
Merging temp files....
SIFT4G Annotation completed !
Output directory:.
Hi, many thanks for developing such useful software.
I have a question about how to use sift4g properly, as usual, we can make a sift4G database and annotate my vcf file to know the deleterious mutation within genes. However, we think this method will introduce reference bias since it is based on reference calling vcf file.
So, in our case, we assembly 4 haplotype genomes for autotetraploid and make sift4G database for each haplotype genome, and then we mark deleterious mutation based on the file chr1_gz
in the directory of name_sift_database
with the command zcat chr/$i/${i}_sift_database/chr${chr}_${hap}.gz |grep 'ref' |awk '$11<0.05 {print}'
. Is it working for detecting deleterious mutation?
For another question, we have compared the deleterious mutation of synteny genes within 4 genomes using up method, we have 23086 synteny genes for 4 genomes.
4 genes with no deleterious mutation 9167
4 genes with only 1 gene has deleterious mutation 1172
4 genes with only 2 genes has deleterious mutation 1079
4 genes with only 3 genes has deleterious mutation 1565
4 genes with 4 genes have deleterious mutation 10103
You can see that the 4 genes with 4 genes have the deleterious mutation have a dominant proportion, to our knowledge, for autotetraploid, 4 genes with 1/2/3 genes have deleterious may have dominant proportion. Do you have any suggestions for us to compare the deleterious mutations within autotetraploid?
many thanks for your help
Hi, I'm working for identifying deleterious mutations using sift4g in model and non-model amphibian species.
To minimize computational time, I'd like to use GPU because of huge data size. However, GPU was not used even when we compile sift4g with 'make gpu'.
How can I utilize my GPU in sift4g?
I'm using nvidia GTX 1650 with cuda 11.5 and sift4g was compiled with 'make gpu' after deleting https://github.com/mkorpar/swsharp/blob/master/swsharp/Makefile#L28-L46 from vendor/swsharp.
Dear SIFT 4G team
I followed the instructions from "https://github.com/pauline-ng/SIFT4G_Create_Genomic_DB" to construct the database for a new organism. In my case, I am constructing the database for Cicer arietinum. I am getting the following error while running the script "make-SIFT-db-all.pl" using the following command:
Command:
perl make-SIFT-db-all.pl -config test_files/cicer_arietinum_config.txt
Log:
perl make-SIFT-db-all.pl -config test_files/cicer_arietinum_config.txt
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
cat: ./test_files/cicer_arietinum_genome/fasta/*.fasta: No such file or directory
/data/ngs/Programs_latest/SIFT4G_v2.0.0/bin/sift4g -d ./test_files/protein_db/uniref90.fasta -q ./test_files/cicer_arietinum_genome/all_prot.fasta --subst ./test_files/cicer_arietinum_genome/subst --out ./test_files/cicer_arietinum_genome/SIFT_predictions --sub-results
** Checking query data and substitutions files **
** EXITING! No valid queries to process. **
I also tried running the same script for the test human dataset provided with the package, but I am observing a different error:
Command:
perl make-SIFT-db-all.pl -config test_files/homo_sapiens-test.txt
Log:
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
/data/ngs/Programs_latest/SIFT4G_v2.0.0/bin/sift4g -d ./test_files/protein_db/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
** Checking query data and substitutions files **
terminate called after throwing an instance of 'std::regex_error'
what(): regex_error
My config file for the Cicer arietinum looks like:
GENETIC_CODE_TABLE=1
GENETIC_CODE_TABLENAME=Standard
MITO_GENETIC_CODE_TABLE=2
MITO_GENETIC_CODE_TABLENAME=Vertebrate Mitochondrial
PARENT_DIR=./test_files/cicer_arietinum_genome
ORG=cicer_arietinum
ORG_VERSION=v1.0
DBSNP_VCF_FILE=
#Running SIFT 4G
SIFT4G_PATH=/data/ngs/Programs_latest/SIFT4G_v2.0.0/bin/sift4g
PROTEIN_DB=./test_files/protein_db/uniref90.fasta
COMPUTER=mrna
GENE_DOWNLOAD_DEST=gene-annotation-src
CHR_DOWNLOAD_DEST=chr-src
LOGFILE=Log.txt
ZLOGFILE=Log2.txt
FASTA_DIR=fasta
SUBST_DIR=subst
ALIGN_DIR=SIFT_alignments
SIFT_SCORE_DIR=SIFT_predictions
SINGLE_REC_BY_CHR_DIR=singleRecords
SINGLE_REC_WITH_SIFTSCORE_DIR=singleRecords_with_scores
DBSNP_DIR=dbSNP
FASTA_LOG=fasta.log
INVALID_LOG=invalid.log
PEPTIDE_LOG=peptide.log
ENS_PATTERN=ENS
SINGLE_RECORD_PATTERN=:change:_aa1valid_dbsnp.singleRecord
I also pulled the latest sift-4g code and recompiled and run the above mentioned perl script to observe the same set of errors.
I need help to resolve this error and construction of the database for my organism.
It would be really appreciable if I can be guided to resolve the error mentioned.
I would be thankful for all the help.
Best regards
Aamir
Dear Robert,
I am unable to create SIFT4G database. Below is my SIFT4G command and screen output,
sift123@sift123-Precision-T5600:/mnt1/scripts_to_build_SIFT_db$ /mnt1/SIFT4G_2.0.0/bin/sift4g -d /mnt1/protein_db/uniprot90_Jul2016/uniref90.fasta -q /mnt1/SIFT_databases//goat/all_prot.fasta --subst /mnt1/SIFT_databases//goat/subst --out /mnt1/SIFT_databases//goat/SIFT_predictions --sub-results
** Checking query data and substitutions files **
** Searching database for candidate sequences **
Killedessing database part 1 (size ~0.25 GB): 97.50/100.00% *
The all_prot.fasta and subst.tar.gz files are attached for debugging purpose. Please let me know if you need any additional information.
Thank you,
-Nilesh
Hi,
I wonder if SIFT can predict synonymous deleterious? I found some novol mutation didn't affect the aa, but with SIFT score <0.05. I wonder how this happen? SIFT is an algorithm that predicts whether an amino acid substitution is deleterious to protein function.
Thanks very mich!
Hello Robert,
I've tried to compile the sift4g
code, and it seems to fail because swsharp headers are missing. Probably got lost somewhere along the way? ;)
[CP] src/sift_prediction.cpp
In file included from src/sift_prediction.cpp:16:
src/sift_scores.hpp:17:10: fatal error: swsharp/swsharp.h: No such file or directory
#include "swsharp/swsharp.h"
^~~~~~~~~~~~~~~~~~~
compilation terminated.
make: *** [Makefile:41: obj/sift_prediction.o] Error 1
>>> vendor/swsharp <<<
[CP] src/swimd/Swimd.cpp
src/swimd/Swimd.cpp:1:18: fatal error: cstdio: No such file or directory
#include <cstdio>
^
compilation terminated.
make[1]: *** [obj/swimd/Swimd.o] Error 1
make: *** [vendor/swsharp] Error 2
when i make sift4g , have this error.
I use git clone --recursive https://github.com/rvaser/sift4g.git sift4g
to download the sift4g.
my gcc and g++ version is V4.9.3 info like this:
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/share/softwares/sift4g/gcc/gcc/libexec/gcc/x86_64-unknown-linux-gnu/4.9.3/lto-wrapper
Target: x86_64-unknown-linux-gnu
Configured with: ./configure --prefix=/share/softwares/sift4g/gcc/gcc-4.9.3 --exec-prefix=/share/softwares/sift4g/gcc/gcc --with-mpfr=/share/softwares/sift4g/gcc/mpfr --with-gmp=/share/softwares/sift4g/gcc/gmp --with-mpc=/share/softwares/sift4g/gcc/mpc --disable-multilib
Thread model: posix
gcc version 4.9.3 (GCC)
Using built-in specs.
COLLECT_GCC=g++
COLLECT_LTO_WRAPPER=/share/softwares/sift4g/gcc/gcc/libexec/gcc/x86_64-unknown-linux-gnu/4.9.3/lto-wrapper
Target: x86_64-unknown-linux-gnu
Configured with: ./configure --prefix=/share/softwares/sift4g/gcc/gcc-4.9.3 --exec-prefix=/share/softwares/sift4g/gcc/gcc --with-mpfr=/share/softwares/sift4g/gcc/mpfr --with-gmp=/share/softwares/sift4g/gcc/gmp --with-mpc=/share/softwares/sift4g/gcc/mpc --disable-multilib
Thread model: posix
gcc version 4.9.3 (GCC)
my system is centos7
Dear Robert,
I met a weird problem when I use sift4g.
