ensembl-gh-mirror issueshttps://gitlab.ebi.ac.uk/groups/ensembl-gh-mirror/-/issues2016-12-07T16:47:00Zhttps://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/30Split HTSLIB_DIR into HTSLIB_LIBDIR and HTSLIB_INCDIR2016-12-07T16:47:00ZMarek SzubaSplit HTSLIB_DIR into HTSLIB_LIBDIR and HTSLIB_INCDIR*Created by: mmokrejs*
Hi,
I am trying to create a package into Gentoo Linux.
The current INSTALL.pl logic does not work on Gentoo Linux, which tries to get around the samtools/htslib mess by installing the headers and libs into su...*Created by: mmokrejs*
Hi,
I am trying to create a package into Gentoo Linux.
The current INSTALL.pl logic does not work on Gentoo Linux, which tries to get around the samtools/htslib mess by installing the headers and libs into subdirectories (see at the end for a list of files). This setup is not detected by your INSTALL.pl script. Here is what happens:
```
>>> Emerging (1 of 1) dev-perl/Bio-DB-HTS-2.3::science
* Bio-DB-HTS-2.3.tar.gz SHA256 SHA512 WHIRLPOOL size ;-) ... [ ok ]
>>> Unpacking source...
>>> Unpacking Bio-DB-HTS-2.3.tar.gz to /scratch/var/tmp/portage/dev-perl/Bio-DB-HTS-2.3/work
>>> Source unpacked in /scratch/var/tmp/portage/dev-perl/Bio-DB-HTS-2.3/work
>>> Preparing source in /scratch/var/tmp/portage/dev-perl/Bio-DB-HTS-2.3/work/Bio-DB-HTS-2.3 ...
>>> Source prepared.
>>> Configuring source in /scratch/var/tmp/portage/dev-perl/Bio-DB-HTS-2.3/work/Bio-DB-HTS-2.3 ...
* Using Module::Build
* perl Build.PL --installdirs=vendor --libdoc= --destdir=/scratch/var/tmp/portage/dev-perl/Bio-DB-HTS-2.3/image/ --create_packlist=1
This module requires htslib (http://htslib/org)
Install it if you have not done so already.
This script will attempt to locate htslib by looking for hts.h and libhts.a in:
1. --htslib command line argument
2. HTSLIB_DIR environment variable
3. --prefix command line argument (which also sets installation location)
4. Alien::HTSlib dependency resolver
5. pkg-config (extra directories can be set in PKG_CONFIG_PATH environment variable)
6. common library locations: /usr/local, /usr/share, /opt/local
* ERROR: dev-perl/Bio-DB-HTS-2.3::science failed (configure phase):
>>> Emerging (1 of 1) dev-perl/Bio-DB-HTS-2.3::science
* Bio-DB-HTS-2.3.tar.gz SHA256 SHA512 WHIRLPOOL size ;-) ... [ ok ]
>>> Unpacking source...
>>> Unpacking Bio-DB-HTS-2.3.tar.gz to /scratch/var/tmp/portage/dev-perl/Bio-DB-HTS-2.3/work
>>> Source unpacked in /scratch/var/tmp/portage/dev-perl/Bio-DB-HTS-2.3/work
>>> Preparing source in /scratch/var/tmp/portage/dev-perl/Bio-DB-HTS-2.3/work/Bio-DB-HTS-2.3 ...
>>> Source prepared.
>>> Configuring source in /scratch/var/tmp/portage/dev-perl/Bio-DB-HTS-2.3/work/Bio-DB-HTS-2.3 ...
* Using Module::Build
* perl Build.PL --installdirs=vendor --libdoc= --destdir=/scratch/var/tmp/portage/dev-perl/Bio-DB-HTS-2.3/image/ --create_packlist=1
This module requires htslib (http://htslib/org)
Install it if you have not done so already.
This script will attempt to locate htslib by looking for hts.h and libhts.a in:
1. --htslib command line argument
2. HTSLIB_DIR environment variable
3. --prefix command line argument (which also sets installation location)
4. Alien::HTSlib dependency resolver
5. pkg-config (extra directories can be set in PKG_CONFIG_PATH environment variable)
6. common library locations: /usr/local, /usr/share, /opt/local
* ERROR: dev-perl/Bio-DB-HTS-2.3::science failed (configure phase):
```
Here is a list of files from htslib and their installation place:
```
# equery files htslib
* Searching for htslib ...
