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I use a 64 bit ubuntu 18.04. I tried to install mrsFAST but I got the following error.
I could not find anything in the manual to help me through this. Would it be possible for you to suggest what I should do to be able to install mrsFAST?

Error details:

cc -fno-pic -DMRSFAST_VERSION=""3.4.0"" -DBUILD_DATE=""Tue Aug 27 14:01:17 IST 2019"" -DSSE4=0 -O2 -c -o baseFAST.o baseFAST.c
cc -fno-pic -DMRSFAST_VERSION=""3.4.0"" -DBUILD_DATE=""Tue Aug 27 14:01:17 IST 2019"" -DSSE4=0 -O2 -c -o Sort.o Sort.c
cc -fno-pic -DMRSFAST_VERSION=""3.4.0"" -DBUILD_DATE=""Tue Aug 27 14:01:17 IST 2019"" -DSSE4=0 -O2 -c -o MrsFAST.o MrsFAST.c
MrsFAST.c: In function ‘initializeFAST’:
MrsFAST.c:202:25: warning: ‘M’ directive writing 1 byte into a region of size between 0 and 4 [-Wformat-overflow=]
sprintf(_msf_cigar, "%dM", SEQ_LENGTH);
^
In file included from /usr/include/stdio.h:862:0,
from MrsFAST.c:36:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:33:10: note: ‘__builtin___sprintf_chk’ output between 3 and 7 bytes into a destination of size 5
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc -fno-pic -DMRSFAST_VERSION=""3.4.0"" -DBUILD_DATE=""Tue Aug 27 14:01:17 IST 2019"" -DSSE4=0 -O2 -c -o Common.o Common.c
cc -fno-pic -DMRSFAST_VERSION=""3.4.0"" -DBUILD_DATE=""Tue Aug 27 14:01:17 IST 2019"" -DSSE4=0 -O2 -c -o CommandLineParser.o CommandLineParser.c
cc -fno-pic -DMRSFAST_VERSION=""3.4.0"" -DBUILD_DATE=""Tue Aug 27 14:01:17 IST 2019"" -DSSE4=0 -O2 -c -o RefGenome.o RefGenome.c
RefGenome.c: In function ‘initLoadingRefGenome’:
RefGenome.c:61:2: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fscanf(_rg_fp, "%c", &ch); // '>'
^~~~~~~~~~~~~~~~~~~~~~~~~
cc -fno-pic -DMRSFAST_VERSION=""3.4.0"" -DBUILD_DATE=""Tue Aug 27 14:01:17 IST 2019"" -DSSE4=0 -O2 -c -o HashTable.o HashTable.c
HashTable.c: In function ‘loadHashTable’:
HashTable.c:646:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&bytesToRead, sizeof(int), 1, _ih_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
HashTable.c:647:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(_ih_IOBuffer, sizeof(unsigned char), bytesToRead, _ih_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc -fno-pic -DMRSFAST_VERSION=""3.4.0"" -DBUILD_DATE=""Tue Aug 27 14:01:17 IST 2019"" -DSSE4=0 -O2 -c -o Reads.o Reads.c
cc -fno-pic -DMRSFAST_VERSION=""3.4.0"" -DBUILD_DATE=""Tue Aug 27 14:01:17 IST 2019"" -DSSE4=0 -O2 -c -o Output.o Output.c
cc -fno-pic -DMRSFAST_VERSION=""3.4.0"" -DBUILD_DATE=""Tue Aug 27 14:01:17 IST 2019"" -DSSE4=0 -O2 -c -o SNPReader.o SNPReader.c
gcc -w baseFAST.o Sort.o MrsFAST.o Common.o CommandLineParser.o RefGenome.o HashTable.o Reads.o Output.o SNPReader.o HELP.o -o mrsfast -lz -lm -pthread -lpthread
/usr/bin/ld: baseFAST.o: relocation R_X86_64_32 against undefined symbol fileName' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: MrsFAST.o: relocation R_X86_64_32S against undefined symbol _msf_numbers' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: Common.o: relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: CommandLineParser.o: relocation R_X86_64_32 against symbol _binary_HELP_start' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: RefGenome.o: relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: HashTable.o: relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: Reads.o: relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: Output.o: relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: SNPReader.o: relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: final link failed: Nonrepresentable section on output
collect2: error: ld returned 1 exit status
Makefile:17: recipe for target 'mrsfast' failed
make: *** [mrsfast] Error 1

Thank you.

Dear Sir,
I have installed mrsfast using gcc4 while it was showing error with other version of gcc. Now after running mrsfast search i am getting the error Segmentation fault (core dumped). Even though I have used small dataset to test but still this error persist. Presently, I am using mrfast also but it is very slow. I would like to know is there any way to speed up this.
Thank you
Waiting for your reply in anticipation

Hello

I am trying to map paired-end samples using mrsFAST and I am encountering the below error (ERR: Inconsistent read length). Any idea on how to resolve this?