The program stuck up when I run a command like that
"home/sift4g/bin/sift4g -d PATH1/uniref90.fasta -q PATH2/all_prot.fasta --subst PATH3/subst --out PATH4/SIFT_predictions --sub-results -t 32
" , As a part of "make-SIFT-db" pipeline.
No CPU time was assigned to sift4g, when the program runs to the "Selecting alignments" sub-step. This state has lasted for almost two days.
The log file and program state are as follow.
pleas let me informed if there is any solution for this issue ,thanks for your time.
best wish
Huang Liang
Hi,rvaser,
Thank you for create a great software,i would like to use it to annotate animal genome. I use conda to install sift4g,when i run the sift4g in test_file,it can not generate anything, i do not know why . Following is issue i meet
I also want to do a datebase for my species,then run the make-SIFT-db-all.pl
But it always processing database part 975,can not go next,so what happened ?i want know,it is a big problem that i can not resolve.
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
/home/Wangpengfei/anaconda3/envs/sift4g/bin/sift4g -d /home/Wangpengfei/sift4g/SIFT4G_Create_Genomic_DB-master/nr -q /home/Wangpengfei/sift4g/SIFT4G_Create_Genomic_DB-master/test_files/bovine_ncbi/all_prot.fasta --subst /home/Wangpengfei/sift4g/SIFT4G_Create_Genomic_DB-master/test_files/bovine_ncbi/subst --out /home/Wangpengfei/sift4g/SIFT4G_Create_Genomic_DB
** Checking query data and substitutions files **
processing queries: 0.00/100.00% ^M processing queries: 0.01/100.00% ^M processing queries: 0.01/100.00% ^M processing queries: 0.01/100.00% ^M processing queries: 0.01/100.00% ^M processing queries: 0.02/100.00% ^M processing queries: 0.02/100.00% ^M processing queries: 0.02/100.00% ^M processing queries: 0.02/100.00% ^M processing querie..............................................................................** Searching database for candidate sequences **
processing database part 1 (size ~0.25 GB): 0.00/100.00% ^M processing database part 1 (size ~0.25 GB): 2.50/100.00%processing database part 975 (size ~0.25 GB): 92.50/100.00% ^M processing database part 975 (size ~0.25 GB): 95.00/100.00% ^M processing database part 975 (size ~0.25 GB): 97.50/100.00% ^M processing database part 975 (size ~0.25 GB): 100.00/100.00%
Dear Robert,
I apologize in advance if this is not a good place to ask these questions.
I was wondering which protein database is the most appropriate for annotation of missense variants in a bacterium? I've ran variant effect prediction on approx. 30k missense mutations in 4k genes. I've tried swissprot and uniref 90 as reference databases. The final stats are like this
Swissprot: 20574 DELETERIOUS 8453 TOLERATED
UniRef 90: 13215 DELETERIOUS 15810 TOLERATED
I am somewhat unsure what are the numbers in sift4g
output. Seems like they are a bit different from classical sift?
P95S DELETERIOUS 0.00 3.74 7 8
A85T DELETERIOUS 0.03 3.74 7 8
From what I understand, last 1 or 2 numbers is the number of reference sequences the prediction is based on. Is the number capped at 400, and how are 400 selected? I've also seen quite a few sequences that are predicted based on 1 sequence - is that OK?
Thank you!
Hi,
I have tried to use the SIFT4G to build my own SIFT database for many times, but it still was unsuccessful. can you help me to check it? The details as bellow:
** Searching database for candidate sequences **
** Aligning queries with candidate sequences **
** Selecting alignments with median threshold: 2.75 **
** Generating SIFT predictions with sequence identity: 100.00% **
done getting all the scores
populating databases
cat: /home/scripts_to_build_SIFT_db/test_files/singleRecords/Chr1.singleRecords: No such file or directory
can't open /home/scripts_to_build_SIFT_db/test_files/singleRecords/Chr1.singleRecords at map-scores-back-to-records.pl line 122.
Unable to read from /home/scripts_to_build_SIFT_db/test_files/singleRecords_with_scores/Chr1_scores.Srecords
cat: /home/scripts_to_build_SIFT_db/test_files/singleRecords/Chr1.singleRecords_noncoding.with_dbSNPid: No such file or directory
Traceback (most recent call last):
File "make_regions_file.py", line 68, in
get_regions (chrom_file, out_file)
File "make_regions_file.py", line 31, in get_regions
pos = get_pos (first_line)
File "make_regions_file.py", line 8, in get_pos
return int (fields[0])
ValueError: invalid literal for int() with base 10: ''
rm: cannot remove '/home/scripts_to_build_SIFT_db/test_files/singleRecords_with_scores/Chr1_scores.Srecords': No such file or directory
many thx.
Hi, I am facing an error when compiling this code on GPU (make gpu).
>>> vendor/swsharp <<<
[CORE] swsharp
[CU] src/evalue.cu
nvcc fatal : Unsupported gpu architecture 'compute_30'
Makefile:111: recipe for target 'obj/evalue.o' failed
make[2]: *** [obj/evalue.o] Error 1
Makefile:51: recipe for target 'swsharp' failed
make[1]: *** [swsharp] Error 2
Makefile:16: recipe for target 'vendor/swsharp' failed
make: *** [vendor/swsharp] Error 2
Could you please help me to fix this error? Thank you so much.
My system infor:
# nvcc -V
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2021 NVIDIA Corporation
Built on Sun_Feb_14_21:12:58_PST_2021
Cuda compilation tools, release 11.2, V11.2.152
Build cuda_11.2.r11.2/compiler.29618528_0
Hello,
I tried using the full path in the parent_dir but still it shows that it can't access the gene-annotation-src file. Can you please help me?
I have attached my config file,
Thanks,
Princy
peas_config.txt
Dear Robert
I met a error when I run sift4g test data .
"./bin/sift4g -q ./test_files/query.fasta --subst ./test_files/ -d ./test_files/sample_protein_database.fa"
** Checking query data and substitutions files **
terminate called after throwing an instance of 'std::regex_error'
what(): regex_error
Aborted (core dumped).
My gcc is gcc-7.3.0, which is gcc 4.9+. Do you know why?
when I construnct the database using "perl make-SIFT-db-all.pl -config test_files/candidatus_carsonella_ruddii_pv_config.txt --ensembl_download"
it says: Possible precedence issue with control flow operator at /usr/local/lib/perl5/site_perl/5.22.0/Bio/DB/IndexedBase.pm line 791.
done making single records template
making noncoding records file
start siftsharp, getting the alignments
/workdir/yw2326/have_check/SIFT/sift4g/bin/sift4g -d /workdir/yw2326/have_check/SIFT/PROTEIN_DB/uniref90.fasta -q /local/workdir/yw2326/have_check/SIFT/SIFT4G_Create_Genomic_DB/database_output/all_prot.fasta --subst /local/workdir/yw2326/have_check/SIFT/SIFT4G_Create_Genomic_DB/database_output/subst --out /local/workdir/yw2326/have_check/SIFT/SIFT4G_Create_Genomic_DB/database_output/SIFT_predictions --sub-results
** Checking query data and substitutions files **
terminate called after throwing an instance of 'std::regex_error'
what(): regex_error
Hello,
I am looking to use SIFT on some E coli genomes that I've aligned but I keep getting the error:
Chromosome WithSIFT4GAnnotations WithoutSIFT4GAnnotations Progress
ERROR! Input VCF file should contain at least 8 columns. See line:
Chromosome,70289,.,C,A,100,0,*,TYPE=SUBSTITUTE
This is even though my vcf file has 8 columns (I added in a dummy column so there are actually 9, 8 of the original vcf file) and follows the layout of the example vcf file in the supplementary of the nature protocols paper. I get this error when using either the GUI or running it in terminal.
Here's a head of my vcf file:
#CHROM,POS,ID,REF,ALT,QUAL,Y,FILTER,INFO
Chromosome,70289,.,C,A,100,0,,TYPE=SUBSTITUTE
Chromosome,366519,.,G,A,100,1,,TYPE=SUBSTITUTE
Chromosome,503429,.,C,T,100,2,,TYPE=SUBSTITUTE
Chromosome,705013,.,A,G,100,3,,TYPE=SUBSTITUTE
Chromosome,1633629,.,T,C,100,4,,TYPE=SUBSTITUTE
Chromosome,1633924,.,C,A,100,5,,TYPE=SUBSTITUTE
Chromosome,1652331,.,T,C,100,6,,TYPE=SUBSTITUTE
Chromosome,2173362,.,CCC,C,100,7,,TYPE=DELETE
Chromosome,2731078,.,C,A,100,8,*,TYPE=SUBSTITUTE
Thanks for your help!
When I use sift4g,some position(114,661/145,218) it predicted to be DELETERIOUS (*WARNING! Low confidence),Can we consider this position as deleterious ?