* Contents of sci-libs/htslib-1.3:
/usr
/usr/bin
/usr/bin/bgzip
/usr/bin/htsfile
/usr/bin/tabix
/usr/include
/usr/include/htslib
/usr/include/htslib/bgzf.h
/usr/include/htslib/cram.h
/usr/include/htslib/faidx.h
/usr/include/htslib/hfile.h
/usr/include/htslib/hts.h
/usr/include/htslib/hts_defs.h
/usr/include/htslib/kbitset.h
/usr/include/htslib/kfunc.h
/usr/include/htslib/khash.h
/usr/include/htslib/khash_str2int.h
/usr/include/htslib/klist.h
/usr/include/htslib/knetfile.h
/usr/include/htslib/kseq.h
/usr/include/htslib/ksort.h
/usr/include/htslib/kstring.h
/usr/include/htslib/regidx.h
/usr/include/htslib/sam.h
/usr/include/htslib/synced_bcf_reader.h
/usr/include/htslib/tbx.h
/usr/include/htslib/vcf.h
/usr/include/htslib/vcf_sweep.h
/usr/include/htslib/vcfutils.h
/usr/lib
/usr/lib/debug
/usr/lib/debug/usr
/usr/lib/debug/usr/bin
/usr/lib/debug/usr/bin/bgzip.debug
/usr/lib/debug/usr/bin/htsfile.debug
/usr/lib/debug/usr/bin/tabix.debug
/usr/lib/debug/usr/lib64
/usr/lib/debug/usr/lib64/libhts.so.1.3.debug
/usr/lib64
/usr/lib64/libhts.so -> libhts.so.1.3
/usr/lib64/libhts.so.1 -> libhts.so.1.3
/usr/lib64/libhts.so.1.3
/usr/lib64/pkgconfig
/usr/lib64/pkgconfig/htslib.pc
/usr/share
/usr/share/doc
/usr/share/doc/htslib-1.3
/usr/share/doc/htslib-1.3/NEWS.bz2
/usr/share/doc/htslib-1.3/README.bz2
/usr/share/man
/usr/share/man/man1
/usr/share/man/man1/htsfile.1.bz2
/usr/share/man/man1/tabix.1.bz2
/usr/share/man/man5
/usr/share/man/man5/faidx.5.bz2
/usr/share/man/man5/sam.5.bz2
/usr/share/man/man5/vcf.5.bz2
```
Maybe I could pursue the `PKG_CONFIG_PATH` way?
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/60HTSfile::reindex with CRAM: renaming after sorting expects BAM2018-03-06T10:05:06ZMarek SzubaHTSfile::reindex with CRAM: renaming after sorting expects BAM*Created by: avullo*
See https://github.com/Ensembl/Bio-DB-HTS/issues/57#issuecomment-364239492*Created by: avullo*
See https://github.com/Ensembl/Bio-DB-HTS/issues/57#issuecomment-364239492https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/66Add memory leak cases to test suite2018-03-20T15:22:18ZMarek SzubaAdd memory leak cases to test suite*Created by: avullo*
The latest, more comprehensive, travis builds have exposed some memory leaks which occur when releasing memory of an index. Ensure these and other types do not occur by adding appropriate tests, e.g. using Test::Lea...*Created by: avullo*
The latest, more comprehensive, travis builds have exposed some memory leaks which occur when releasing memory of an index. Ensure these and other types do not occur by adding appropriate tests, e.g. using Test::LeakTrace.https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/63Travis to test with multiple htslib versions2018-03-14T17:06:18ZMarek SzubaTravis to test with multiple htslib versions*Created by: avullo*
Both ensembl web and vep rely on htslib 1.3.1, but development and enhancements are tied to newer library versions. So far, we've observed installation issues and also some header reading incompatibilities, see e.g....*Created by: avullo*
Both ensembl web and vep rely on htslib 1.3.1, but development and enhancements are tied to newer library versions. So far, we've observed installation issues and also some header reading incompatibilities, see e.g. #62 and #54.