[@fn-0001 mrsfast-3.4.0]$ ./mrsfast --search /gpfs/data/lab/raa04/conifer/hg19.fa --seq1 /gpfs/data/lab/raa04/conifer/AMV1_R1.fastq --seq2 /gpfs/data/lab/raa04/conifer/AMV1_R2.fastq --pe -o output.sam -e 2 --crop 36
==> This version is compiled without any SSE4 optimization <==
Threads: 1
| Genome Name | Loading Time | Mapping Time | Memory Usage(M) | Total Mappings Mapped reads |

ERR: Inconsistent read length for @NB501457:38:HWNTKBGXY:1:11101:16080:1853

Hi,
I encountered a problem. I ran the command and mrsfast-ultra. (Version: 3.4.0 Build Date: Tue Dec 27 19:23:16 ACDT 2016)
The command line I was using mrsfast --search ref.fasta --pe --discordant-vh --threads 24 --seqcomp --seq1 ${}.R1.fastq.gz --seq2 ${}.R2.fastq.gz --crop ${readlength} --min ${minimum} --max ${maximum} --disable-nohits
Input files are paired-end and consistent length.

It gave me Errors:8.

# Threads: 24

# Errors: 8

How can I fix this?
Thank you.

If you use gcc 9.3.0, it fails: seems that Makefile requires both major and minor version to be greater or equal than 4 for SSE to work.

Hi,
A paper said mrsfast can predict segmental duplications based on read depth. However, I didn't find this function. Did I miss anything?

from the Supplementary Material of Great ape genetic diversity and population history

Hi,

I am getting Error: 2 (full sensitivity) but the alignment finished normally apparently. Should I be worried about it?

==> This version is compiled without any SSE4 optimization <==
# Threads: 8
# Error: 2 (full sensitivity)
-----------------------------------------------------------------------------------------------------------
|     Genome Name |    Loading Time |    Mapping Time | Memory Usage(M) |  Total Mappings    Mapped reads |
-----------------------------------------------------------------------------------------------------------
| *Reading Input* |          101.49 | XXXXXXXXXXXXXXX |        15249.37 | XXXXXXXXXXXXXXX        22509475 |
|               1 |           20.67 |         1014.60 |        15305.37 |       784211141         3272412 |
|               2 |           18.19 |          775.10 |        15305.37 |      1391848098         5319167 |
|               3 |           10.91 |          881.47 |        15305.37 |      2013766521         6222282 |
|               4 |           11.10 |          742.13 |        15305.37 |      2453996439         7552566 |
|               5 |           11.76 |          607.03 |        15305.37 |      2766780248         8787975 |
|               6 |           11.27 |          616.60 |        15305.37 |      3135674544         9643657 |
|               7 |           10.59 |          530.96 |        15305.37 |      3443821878        10952447 |
|               8 |            9.67 |          404.34 |        15305.37 |      3658669007        11977026 |
|               9 |            9.81 |          397.37 |        15305.37 |      3875029613        13006889 |
|              10 |           10.10 |          445.17 |        15305.37 |      4090826446        13920444 |
|              11 |            8.73 |          258.38 |        15305.37 |      4221818024        15438502 |
|              12 |            9.13 |          378.36 |        15305.37 |      4426165929        16148926 |
|              13 |            9.20 |          337.87 |        15305.37 |      4615630769        16880576 |
|              14 |            9.52 |          366.32 |        15305.37 |      4825804624        17557153 |
|              15 |            8.72 |          325.23 |        15305.37 |      5016311851        18338565 |
|              16 |            8.71 |          325.83 |        15305.37 |      5209792377        18909564 |
|              17 |            7.83 |          226.73 |        15305.37 |      5335656468        19879302 |
|              18 |            7.61 |          261.11 |        15305.37 |      5493821851        20402467 |
|              19 |            5.00 |          111.80 |        15305.37 |      5557757374        20999127 |
|               X |           14.14 |          811.40 |        15305.37 |      6091814176        21342427 |
|               Y |            7.08 |         5114.34 |        15305.37 |      6191351373        21374949 |
----------------------------------------------------------------------------------------------------------
             Total:          321.30          14932.14

Total Time:                     15253.44
Total No. of Reads:             22509475
Total No. of Mappings:        6191351373
[Wed Jan 27 20:26:02 2021]
Finished job 0.
1 of 1 steps (100%) done


 ## The table is composed of single-end and paired-end experiments ##

Thx

Dear,
I created the SNP index based on the vcf file of dbSNP156.
An error occurs when performing SNP comparison:
mrsfast --search hg38.fa --seq ./test/rfx5.fa --threads 6 -e 100 --disable-sam-header --snp dbsnp156Common
ERROR :

==> This version is compiled without any SSE4 optimization <==
# Threads: 6
# Error: 2 (full sensitivity)
*** buffer overflow detected ***: terminated
Aborted

My vcf file like this:

And snp index created successfully:

Pre-processing VCF file ...
Chromosomes: 1027
Valid SNP locations: 21066777
Reading SNP locations .......
Reformatting data ...
Creating output in dbsnp156Common
21066777 SNP locations registered successfully

I performed an operation on the vcf file. If the two candidate alleles of a site are both greater than 0.5%, then the two SNPs are split into two lines, like the following:

Hi,

Is there a way to enable stdout, as we need to compress sam to bam using samtools somtimes.