Why have this happened? Because SIFT4G_Create_Genomic_DB run the result?My CHECK_GENES.LOG Pos with Confident Scores are around 60% to 70%.
i use taurine reference genome ARS_UCD1.2 and uniref 90 to creat sift4g_genomic_DB, ORG be setting as bovine its right? my vcf file used to be predicted contain taurine and indicine ,but ARS_UCD1.2 reference genome is taurine ,and ORG seeting is bovine not taurine or indicine its problem? Do I need to consider the bias of the reference genome?
Hi Robert,
The output .SIFTprediction tables contain scores rounded to 2 decimal places and it would be useful for my work to have more precision. I only occasionally use C++ but as far as I can tell this rounding is done just before writing the output table (e.g. the print_double functions at line 303 of sift_scores.cpp) with no option to change it.
Is there an important reason to round like this? or would I be able to simply change the precision when writing the output table and get more detailed scores?
Thanks,
Ally
Hello,
I'm getting an error when trying to compile sift4g on a Mac running Catalina. Any ideas what could be going on? See below the result of 'gcc -v' and 'make' below that
Thanks!
jah1$ gcc -v
Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/c++/4.2.1
Apple clang version 12.0.0 (clang-1200.0.32.29)
Target: x86_64-apple-darwin19.6.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin
h80ad4bb7:sift4g jah1$ make
vendor/swsharp <<<
[CORE] swsharp
[CP] src/nw_find_score_gpu.cu
[CC] src/thread.c
[CC] src/constants.c
[CP] src/ov_end_data_gpu.cu
[CC] src/reconstruct.c
[CC] src/ssw/ssw.c
[CC] src/sse_module.c
[CC] src/database.c
[CC] src/post_proc.c
[CP] src/score_database_gpu.cu
[CP] src/score_database_gpu_short.cu
[CP] src/nw_linear_data_gpu.cu
[CC] src/align.c
[CC] src/utils.c
[CC] src/chain.c
[CP] src/hw_end_data_gpu.cu
[CC] src/threadpool.c
[CC] src/alignment.c
[CC] src/db_alignment.c
[CP] src/sw_end_data_gpu.cu
[CP] src/evalue.cu
[CP] src/score_database_gpu_long.cu
[CP] src/cuda_utils.cu
[CP] src/ov_find_score_gpu.cu
[CP] src/swimd/Swimd.cpp
[CC] src/pre_proc.c
[CC] src/scorer.c
[CP] src/gpu_module.cu
[CC] src/cpu_module.c
[AR] ../lib/libswsharp.a
[CP] ../include/swsharp/align.h
[CP] ../include/swsharp/alignment.h
[CP] ../include/swsharp/chain.h
[CP] ../include/swsharp/constants.h
[CP] ../include/swsharp/cpu_module.h
[CP] ../include/swsharp/cuda_utils.h
[CP] ../include/swsharp/database.h
[CP] ../include/swsharp/db_alignment.h
[CP] ../include/swsharp/evalue.h
[CP] ../include/swsharp/gpu_module.h
[CP] ../include/swsharp/post_proc.h
[CP] ../include/swsharp/pre_proc.h
[CP] ../include/swsharp/reconstruct.h
[CP] ../include/swsharp/scorer.h
[CP] ../include/swsharp/swsharp.h
[CP] ../include/swsharp/thread.h
[CP] ../include/swsharp/threadpool.h
[CP] ../swsharpwin/swsharp/chain.h
[CP] ../swsharpwin/swsharp/error.h
[CP] ../swsharpwin/swsharp/utils.h
[CP] ../swsharpwin/swsharp/score_database_gpu_short.h
[CP] ../swsharpwin/swsharp/ssw/ssw.h
[CP] ../swsharpwin/swsharp/align.h
[CP] ../swsharpwin/swsharp/score_database_gpu_long.h
[CP] ../swsharpwin/swsharp/db_alignment.h
[CP] ../swsharpwin/swsharp/threadpool.h
[CP] ../swsharpwin/swsharp/alignment.h
[CP] ../swsharpwin/swsharp/swsharp.h
[CP] ../swsharpwin/swsharp/cpu_module.h
[CP] ../swsharpwin/swsharp/scorer.h
[CP] ../swsharpwin/swsharp/pre_proc.h
[CP] ../swsharpwin/swsharp/reconstruct.h
[CP] ../swsharpwin/swsharp/constants.h
[CP] ../swsharpwin/swsharp/thread.h
[CP] ../swsharpwin/swsharp/database.h
[CP] ../swsharpwin/swsharp/sse_module.h
[CP] ../swsharpwin/swsharp/cuda_utils.h
[CP] ../swsharpwin/swsharp/swimd/Swimd.h
[CP] ../swsharpwin/swsharp/evalue.h
[CP] ../swsharpwin/swsharp/post_proc.h
[CP] ../swsharpwin/swsharp/gpu_module.h
[CP] ../swsharpwin/swsharp/nw_find_score_gpu.cu
[CP] ../swsharpwin/swsharp/thread.c
[CP] ../swsharpwin/swsharp/constants.c
[CP] ../swsharpwin/swsharp/ov_end_data_gpu.cu
[CP] ../swsharpwin/swsharp/reconstruct.c
[CP] ../swsharpwin/swsharp/ssw/ssw.c
[CP] ../swsharpwin/swsharp/sse_module.c
[CP] ../swsharpwin/swsharp/database.c
[CP] ../swsharpwin/swsharp/post_proc.c
[CP] ../swsharpwin/swsharp/score_database_gpu.cu
[CP] ../swsharpwin/swsharp/score_database_gpu_short.cu
[CP] ../swsharpwin/swsharp/nw_linear_data_gpu.cu
[CP] ../swsharpwin/swsharp/align.c
[CP] ../swsharpwin/swsharp/utils.c
[CP] ../swsharpwin/swsharp/chain.c
[CP] ../swsharpwin/swsharp/hw_end_data_gpu.cu
[CP] ../swsharpwin/swsharp/threadpool.c
[CP] ../swsharpwin/swsharp/alignment.c
[CP] ../swsharpwin/swsharp/db_alignment.c
[CP] ../swsharpwin/swsharp/sw_end_data_gpu.cu
[CP] ../swsharpwin/swsharp/evalue.cu
[CP] ../swsharpwin/swsharp/score_database_gpu_long.cu
[CP] ../swsharpwin/swsharp/cuda_utils.cu
[CP] ../swsharpwin/swsharp/ov_find_score_gpu.cu
[CP] ../swsharpwin/swsharp/swimd/Swimd.cpp
[CP] ../swsharpwin/swsharp/pre_proc.c
[CP] ../swsharpwin/swsharp/scorer.c
[CP] ../swsharpwin/swsharp/gpu_module.cu
[CP] ../swsharpwin/swsharp/cpu_module.c
[MOD] swsharpn
[CC] src/main.c
[LD] swsharpn
[CP] ../bin/swsharpn
[CP] ../swsharpwin/swsharpn/main.c
[MOD] swsharpp
[CC] src/main.c
[LD] swsharpp
[CP] ../bin/swsharpp
[CP] ../swsharpwin/swsharpp/main.c
[MOD] swsharpnc
[CC] src/main.c
[LD] swsharpnc
[CP] ../bin/swsharpnc
[CP] ../swsharpwin/swsharpnc/main.c
[MOD] swsharpdb
[CC] src/main.c
[LD] swsharpdb
[CP] ../bin/swsharpdb
[CP] ../swsharpwin/swsharpdb/main.c
[MOD] swsharpout
[CC] src/main.c
[LD] swsharpout
[CP] ../bin/swsharpout
[CP] ../swsharpwin/swsharpout/main.c
sift4g <<<
[CP] src/database_search.cpp
[CP] src/utils.cpp
[CP] src/sift_prediction.cpp
[CP] src/select_alignments.cpp
[CP] src/database_alignment.cpp
[CP] src/sift_scores.cpp
src/sift_scores.cpp:242:23: error: implicit instantiation of undefined template
'std::__1::basic_stringstream<char, std::__1::char_traits,
std::__1::allocator >'
std::stringstream stream;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/iosfwd:139:32: note:
template is declared here
class _LIBCPP_TEMPLATE_VIS basic_stringstream;
^
src/sift_scores.cpp:280:35: error: implicit instantiation of undefined template
'std::__1::basic_stringstream<char, std::__1::char_traits,
std::__1::allocator >'
std::stringstream ss(std::stringstream::in | std::stringstream::out);
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/iosfwd:139:32: note:
template is declared here
class _LIBCPP_TEMPLATE_VIS basic_stringstream;
^
src/sift_scores.cpp:280:59: error: implicit instantiation of undefined template
'std::__1::basic_stringstream<char, std::__1::char_traits,
std::__1::allocator >'
std::stringstream ss(std::stringstream::in | std::stringstream::out);
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/iosfwd:139:32: note:
template is declared here
class _LIBCPP_TEMPLATE_VIS basic_stringstream;
^
src/sift_scores.cpp:280:27: error: implicit instantiation of undefined template
'std::__1::basic_stringstream<char, std::__1::char_traits,
std::__1::allocator >'
std::stringstream ss(std::stringstream::in | std::stringstream::out);
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/iosfwd:139:32: note:
template is declared here
class _LIBCPP_TEMPLATE_VIS basic_stringstream;
^
4 errors generated.
make[1]: *** [obj/sift_scores.o] Error 1
make: *** [sift4g] Error 2
Hello,
I am continuing an issue here that began with this thread: pauline-ng/SIFT4G_Create_Genomic_DB#70
The current issue is that I run into a segmentation fault when running the sift4g command to generate SIFT_predictions.