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/57Does not support csi index2018-03-05T17:15:27ZMarek SzubaDoes not support csi index*Created by: keiranmraine*
The perl code doesn't handle the more efficient `csi` index for bam files:
https://github.com/Ensembl/Bio-DB-HTS/blob/master/lib/Bio/DB/HTS.pm#L2146*Created by: keiranmraine*
The perl code doesn't handle the more efficient `csi` index for bam files:
https://github.com/Ensembl/Bio-DB-HTS/blob/master/lib/Bio/DB/HTS.pm#L2146https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/55BCF indexing2018-04-16T15:50:47ZMarek SzubaBCF indexing*Created by: rishidev*
It would be good to be able to have the ability to jump straight into an indexed BCF file, perhaps using the bcf_sr_seek function in HTSlib.*Created by: rishidev*
It would be good to be able to have the ability to jump straight into an indexed BCF file, perhaps using the bcf_sr_seek function in HTSlib.https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/59Archives install script tied to master2018-03-15T14:35:28ZMarek SzubaArchives install script tied to master*Created by: avullo*
The install script for previous releases downloads and builds the master branch code.
An excerpt from running it for 2.7, showing how it is bound to the current release number as set in master (2.9):
*** Buildin...*Created by: avullo*
The install script for previous releases downloads and builds the master branch code.
An excerpt from running it for 2.7, showing how it is bound to the current release number as set in master (2.9):
*** Building Bio::DB::HTS ***
***CMD*** : env HTSLIB_DIR=/tmp/lCFQHly_Rz/htslib perl Build.PL
Created MYMETA.yml and MYMETA.json
Creating new 'Build' script for 'Bio-DB-HTS' version '2.9'
Building Bio-DB-HTS
cc -I/tmp/lCFQHly_Rz/htslib/htslib -I/home/avullo/perl5/perlbrew/perls/perl-5.16.0/lib/5.16.0/x86_64-linux/CORE -DXS_VERSION="2.9" -DVERSION="2.9" -fPIC -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -Wno-error -Wno-unused-result -c -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -o lib/Bio/DB/HTS.o lib/Bio/DB/HTS.c
ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/HTS/HTS.bs')
...
This is about introducing a version variable in the install script, and keeping it in sync at release time with the version number as set in the various modules.https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/14Functionality to write bam file2016-05-19T09:39:20ZMarek SzubaFunctionality to write bam file*Created by: sb43*
Would be handy to have method available in bio::db::sam that writes bam file.
*Created by: sb43*
Would be handy to have method available in bio::db::sam that writes bam file.
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/44The install script fails with GNU Wget 1.122017-06-17T13:09:49ZMarek SzubaThe install script fails with GNU Wget 1.12*Created by: dbolser-ebi*
I don't know why, but this version of wget trims off the file extension while downloading, breaking the logic of the install script:
```
[dbolser@gunpowder Bio-DB-HTS]$ perl INSTALL.pl --prefix $PWD/build
/n...*Created by: dbolser-ebi*
I don't know why, but this version of wget trims off the file extension while downloading, breaking the logic of the install script:
```
[dbolser@gunpowder Bio-DB-HTS]$ perl INSTALL.pl --prefix $PWD/build
/nfs/production/panda/ensemblgenomes/development/dbolser/Web/Ensembl/Test_Ensembl_89/Bio-DB-HTS
*** Performing build in /tmp/PrkgGdxgMT ***
*** Checking out HTSlib v1.3.1 ***
1.3.1.zip
--2017-06-16 10:53:32-- https://github.com/samtools/htslib/archive/1.3.1.zip
Resolving github.com... 192.30.253.113, 192.30.253.112
Connecting to github.com|192.30.253.113|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://codeload.github.com/samtools/htslib/zip/1.3.1 [following]
--2017-06-16 10:53:32-- https://codeload.github.com/samtools/htslib/zip/1.3.1
Resolving codeload.github.com... 192.30.253.121, 192.30.253.120
Connecting to codeload.github.com|192.30.253.121|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 1170333 (1.1M) [application/zip]
Saving to: `1.3.1'
100%[================================================================================================>] 1,170,333 1.47M/s in 0.8s
2017-06-16 10:53:34 (1.47 MB/s) - `1.3.1' saved [1170333/1170333]
Could not fetch HTSlib archive https://github.com/samtools/htslib/archive/1.3.1.zip at INSTALL.pl line 104.