Best,
Kun

Hi,

I'm trying to map some 14bp sequences to the human genome with max 2 mismatches allowed. However, no matter how I adjust the -e option, the program only checks for the perfect match.

for example:
mrsfast --search hg19.fasta --seq mrsfast_test.fq -e 2 --threads 4 -o mrsfast_out.sam
# Threads: 4
# Error: 0 (full sensitivity)
..

Is there a way to fix this?

I'm using mrsFAST-Ultra Version: 3.4.0.

Thank you!

I received segmentation fault
14285 Segmentation fault (core dumped)$path/mrsfast --search GRCh38_full_analysis_set.fa --pe --discordant-vh --seq1 R1.group_1.fastq --seq2 R2.group_1.fastq --crop 148 --min 297 --max 848 > mrsfast.seq1.log 2>&1

The result of make command gave me the following,
cc -fno-pic -DMRSFAST_VERSION=\""3.4.0"\" -DBUILD_DATE=\""Thu May 18 21:00:15 ACST 2017"\" -DSSE4=0 -O2 -c -o baseFAST.o baseFAST.c cc -fno-pic -DMRSFAST_VERSION=\""3.4.0"\" -DBUILD_DATE=\""Thu May 18 21:00:15 ACST 2017"\" -DSSE4=0 -O2 -c -o Sort.o Sort.c cc -fno-pic -DMRSFAST_VERSION=\""3.4.0"\" -DBUILD_DATE=\""Thu May 18 21:00:15 ACST 2017"\" -DSSE4=0 -O2 -c -o MrsFAST.o MrsFAST.c cc -fno-pic -DMRSFAST_VERSION=\""3.4.0"\" -DBUILD_DATE=\""Thu May 18 21:00:15 ACST 2017"\" -DSSE4=0 -O2 -c -o Common.o Common.c cc -fno-pic -DMRSFAST_VERSION=\""3.4.0"\" -DBUILD_DATE=\""Thu May 18 21:00:15 ACST 2017"\" -DSSE4=0 -O2 -c -o CommandLineParser.o CommandLineParser.c cc -fno-pic -DMRSFAST_VERSION=\""3.4.0"\" -DBUILD_DATE=\""Thu May 18 21:00:15 ACST 2017"\" -DSSE4=0 -O2 -c -o RefGenome.o RefGenome.c cc -fno-pic -DMRSFAST_VERSION=\""3.4.0"\" -DBUILD_DATE=\""Thu May 18 21:00:15 ACST 2017"\" -DSSE4=0 -O2 -c -o HashTable.o HashTable.c cc -fno-pic -DMRSFAST_VERSION=\""3.4.0"\" -DBUILD_DATE=\""Thu May 18 21:00:15 ACST 2017"\" -DSSE4=0 -O2 -c -o Reads.o Reads.c cc -fno-pic -DMRSFAST_VERSION=\""3.4.0"\" -DBUILD_DATE=\""Thu May 18 21:00:15 ACST 2017"\" -DSSE4=0 -O2 -c -o Output.o Output.c cc -fno-pic -DMRSFAST_VERSION=\""3.4.0"\" -DBUILD_DATE=\""Thu May 18 21:00:15 ACST 2017"\" -DSSE4=0 -O2 -c -o SNPReader.o SNPReader.c gcc -w baseFAST.o Sort.o MrsFAST.o Common.o CommandLineParser.o RefGenome.o HashTable.o Reads.o Output.o SNPReader.o HELP.o -o mrsfast -lz -lm -pthread -lpthread cc -fno-pic -DMRSFAST_VERSION=\""3.4.0"\" -DBUILD_DATE=\""Thu May 18 21:00:15 ACST 2017"\" -DSSE4=0 -O2 -c -o SNPIndexer.o SNPIndexer.c gcc SNPIndexer.o -o snp_indexer -lz -lm -pthread -lpthread

But the log file contains ==> This version is compiled without any SSE4 optimization <==
I tried multiple times, but it worked until first chr3 and it stopped.

I hope you gives me any advice on this issue.

Dear developer,
I have been using version 3.4.2 of mrsfast for alignment,
and I've found that the -e parameter is ineffective. It always retains its default value. Here are the results:
For -e 4:

For -e 9:

Dear,
I want to use snp-aware for sequence comparison.
I looked at the sample data you gave.
I would like to ask if I have small INDEl mrsfast tool in my vcf file can I handle it?
For example:
REF ATL
AGGC---->G
G------->CGCG

Thanks.