This is the most recent output I get:
** Aligning queries with candidate sequences **
processing database part 1 (size ~1.00 GB): 0.00/100.00% *
processing database part 1 (size ~1.00 GB): 2.50/100.00% *
processing database part 1 (size ~1.00 GB): 5.00/100.00% *
processing database part 1 (size ~1.00 GB): 7.50/100.00% *
processing database part 1 (size ~1.00 GB): 10.00/100.00% *
processing database part 1 (size ~1.00 GB): 12.50/100.00% *
/cm/local/apps/slurm/var/spool/job391367/slurm_script: line 16: 18084 Segmentation fault sift4g -t 20 -q /home/npb0015/reinforcement_project/all_prot.fasta -d /home/npb0015/reinforcement_project/Reference_files/uniprot_sprot.fasta --subst /home/npb0015/reinforcement_project/subst --out /home/npb0015/reinforcement_project/SIFT_predictions/ --sub-results
This error comes from running the sift4g command given in the error, which is essentially the same as that suggested on October 16th in the original thread (I get the same error running that command exactly as is). Since a segmentation fault usually means an inability to access the memory required I've tried runs as high as 248GB RAM but still receive the same error, so I assume that is not the issue.
Here I will also provide a link to dropbox for the all_prot.fasta file that has been generated by earlier steps in the database creation.
https://www.dropbox.com/s/ggfgs7senvh3vaf/all_prot.fasta?dl=0
Hi @rvaser and @pauline-ng ,
I'm installing sift4g using the command 'make' as the readme file. And it success installed under gcc-4.8.5.
>>> sift4g <<<
[CP] src/database_alignment.cpp
[CP] src/database_search.cpp
[CP] src/hash.cpp
[CP] src/main.cpp
[CP] src/select_alignments.cpp
[CP] src/sift_prediction.cpp
[CP] src/sift_scores.cpp
[CP] src/utils.cpp
[LD] ../bin/sift4g
while running the test command, it failed with:
./bin/sift4g -q ./test_files/query.fasta --subst ./test_files/ -d ./test_files/sample_protein_database.fa
** Checking query data and substitutions files **
terminate called after throwing an instance of 'std::regex_error'
what(): regex_error
Aborted (core dumped)
According to the answer suggested in google, is about the gcc version(but the readme file suggest 4.8+). But I still try to use another gcc version , failed while running make
in gcc-5.4 or gcc-6.2 as below:
>>> sift4g <<<
[CP] src/database_alignment.cpp
[CP] src/database_search.cpp
src/database_search.cpp: In function ‘int32_t longestIncreasingSubsequence(const std::vector<int>&)’:
src/database_search.cpp:264:40: error: ‘floor’ was not declared in this scope
temp = floor((l + u) / 2.0f);
^
make[1]: *** [obj/database_search.o] Error 1
make: *** [sift4g] Error 2
Sincerely hope can get some advise about you. And thanks in advance.
Hi @rvaser,
I'm trying to make a SIFT database using @pauline-ng 's SIFT4G_Create_Genomic_DB (which requires sift4g). When I'm trying to install sift4g I'm getting a slew of error messages. Here is what I did to get the repository:
git clone --recursive https://github.com/rvaser/sift4g.git sift4g
cd sift4g/
make
I have GNU Make 4.1 and g++ (GCC) 4.9.3
Any ideas on what might be causing this issue and suggestions on how to fix it?
Thanks,
Randy
Here is the error message:
>>> vendor/swsharp <<< [CORE] swsharp [CP] src/swimd/Swimd.cpp /tmp/cclpPiBu.s: Assembler messages: /tmp/cclpPiBu.s:185: Error: suffix or operands invalid for
vbroadcastss'
/tmp/cclpPiBu.s:188: Error: suffix or operands invalid for vbroadcastss' /tmp/cclpPiBu.s:189: Error: suffix or operands invalid for
vpsubd'
/tmp/cclpPiBu.s:210: Error: suffix or operands invalid for vpsubd' /tmp/cclpPiBu.s:219: Error: suffix or operands invalid for
vpsubd'
/tmp/cclpPiBu.s:401: Error: suffix or operands invalid for vpand' /tmp/cclpPiBu.s:404: Error: suffix or operands invalid for
vpsubd'
/tmp/cclpPiBu.s:417: Error: suffix or operands invalid for vpsubd' /tmp/cclpPiBu.s:421: Error: suffix or operands invalid for
vpsubd'
/tmp/cclpPiBu.s:422: Error: suffix or operands invalid for vpsubd' /tmp/cclpPiBu.s:423: Error: suffix or operands invalid for
vpmaxsd'
/tmp/cclpPiBu.s:426: Error: suffix or operands invalid for vpsubd' /tmp/cclpPiBu.s:428: Error: suffix or operands invalid for
vpmaxsd'
/tmp/cclpPiBu.s:429: Error: suffix or operands invalid for vpaddd' /tmp/cclpPiBu.s:431: Error: suffix or operands invalid for
vpmaxsd'
/tmp/cclpPiBu.s:432: Error: suffix or operands invalid for vpmaxsd' /tmp/cclpPiBu.s:724: Error: suffix or operands invalid for
vpand'
/tmp/cclpPiBu.s:731: Error: suffix or operands invalid for vpand' /tmp/cclpPiBu.s:732: Error: suffix or operands invalid for
vpaddd'
/tmp/cclpPiBu.s:740: Error: suffix or operands invalid for vpand' /tmp/cclpPiBu.s:744: Error: suffix or operands invalid for
vpand'
/tmp/cclpPiBu.s:749: Error: suffix or operands invalid for vpsubd' /tmp/cclpPiBu.s:750: Error: suffix or operands invalid for
vpand'
/tmp/cclpPiBu.s:751: Error: suffix or operands invalid for vpaddd' /tmp/cclpPiBu.s:759: Error: suffix or operands invalid for
vpand'
/tmp/cclpPiBu.s:760: Error: suffix or operands invalid for vpand' /tmp/cclpPiBu.s:762: Error: suffix or operands invalid for
vpaddd'
/tmp/cclpPiBu.s:811: Error: suffix or operands invalid for vpsubd' /tmp/cclpPiBu.s:1012: Error: no such instruction:
vpbroadcastb %xmm7,%xmm7'
/tmp/cclpPiBu.s:1013: Error: no such instruction: vpbroadcastb %xmm5,%xmm5' /tmp/cclpPiBu.s:1015: Error: no such instruction:
vinserti128 $1,%xmm7,%ymm7,%ymm7'
/tmp/cclpPiBu.s:1017: Error: no such instruction: vinserti128 $1,%xmm5,%ymm5,%ymm5' /tmp/cclpPiBu.s:1105: Error: suffix or operands invalid for
vpsubsb'
/tmp/cclpPiBu.s:1109: Error: suffix or operands invalid for vpsubsb' /tmp/cclpPiBu.s:1110: Error: suffix or operands invalid for
vpsubsb'
/tmp/cclpPiBu.s:1112: Error: suffix or operands invalid for vpmaxub' /tmp/cclpPiBu.s:1113: Error: suffix or operands invalid for
vpsubsb'
/tmp/cclpPiBu.s:1114: Error: suffix or operands invalid for vpaddsb' /tmp/cclpPiBu.s:1115: Error: suffix or operands invalid for
vpmaxub'
/tmp/cclpPiBu.s:1118: Error: suffix or operands invalid for vpmaxub' /tmp/cclpPiBu.s:1119: Error: suffix or operands invalid for
vpmaxub'
/tmp/cclpPiBu.s:1120: Error: suffix or operands invalid for vpand' /tmp/cclpPiBu.s:1125: Error: suffix or operands invalid for