```
There is probably a library to abstract downloads in Perl.https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/46Switch to using hisremote2017-06-17T13:09:01ZMarek SzubaSwitch to using hisremote*Created by: andrewyatz*
Currently Bio::HTS::Lib has its own routine for deciding if a given location is a remote or locally hosted file. htslib now has `hisremote()`, which does the same thing. We should switch to using this routine ra...*Created by: andrewyatz*
Currently Bio::HTS::Lib has its own routine for deciding if a given location is a remote or locally hosted file. htslib now has `hisremote()`, which does the same thing. We should switch to using this routine rather than using our own versionhttps://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/27system exit codes not checked - silent install failures2016-08-04T10:50:27ZMarek Szubasystem exit codes not checked - silent install failures*Created by: keiranmraine*
The system calls aren't being checked. Causes specific issues on minimal installs if `wget` not present:
https://github.com/Ensembl/Bio-HTS/blob/master/INSTALL.pl#L83
*Created by: keiranmraine*
The system calls aren't being checked. Causes specific issues on minimal installs if `wget` not present:
https://github.com/Ensembl/Bio-HTS/blob/master/INSTALL.pl#L83
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/2Looking for some examples of basic FASTA/Q handling with Bio::DB::HTS2016-05-25T08:20:21ZMarek SzubaLooking for some examples of basic FASTA/Q handling with Bio::DB::HTS*Created by: sestaton*
First, thanks for the work on this and for making it available on CPAN. I would like to know if there are any plans to add bindings to the FASTA/Q parsing methods in kseq.h of htslib? This may be possible already ...*Created by: sestaton*
First, thanks for the work on this and for making it available on CPAN. I would like to know if there are any plans to add bindings to the FASTA/Q parsing methods in kseq.h of htslib? This may be possible already or by some other method but it is not clear. For reference, @cjfields has already written bindings to kseq.h in the [Bio::Kseq](https://github.com/cjfields/Bio-Kseq) module, which is extremely useful because it is much faster than any pure-Perl parser. I think it would be great to have those basic sequence reading methods in one package along with all the alignment methods.
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/28Does Bio-HTS use ENA for CRAM tests?2016-10-20T10:59:03ZMarek SzubaDoes Bio-HTS use ENA for CRAM tests?*Created by: andrewyatz*
I've seen some odd behaviour running tests on the Ensembl REST API. It seems that travis build failed because of issues with accessing ENA (I've been told this but have not verified the problem). Do we go to ENA...*Created by: andrewyatz*
I've seen some odd behaviour running tests on the Ensembl REST API. It seems that travis build failed because of issues with accessing ENA (I've been told this but have not verified the problem). Do we go to ENA for any entries in the CRAM registry or do we always use the locally available FASTA file?
If we do then we should either make it an optional test pending if CRAM registry is available or switch to using a local file system or mock HTTP server using [Test::Fake::HTTPD](http://search.cpan.org/~masaki/Test-Fake-HTTPD/README.pod). There's a good example of how to configure it in the [Ensembl core test suite for network downloads](https://github.com/Ensembl/ensembl/blob/release/84/modules/t/utilsNet.t#L70). Happy to lend a hand
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/31Why didn't you just rename the repo?2016-08-05T12:42:08ZMarek SzubaWhy didn't you just rename the repo?*Created by: keiranmraine*
All links are maintained if you rename the repo so legacy docs just magically get redirected.
*Created by: keiranmraine*
All links are maintained if you rename the repo so legacy docs just magically get redirected.
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/32Ancillary items from Bio-SamTools2016-08-10T09:04:20ZMarek SzubaAncillary items from Bio-SamTools*Created by: drjsanger*
@keiranmraine created a ticket on the perviously copied repo, so I'm reopening it as it's been lost.
bam2bedgraph is missing, however Bio-DB-HTS also doesn't include the utility perl scripts that use it.
I hav...*Created by: drjsanger*
@keiranmraine created a ticket on the perviously copied repo, so I'm reopening it as it's been lost.
bam2bedgraph is missing, however Bio-DB-HTS also doesn't include the utility perl scripts that use it.
I have written an htslib dependant version of bam2bedgraph **(NB the input style is slightly different)**.