vpmaxub'
/tmp/cclpPiBu.s:1251: Error: suffix or operands invalid for vpaddsb' /tmp/cclpPiBu.s:1261: Error: suffix or operands invalid for
vpaddsb'
/tmp/cclpPiBu.s:1268: Error: suffix or operands invalid for vpaddsb' /tmp/cclpPiBu.s:1496: Error: no such instruction:
vpbroadcastb %xmm0,%xmm0'
/tmp/cclpPiBu.s:1497: Error: no such instruction: vinserti128 $1,%xmm0,%ymm0,%ymm0' /tmp/cclpPiBu.s:1580: Error: no such instruction:
vpbroadcastb %xmm9,%xmm9'
/tmp/cclpPiBu.s:1581: Error: no such instruction: vpbroadcastb %xmm4,%xmm4' /tmp/cclpPiBu.s:1582: Error: no such instruction:
vpbroadcastb %xmm5,%xmm5'
/tmp/cclpPiBu.s:1583: Error: no such instruction: vinserti128 $1,%xmm9,%ymm9,%ymm9' /tmp/cclpPiBu.s:1586: Error: no such instruction:
vinserti128 $1,%xmm4,%ymm4,%ymm4'
/tmp/cclpPiBu.s:1588: Error: no such instruction: vinserti128 $1,%xmm5,%ymm5,%ymm5' /tmp/cclpPiBu.s:1652: Error: no such instruction:
vpbroadcastb %xmm6,%xmm6'
/tmp/cclpPiBu.s:1653: Error: no such instruction: vinserti128 $1,%xmm6,%ymm6,%ymm6' /tmp/cclpPiBu.s:1670: Error: suffix or operands invalid for
vpsubsb'
/tmp/cclpPiBu.s:1674: Error: suffix or operands invalid for vpsubsb' /tmp/cclpPiBu.s:1675: Error: suffix or operands invalid for
vpsubsb'
/tmp/cclpPiBu.s:1676: Error: suffix or operands invalid for vpmaxsb' /tmp/cclpPiBu.s:1679: Error: suffix or operands invalid for
vpsubsb'
/tmp/cclpPiBu.s:1681: Error: suffix or operands invalid for vpmaxsb' /tmp/cclpPiBu.s:1682: Error: suffix or operands invalid for
vpaddsb'
/tmp/cclpPiBu.s:1684: Error: suffix or operands invalid for vpminsb' /tmp/cclpPiBu.s:1685: Error: suffix or operands invalid for
vpmaxsb'
/tmp/cclpPiBu.s:1686: Error: suffix or operands invalid for vpmaxsb' /tmp/cclpPiBu.s:1690: Error: suffix or operands invalid for
vpmaxsb'
/tmp/cclpPiBu.s:1695: Error: suffix or operands invalid for vpmaxsb' /tmp/cclpPiBu.s:1702: Error: suffix or operands invalid for
vpminsb'
/tmp/cclpPiBu.s:1707: Error: suffix or operands invalid for vpminsb' /tmp/cclpPiBu.s:1754: Error: suffix or operands invalid for
vpand'
/tmp/cclpPiBu.s:1761: Error: suffix or operands invalid for vpand' /tmp/cclpPiBu.s:1762: Error: suffix or operands invalid for
vpaddsb'
/tmp/cclpPiBu.s:1772: Error: suffix or operands invalid for vpand' /tmp/cclpPiBu.s:1778: Error: suffix or operands invalid for
vpand'
/tmp/cclpPiBu.s:1779: Error: suffix or operands invalid for vpand' /tmp/cclpPiBu.s:1781: Error: suffix or operands invalid for
vpaddsb'
/tmp/cclpPiBu.s:1902: Error: suffix or operands invalid for vpmaxsb' /tmp/cclpPiBu.s:2029: Error: suffix or operands invalid for
vpmaxsb'
/tmp/cclpPiBu.s:2166: Error: no such instruction: vpbroadcastb %xmm0,%xmm0' /tmp/cclpPiBu.s:2167: Error: no such instruction:
vinserti128 $1,%xmm0,%ymm0,%ymm0'
/tmp/cclpPiBu.s:2204: Error: no such instruction: vpbroadcastb %xmm5,%xmm5' /tmp/cclpPiBu.s:2205: Error: no such instruction:
vpbroadcastb %xmm6,%xmm6'
/tmp/cclpPiBu.s:2207: Error: no such instruction: vinserti128 $1,%xmm5,%ymm5,%ymm5' /tmp/cclpPiBu.s:2208: Error: no such instruction:
vinserti128 $1,%xmm6,%ymm6,%ymm6'
/tmp/cclpPiBu.s:2225: Error: suffix or operands invalid for vpsubsb' /tmp/cclpPiBu.s:2230: Error: suffix or operands invalid for
vpsubsb'
/tmp/cclpPiBu.s:2245: Error: no such instruction: vpbroadcastb %xmm4,%xmm4' /tmp/cclpPiBu.s:2246: Error: no such instruction:
vinserti128 $1,%xmm4,%ymm4,%ymm4'
/tmp/cclpPiBu.s:2309: Error: no such instruction: vpbroadcastb %xmm7,%xmm7' /tmp/cclpPiBu.s:2310: Error: no such instruction:
vinserti128 $1,%xmm7,%ymm7,%ymm7'
/tmp/cclpPiBu.s:2327: Error: suffix or operands invalid for vpsubsb' /tmp/cclpPiBu.s:2332: Error: suffix or operands invalid for
vpsubsb'
/tmp/cclpPiBu.s:2334: Error: suffix or operands invalid for vpsubsb' /tmp/cclpPiBu.s:2335: Error: suffix or operands invalid for
vpsubsb'
/tmp/cclpPiBu.s:2336: Error: suffix or operands invalid for vpmaxsb' /tmp/cclpPiBu.s:2337: Error: suffix or operands invalid for
vpmaxsb'
/tmp/cclpPiBu.s:2338: Error: suffix or operands invalid for vpaddsb' /tmp/cclpPiBu.s:2340: Error: suffix or operands invalid for
vpmaxsb'
/tmp/cclpPiBu.s:2342: Error: suffix or operands invalid for vpminsb' /tmp/cclpPiBu.s:2343: Error: suffix or operands invalid for
vpmaxsb'
/tmp/cclpPiBu.s:2347: Error: suffix or operands invalid for vpmaxsb' /tmp/cclpPiBu.s:2352: Error: suffix or operands invalid for
vpmaxsb'
/tmp/cclpPiBu.s:2358: Error: suffix or operands invalid for vpminsb' /tmp/cclpPiBu.s:2363: Error: suffix or operands invalid for
vpminsb'
/tmp/cclpPiBu.s:2410: Error: suffix or operands invalid for vpand' /tmp/cclpPiBu.s:2417: Error: suffix or operands invalid for
vpand'
/tmp/cclpPiBu.s:2418: Error: suffix or operands invalid for vpaddsb' /tmp/cclpPiBu.s:2425: Error: suffix or operands invalid for
vpand'
/tmp/cclpPiBu.s:2431: Error: suffix or operands invalid for vpand' /tmp/cclpPiBu.s:2436: Error: suffix or operands invalid for
vpsubsb'
/tmp/cclpPiBu.s:2437: Error: suffix or operands invalid for vpand' /tmp/cclpPiBu.s:2438: Error: suffix or operands invalid for
vpaddsb'
/tmp/cclpPiBu.s:2446: Error: suffix or operands invalid for vpand' /tmp/cclpPiBu.s:2447: Error: suffix or operands invalid for
vpand'
/tmp/cclpPiBu.s:2449: Error: suffix or operands invalid for vpaddsb' /tmp/cclpPiBu.s:2690: Error: suffix or operands invalid for
vpmaxsb'
/tmp/cclpPiBu.s:2700: Error: suffix or operands invalid for vpsubsb' /tmp/cclpPiBu.s:2825: Error: no such instruction:
vpbroadcastb %xmm0,%xmm0'
/tmp/cclpPiBu.s:2829: Error: no such instruction: vinserti128 $1,%xmm0,%ymm0,%ymm0' /tmp/cclpPiBu.s:2837: Error: no such instruction:
vpbroadcastb %xmm0,%xmm0'
/tmp/cclpPiBu.s:2838: Error: no such instruction: vinserti128 $1,%xmm0,%ymm0,%ymm0' /tmp/cclpPiBu.s:2875: Error: no such instruction:
vpbroadcastb %xmm6,%xmm6'
/tmp/cclpPiBu.s:2876: Error: no such instruction: vinserti128 $1,%xmm6,%ymm6,%ymm6' /tmp/cclpPiBu.s:2881: Error: no such instruction:
vpbroadcastb %xmm7,%xmm7'
/tmp/cclpPiBu.s:2883: Error: no such instruction: vinserti128 $1,%xmm7,%ymm7,%ymm7' /tmp/cclpPiBu.s:2897: Error: suffix or operands invalid for
vpsubsb'
/tmp/cclpPiBu.s:2902: Error: suffix or operands invalid for vpsubsb' /tmp/cclpPiBu.s:2911: Error: suffix or operands invalid for
vpsubsb'
/tmp/cclpPiBu.s:2996: Error: suffix or operands invalid for vpand' /tmp/cclpPiBu.s:2999: Error: suffix or operands invalid for
vpsubsb'
/tmp/cclpPiBu.s:3003: Error: no such instruction: vpbroadcastb %xmm3,%xmm3' /tmp/cclpPiBu.s:3004: Error: no such instruction:
vinserti128 $1,%xmm3,%ymm3,%ymm3'
/tmp/cclpPiBu.s:3020: Error: suffix or operands invalid for vpsubsb' /tmp/cclpPiBu.s:3024: Error: suffix or operands invalid for
vpsubsb'
/tmp/cclpPiBu.s:3025: Error: suffix or operands invalid for vpsubsb' /tmp/cclpPiBu.s:3027: Error: suffix or operands invalid for
vpmaxsb'
/tmp/cclpPiBu.s:3028: Error: suffix or operands invalid for vpsubsb' /tmp/cclpPiBu.s:3029: Error: suffix or operands invalid for
vpmaxsb'
/tmp/cclpPiBu.s:3030: Error: suffix or operands invalid for vpaddsb' /tmp/cclpPiBu.s:3033: Error: suffix or operands invalid for
vpminsb'
/tmp/cclpPiBu.s:3034: Error: suffix or operands invalid for vpmaxsb' /tmp/cclpPiBu.s:3035: Error: suffix or operands invalid for
vpmaxsb'
/tmp/cclpPiBu.s:3040: Error: suffix or operands invalid for vpmaxsb' /tmp/cclpPiBu.s:3049: Error: suffix or operands invalid for
vpminsb'
/tmp/cclpPiBu.s:3054: Error: suffix or operands invalid for vpminsb' /tmp/cclpPiBu.s:3342: Error: suffix or operands invalid for
vpand'
/tmp/cclpPiBu.s:3349: Error: suffix or operands invalid for vpand' /tmp/cclpPiBu.s:3350: Error: suffix or operands invalid for
vpaddsb'
/tmp/cclpPiBu.s:3357: Error: suffix or operands invalid for vpand' /tmp/cclpPiBu.s:3363: Error: suffix or operands invalid for
vpand'
/tmp/cclpPiBu.s:3368: Error: suffix or operands invalid for vpsubsb' /tmp/cclpPiBu.s:3369: Error: suffix or operands invalid for
vpand'
/tmp/cclpPiBu.s:3370: Error: suffix or operands invalid for vpaddsb' /tmp/cclpPiBu.s:3378: Error: suffix or operands invalid for
vpand'
/tmp/cclpPiBu.s:3379: Error: suffix or operands invalid for vpand' /tmp/cclpPiBu.s:3381: Error: suffix or operands invalid for
vpaddsb'
/tmp/cclpPiBu.s:3404: Error: suffix or operands invalid for vpsubsb' /tmp/cclpPiBu.s:3574: Error: no such instruction:
vpbroadcastw %xmm9,%xmm9'
/tmp/cclpPiBu.s:3575: Error: no such instruction: vpbroadcastw %xmm6,%xmm6' /tmp/cclpPiBu.s:3579: Error: no such instruction:
vinserti128 $1,%xmm9,%ymm9,%ymm9'
/tmp/cclpPiBu.s:3580: Error: no such instruction: vinserti128 $1,%xmm6,%ymm6,%ymm6' /tmp/cclpPiBu.s:3846: Error: suffix or operands invalid for
vpsubsw'
/tmp/cclpPiBu.s:3847: Error: suffix or operands invalid for vpsubsw' /tmp/cclpPiBu.s:3850: Error: suffix or operands invalid for
vpmaxsw'
/tmp/cclpPiBu.s:3853: Error: suffix or operands invalid for vpsubsw' /tmp/cclpPiBu.s:3854: Error: suffix or operands invalid for
vpsubsw'
/tmp/cclpPiBu.s:3856: Error: suffix or operands invalid for vpmaxsw' /tmp/cclpPiBu.s:3857: Error: suffix or operands invalid for
vpaddsw'
/tmp/cclpPiBu.s:3858: Error: suffix or operands invalid for vpmaxsw' /tmp/cclpPiBu.s:3860: Error: suffix or operands invalid for
vpmaxsw'
/tmp/cclpPiBu.s:3861: Error: suffix or operands invalid for vpmaxsw' /tmp/cclpPiBu.s:3866: Error: suffix or operands invalid for
vpmaxsw'
/tmp/cclpPiBu.s:4227: Error: suffix or operands invalid for vpand' /tmp/cclpPiBu.s:4237: Error: suffix or operands invalid for
vpand'
/tmp/cclpPiBu.s:4244: Error: suffix or operands invalid for vpand' /tmp/cclpPiBu.s:4510: Error: no such instruction:
vpbroadcastw %xmm9,%xmm9'
/tmp/cclpPiBu.s:4513: Error: no such instruction: vinserti128 $1,%xmm9,%ymm9,%ymm9' /tmp/cclpPiBu.s:4518: Error: no such instruction:
vpbroadcastw %xmm0,%xmm0'
/tmp/cclpPiBu.s:4519: Error: no such instruction: vinserti128 $1,%xmm0,%ymm0,%ymm0' /tmp/cclpPiBu.s:4559: Error: no such instruction:
vpbroadcastw %xmm4,%xmm4'
/tmp/cclpPiBu.s:4560: Error: no such instruction: vpbroadcastw %xmm5,%xmm5' /tmp/cclpPiBu.s:4563: Error: no such instruction:
vinserti128 $1,%xmm4,%ymm4,%ymm4'
/tmp/cclpPiBu.s:4564: Error: no such instruction: vinserti128 $1,%xmm5,%ymm5,%ymm5' /tmp/cclpPiBu.s:4838: Error: no such instruction:
vpbroadcastw %xmm6,%xmm6'
/tmp/cclpPiBu.s:4839: Error: no such instruction: vinserti128 $1,%xmm6,%ymm6,%ymm6' /tmp/cclpPiBu.s:4854: Error: suffix or operands invalid for
vpsubsw'
/tmp/cclpPiBu.s:4858: Error: suffix or operands invalid for vpsubsw' /tmp/cclpPiBu.s:4859: Error: suffix or operands invalid for
vpsubsw'
/tmp/cclpPiBu.s:4860: Error: suffix or operands invalid for vpmaxsw' /tmp/cclpPiBu.s:4863: Error: suffix or operands invalid for
vpsubsw'
/tmp/cclpPiBu.s:4865: Error: suffix or operands invalid for vpmaxsw' /tmp/cclpPiBu.s:4866: Error: suffix or operands invalid for
vpaddsw'
/tmp/cclpPiBu.s:4868: Error: suffix or operands invalid for vpminsw' /tmp/cclpPiBu.s:4869: Error: suffix or operands invalid for
vpmaxsw'
/tmp/cclpPiBu.s:4870: Error: suffix or operands invalid for vpmaxsw' /tmp/cclpPiBu.s:4874: Error: suffix or operands invalid for
vpmaxsw'
/tmp/cclpPiBu.s:4879: Error: suffix or operands invalid for vpmaxsw' /tmp/cclpPiBu.s:4885: Error: suffix or operands invalid for
vpminsw'
/tmp/cclpPiBu.s:4890: Error: suffix or operands invalid for vpminsw' /tmp/cclpPiBu.s:5136: Error: suffix or operands invalid for
vpmaxsw'
/tmp/cclpPiBu.s:5359: Error: suffix or operands invalid for vpand' /tmp/cclpPiBu.s:5366: Error: suffix or operands invalid for
vpand'
/tmp/cclpPiBu.s:5367: Error: suffix or operands invalid for vpaddsw' /tmp/cclpPiBu.s:5377: Error: suffix or operands invalid for
vpand'
/tmp/cclpPiBu.s:5383: Error: suffix or operands invalid for vpand' /tmp/cclpPiBu.s:5384: Error: suffix or operands invalid for
vpand'
/tmp/cclpPiBu.s:5386: Error: suffix or operands invalid for vpaddsw' /tmp/cclpPiBu.s:5396: Error: suffix or operands invalid for
vpmaxsw'
/tmp/cclpPiBu.s:5528: Error: no such instruction: vpbroadcastw %xmm4,%xmm4' /tmp/cclpPiBu.s:5531: Error: no such instruction:
vinserti128 $1,%xmm4,%ymm4,%ymm4'
/tmp/cclpPiBu.s:5536: Error: no such instruction: vpbroadcastw %xmm0,%xmm0' /tmp/cclpPiBu.s:5537: Error: no such instruction:
vinserti128 $1,%xmm0,%ymm0,%ymm0'
/tmp/cclpPiBu.s:5577: Error: no such instruction: vpbroadcastw %xmm6,%xmm6' /tmp/cclpPiBu.s:5578: Error: no such instruction:
vpbroadcastw %xmm5,%xmm5'
/tmp/cclpPiBu.s:5580: Error: no such instruction: vinserti128 $1,%xmm6,%ymm6,%ymm6' /tmp/cclpPiBu.s:5581: Error: no such instruction:
vinserti128 $1,%xmm5,%ymm5,%ymm5'
/tmp/cclpPiBu.s:5602: Error: suffix or operands invalid for vpsubsw' /tmp/cclpPiBu.s:5609: Error: suffix or operands invalid for
vpsubsw'
/tmp/cclpPiBu.s:5839: Error: no such instruction: vpbroadcastw %xmm7,%xmm7' /tmp/cclpPiBu.s:5840: Error: no such instruction:
vinserti128 $1,%xmm7,%ymm7,%ymm7'
/tmp/cclpPiBu.s:5855: Error: suffix or operands invalid for vpsubsw' /tmp/cclpPiBu.s:5860: Error: suffix or operands invalid for
vpsubsw'
/tmp/cclpPiBu.s:5862: Error: suffix or operands invalid for vpsubsw' /tmp/cclpPiBu.s:5863: Error: suffix or operands invalid for
vpsubsw'
/tmp/cclpPiBu.s:5864: Error: suffix or operands invalid for vpmaxsw' /tmp/cclpPiBu.s:5865: Error: suffix or operands invalid for
vpmaxsw'
/tmp/cclpPiBu.s:5866: Error: suffix or operands invalid for vpaddsw' /tmp/cclpPiBu.s:5868: Error: suffix or operands invalid for
vpmaxsw'
/tmp/cclpPiBu.s:5870: Error: suffix or operands invalid for vpminsw' /tmp/cclpPiBu.s:5871: Error: suffix or operands invalid for
vpmaxsw'
/tmp/cclpPiBu.s:5875: Error: suffix or operands invalid for vpmaxsw' /tmp/cclpPiBu.s:5880: Error: suffix or operands invalid for
vpmaxsw'
/tmp/cclpPiBu.s:5885: Error: suffix or operands invalid for vpminsw' /tmp/cclpPiBu.s:5890: Error: suffix or operands invalid for
vpminsw'
/tmp/cclpPiBu.s:6358: Error: suffix or operands invalid for vpand' /tmp/cclpPiBu.s:6365: Error: suffix or operands invalid for
vpand'
/tmp/cclpPiBu.s:6366: Error: suffix or operands invalid for vpaddsw' /tmp/cclpPiBu.s:6374: Error: suffix or operands invalid for
vpand'
/tmp/cclpPiBu.s:6378: Error: suffix or operands invalid for vpand' /tmp/cclpPiBu.s:6383: Error: suffix or operands invalid for
vpsubsw'
/tmp/cclpPiBu.s:6384: Error: suffix or operands invalid for vpand' /tmp/cclpPiBu.s:6385: Error: suffix or operands invalid for
vpaddsw'
/tmp/cclpPiBu.s:6393: Error: suffix or operands invalid for vpand' /tmp/cclpPiBu.s:6394: Error: suffix or operands invalid for
vpand'
/tmp/cclpPiBu.s:6396: Error: suffix or operands invalid for vpaddsw' /tmp/cclpPiBu.s:6406: Error: suffix or operands invalid for
vpmaxsw'
/tmp/cclpPiBu.s:6419: Error: suffix or operands invalid for vpsubsw' /tmp/cclpPiBu.s:6545: Error: no such instruction:
vpbroadcastw %xmm0,%xmm0'
/tmp/cclpPiBu.s:6548: Error: no such instruction: vinserti128 $1,%xmm0,%ymm0,%ymm0' /tmp/cclpPiBu.s:6554: Error: no such instruction:
vpbroadcastw %xmm0,%xmm0'
/tmp/cclpPiBu.s:6555: Error: no such instruction: vinserti128 $1,%xmm0,%ymm0,%ymm0' /tmp/cclpPiBu.s:6595: Error: no such instruction:
vpbroadcastw %xmm7,%xmm7'
/tmp/cclpPiBu.s:6596: Error: no such instruction: vpbroadcastw %xmm6,%xmm6' /tmp/cclpPiBu.s:6598: Error: no such instruction:
vinserti128 $1,%xmm7,%ymm7,%ymm7'
/tmp/cclpPiBu.s:6599: Error: no such instruction: vinserti128 $1,%xmm6,%ymm6,%ymm6' /tmp/cclpPiBu.s:6620: Error: suffix or operands invalid for
vpsubsw'
/tmp/cclpPiBu.s:6627: Error: suffix or operands invalid for vpsubsw' /tmp/cclpPiBu.s:6636: Error: suffix or operands invalid for
vpsubsw'
/tmp/cclpPiBu.s:6943: Error: suffix or operands invalid for vpand' /tmp/cclpPiBu.s:6946: Error: suffix or operands invalid for
vpsubsw'
/tmp/cclpPiBu.s:6950: Error: no such instruction: vpbroadcastw %xmm3,%xmm3' /tmp/cclpPiBu.s:6951: Error: no such instruction:
vinserti128 $1,%xmm3,%ymm3,%ymm3'
/tmp/cclpPiBu.s:6965: Error: suffix or operands invalid for vpsubsw' /tmp/cclpPiBu.s:6969: Error: suffix or operands invalid for
vpsubsw'
/tmp/cclpPiBu.s:6970: Error: suffix or operands invalid for vpsubsw' /tmp/cclpPiBu.s:6972: Error: suffix or operands invalid for
vpmaxsw'
/tmp/cclpPiBu.s:6973: Error: suffix or operands invalid for vpsubsw' /tmp/cclpPiBu.s:6974: Error: suffix or operands invalid for
vpmaxsw'
/tmp/cclpPiBu.s:6975: Error: suffix or operands invalid for vpaddsw' /tmp/cclpPiBu.s:6978: Error: suffix or operands invalid for
vpminsw'
/tmp/cclpPiBu.s:6979: Error: suffix or operands invalid for vpmaxsw' /tmp/cclpPiBu.s:6980: Error: suffix or operands invalid for
vpmaxsw'
/tmp/cclpPiBu.s:6985: Error: suffix or operands invalid for vpmaxsw' /tmp/cclpPiBu.s:6993: Error: suffix or operands invalid for
vpminsw'
/tmp/cclpPiBu.s:6998: Error: suffix or operands invalid for vpminsw' /tmp/cclpPiBu.s:7474: Error: suffix or operands invalid for
vpand'
/tmp/cclpPiBu.s:7481: Error: suffix or operands invalid for vpand' /tmp/cclpPiBu.s:7482: Error: suffix or operands invalid for
vpaddsw'
/tmp/cclpPiBu.s:7490: Error: suffix or operands invalid for vpand' /tmp/cclpPiBu.s:7494: Error: suffix or operands invalid for
vpand'
/tmp/cclpPiBu.s:7499: Error: suffix or operands invalid for vpsubsw' /tmp/cclpPiBu.s:7500: Error: suffix or operands invalid for
vpand'
/tmp/cclpPiBu.s:7501: Error: suffix or operands invalid for vpaddsw' /tmp/cclpPiBu.s:7509: Error: suffix or operands invalid for
vpand'
/tmp/cclpPiBu.s:7510: Error: suffix or operands invalid for vpand' /tmp/cclpPiBu.s:7512: Error: suffix or operands invalid for
vpaddsw'
/tmp/cclpPiBu.s:7545: Error: suffix or operands invalid for vpsubsw' /tmp/cclpPiBu.s:7708: Error: suffix or operands invalid for
vbroadcastss'
/tmp/cclpPiBu.s:7890: Error: suffix or operands invalid for vpsubd' /tmp/cclpPiBu.s:7894: Error: suffix or operands invalid for
vpsubd'
/tmp/cclpPiBu.s:7895: Error: suffix or operands invalid for vpsubd' /tmp/cclpPiBu.s:7896: Error: suffix or operands invalid for
vpmaxsd'
/tmp/cclpPiBu.s:7897: Error: suffix or operands invalid for vpsubd' /tmp/cclpPiBu.s:7898: Error: suffix or operands invalid for
vpmaxsd'
/tmp/cclpPiBu.s:7902: Error: suffix or operands invalid for vpmaxsd' /tmp/cclpPiBu.s:7903: Error: suffix or operands invalid for
vpaddd'
/tmp/cclpPiBu.s:7904: Error: suffix or operands invalid for vpmaxsd' /tmp/cclpPiBu.s:7905: Error: suffix or operands invalid for
vpmaxsd'
/tmp/cclpPiBu.s:7906: Error: suffix or operands invalid for vpminsd' /tmp/cclpPiBu.s:7911: Error: suffix or operands invalid for
vpmaxsd'
/tmp/cclpPiBu.s:8152: Error: suffix or operands invalid for vpand' /tmp/cclpPiBu.s:8162: Error: suffix or operands invalid for
vpand'
/tmp/cclpPiBu.s:8169: Error: suffix or operands invalid for vpand' /tmp/cclpPiBu.s:8424: Error: suffix or operands invalid for
vbroadcastss'
/tmp/cclpPiBu.s:8468: Error: suffix or operands invalid for vbroadcastss' /tmp/cclpPiBu.s:8469: Error: suffix or operands invalid for
vbroadcastss'
/tmp/cclpPiBu.s:8668: Error: suffix or operands invalid for vpsubd' /tmp/cclpPiBu.s:8672: Error: suffix or operands invalid for
vpsubd'
/tmp/cclpPiBu.s:8673: Error: suffix or operands invalid for vpsubd' /tmp/cclpPiBu.s:8674: Error: suffix or operands invalid for
vpmaxsd'
/tmp/cclpPiBu.s:8677: Error: suffix or operands invalid for vpsubd' /tmp/cclpPiBu.s:8679: Error: suffix or operands invalid for
vpmaxsd'
/tmp/cclpPiBu.s:8680: Error: suffix or operands invalid for vpaddd' /tmp/cclpPiBu.s:8682: Error: suffix or operands invalid for
vpmaxsd'
/tmp/cclpPiBu.s:8683: Error: suffix or operands invalid for vpmaxsd' /tmp/cclpPiBu.s:8687: Error: suffix or operands invalid for
vpmaxsd'
/tmp/cclpPiBu.s:8691: Error: suffix or operands invalid for vpmaxsd' /tmp/cclpPiBu.s:8832: Error: suffix or operands invalid for
vpmaxsd'
/tmp/cclpPiBu.s:8975: Error: suffix or operands invalid for vpand' /tmp/cclpPiBu.s:8982: Error: suffix or operands invalid for
vpand'
/tmp/cclpPiBu.s:8983: Error: suffix or operands invalid for vpaddd' /tmp/cclpPiBu.s:8993: Error: suffix or operands invalid for
vpand'
/tmp/cclpPiBu.s:8999: Error: suffix or operands invalid for vpand' /tmp/cclpPiBu.s:9000: Error: suffix or operands invalid for
vpand'
/tmp/cclpPiBu.s:9002: Error: suffix or operands invalid for vpaddd' /tmp/cclpPiBu.s:9026: Error: suffix or operands invalid for
vpmaxsd'
/tmp/cclpPiBu.s:9198: Error: suffix or operands invalid for vbroadcastss' /tmp/cclpPiBu.s:9241: Error: suffix or operands invalid for
vbroadcastss'
/tmp/cclpPiBu.s:9243: Error: suffix or operands invalid for vbroadcastss' /tmp/cclpPiBu.s:9245: Error: suffix or operands invalid for
vpsubd'
/tmp/cclpPiBu.s:9266: Error: suffix or operands invalid for vpsubd' /tmp/cclpPiBu.s:9425: Error: suffix or operands invalid for
vpsubd'
/tmp/cclpPiBu.s:9430: Error: suffix or operands invalid for vpsubd' /tmp/cclpPiBu.s:9432: Error: suffix or operands invalid for
vpsubd'
/tmp/cclpPiBu.s:9433: Error: suffix or operands invalid for vpsubd' /tmp/cclpPiBu.s:9434: Error: suffix or operands invalid for
vpmaxsd'
/tmp/cclpPiBu.s:9435: Error: suffix or operands invalid for vpmaxsd' /tmp/cclpPiBu.s:9436: Error: suffix or operands invalid for
vpaddd'
/tmp/cclpPiBu.s:9438: Error: suffix or operands invalid for vpmaxsd' /tmp/cclpPiBu.s:9440: Error: suffix or operands invalid for
vpmaxsd'
/tmp/cclpPiBu.s:9447: Error: suffix or operands invalid for vpmaxsd' /tmp/cclpPiBu.s:9729: Error: suffix or operands invalid for
vpand'
/tmp/cclpPiBu.s:9736: Error: suffix or operands invalid for vpand' /tmp/cclpPiBu.s:9737: Error: suffix or operands invalid for
vpaddd'
/tmp/cclpPiBu.s:9745: Error: suffix or operands invalid for vpand' /tmp/cclpPiBu.s:9749: Error: suffix or operands invalid for
vpand'
/tmp/cclpPiBu.s:9754: Error: suffix or operands invalid for vpsubd' /tmp/cclpPiBu.s:9755: Error: suffix or operands invalid for
vpand'
/tmp/cclpPiBu.s:9756: Error: suffix or operands invalid for vpaddd' /tmp/cclpPiBu.s:9764: Error: suffix or operands invalid for
vpand'
/tmp/cclpPiBu.s:9765: Error: suffix or operands invalid for vpand' /tmp/cclpPiBu.s:9767: Error: suffix or operands invalid for
vpaddd'
/tmp/cclpPiBu.s:9791: Error: suffix or operands invalid for vpmaxsd' /tmp/cclpPiBu.s:9814: Error: suffix or operands invalid for
vpsubd'
Makefile:106: recipe for target 'obj/swimd/Swimd.o' failed
make[2]: *** [obj/swimd/Swimd.o] Error 1
Makefile:51: recipe for target 'swsharp' failed
make[1]: *** [swsharp] Error 2
Makefile:16: recipe for target 'vendor/swsharp' failed
make: *** [vendor/swsharp] Error 2`
Hi, Robert
with pauline's help, sift4g can bring predictions. But still many errors in log file like this:
Use of uninitialized value $aa in string eq at make-single-records-BIOPERL.pl line 270 Use of uninitialized value $aa in concatenation (.) or string at make-single-records-BIOPERL.pl line 276 Use of uninitialized value $mutated_aa in string eq at make-single-records-BIOPERL.pl line 547. Use of uninitialized value in concatenation (.) or string at make-single-records-BIOPERL.pl line 301. Use of uninitialized value $aa2 in string eq at generate-fasta-subst-files-BIOPERL.pl line 615. Use of uninitialized value $aa2 in string ne at generate-fasta-subst-files-BIOPERL.pl line 620. Use of uninitialized value $mutated_aa in string eq at generate-fasta-subst-files-BIOPERL.pl line 888.
It seems sift4g breaks when deal with CDS with "NNNN". For example,
Maybe I should ignore this transcript. I don't know but any way to resolve these errors?
Thanks,
Lipeng
Hello,
I am trying to create sift database for peas. I have my files downloaded. I am getting an error that says it cannot access my gene-annotation-src
Error:
entered mkdir ./newpeas
/Pisum_sativum_v1awpeas
converting gene format to use-able input
ls: cannot access '/gene-annotation-src': No such file or directory
Unable to open for reading
done converting gene format
/*.gz: No such file or directory
DNA files do not exist or did not unzip properly
Config file:
GENETIC_CODE_TABLE=1
GENETIC_CODE_TABLENAME=Standard
MITO_GENETIC_CODE_TABLE=1
MITO_GENETIC_CODE_TABLENAME=Plant Plastid Code
PARENT_DIR=./newpeas/peas
ORG=Pisum_sativum
ORG_VERSION=Pisum_sativum_v1a
DBSNP_VCF_FILE=SNPD4.vcf.gz
#Running SIFT 4G
SIFT4G_PATH=./sift4g/bin/sift4g
PROTEIN_DB=./scripts_to_build_SIFT_db/test_files/fastafiles/uniprot-pisum.fasta
GENE_DOWNLOAD_DEST=gene-annotation-src
CHR_DOWNLOAD_DEST=chr-src
LOGFILE=Log.txt
ZLOGFILE=Log2.txt
FASTA_DIR=fasta
SUBST_DIR=subst
ALIGN_DIR=SIFT_alignments
SIFT_SCORE_DIR=SIFT_predictions
SINGLE_REC_BY_CHR_DIR=singleRecords
SINGLE_REC_WITH_SIFTSCORE_DIR=singleRecords_with_scores
DBSNP_DIR=dbSNP
FASTA_LOG=fasta.log
INVALID_LOG=invalid.log
PEPTIDE_LOG=peptide.log
ENS_PATTERN=ENS
SINGLE_RECORD_PATTERN=:change:_aa1valid_dbsnp.singleRecord
A declarative, efficient, and flexible JavaScript library for building user interfaces.
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google ❤️ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.