Should you choose to include it you can find it here:
https://github.com/ICGC-TCGA-PanCancer/PCAP-core/blob/dev/c/bam2bedgraph.c
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/17Memory leak: Bio::DB::HTS::Tabix - very reproducible2016-05-20T16:01:42ZMarek SzubaMemory leak: Bio::DB::HTS::Tabix - very reproducible*Created by: keiranmraine*
Use the following small bit of code to reproduce with a tabix indexed BED file:
```
#!/usr/bin/perl
use strict;
use Bio::DB::HTS::Tabix;
my ($file, $search, $iterations) = @ARGV;
my $brass_np = Bio::DB::HTS...*Created by: keiranmraine*
Use the following small bit of code to reproduce with a tabix indexed BED file:
```
#!/usr/bin/perl
use strict;
use Bio::DB::HTS::Tabix;
my ($file, $search, $iterations) = @ARGV;
my $brass_np = Bio::DB::HTS::Tabix->new(filename => $file);
for(0..$iterations) {
my $iter = $brass_np->query($search);
while(my $record = $iter->next){ }
}
```
Example runs (coordinate must hit records):
```
$ /usr/bin/time -f '%Mk maxresident' perl htsTabix_mem.pl test.bed.gz 1:9551-10140 1
102848k maxresident
$ /usr/bin/time -f '%Mk maxresident' perl htsTabix_mem.pl test.bed.gz 1:9551-10140 10
108128k maxresident
$ /usr/bin/time -f '%Mk maxresident' perl htsTabix_mem.pl test.bed.gz 1:9551-10140 100
160880k maxresident
$ /usr/bin/time -f '%Mk maxresident' perl htsTabix_mem.pl test.bed.gz 1:9551-10140 1000
688240k maxresident
```
Seems a very similar problem to `Bio::DB::HTS::Faidx`
This is pretty critical as we've discovered this in the middle of a pre-release test cycle
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/15INSTALL.pl - use master.zip instead of git clone2016-08-04T10:50:13ZMarek SzubaINSTALL.pl - use master.zip instead of git clone*Created by: keiranmraine*
Hi,
Have you considered just using the standard 'master.zip' instead of cloning the repository? It should be a much smaller download, especially for htslib, e.g.
```
curl -sSL --retry 10 -o master.zip https...*Created by: keiranmraine*
Hi,
Have you considered just using the standard 'master.zip' instead of cloning the repository? It should be a much smaller download, especially for htslib, e.g.
```
curl -sSL --retry 10 -o master.zip https://github.com/Ensembl/Bio-HTS/archive/master.zip
```
Keiran
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/13Bio::DB::HTS::Tabix - docs not accurate2016-05-03T12:40:09ZMarek SzubaBio::DB::HTS::Tabix - docs not accurate*Created by: keiranmraine*
The docs need rewording for 'query' to make it very clear that the coordinate format is 1-based for start and stop, unlike the legacy Tabix module (which was 0-based start).
It is also inaccurate to say that ...*Created by: keiranmraine*
The docs need rewording for 'query' to make it very clear that the coordinate format is 1-based for start and stop, unlike the legacy Tabix module (which was 0-based start).
It is also inaccurate to say that to retrieve 1 coordinate that a string of '12:5000000-5000001' is required:
```
$ zcat test.bed.gz
1 9 10 . stuff
1 10 11 . more
$ perl htsTabix.pl test.bed.gz 1 9 10
1 9 10 . stuff
$ perl htsTabix.pl test.bed.gz 1 9 11
1 9 10 . stuff
1 10 11 . more
$ perl htsTabix.pl test.bed.gz 1 10 11
1 9 10 . stuff
1 10 11 . more
$ perl htsTabix.pl test.bed.gz 1 11 11
1 10 11 . more
$ perl htsTabix.pl test.bed.gz 1 12 12
```
script:
```
use strict;
use warnings;
use Bio::DB::HTS::Tabix;
my $file = shift @ARGV;
my $tabix = Bio::DB::HTS::Tabix->new(filename => $file);
my $iter = $tabix->query(sprintf '%s:%d-%d', @ARGV);
while(my $l = $iter->next) {
print $l, "\n";
}
```
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/8BioPerl version2016-03-18T10:12:14ZMarek SzubaBioPerl version*Created by: andrewyatz*
Just tried to install from CPAN via cpanm and noticed that it installed BioPerl version 1.69. Is there any particular reason why we need such a late version of BioPerl? Not that I've got any issues surrounding i...*Created by: andrewyatz*
Just tried to install from CPAN via cpanm and noticed that it installed BioPerl version 1.69. Is there any particular reason why we need such a late version of BioPerl? Not that I've got any issues surrounding it just could/should it be relaxed?
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/6Memory leak in Faidx.pm/xs2016-03-15T17:44:36ZMarek SzubaMemory leak in Faidx.pm/xs*Created by: keiranmraine*
Hi,
It looks like there is a mem leak in the Faidx.pm/xs module:
```
$ /usr/bin/time perl snpPanelGcCorrections.pl genome.fa SnpPositions.tsv
Chr Position ...
AUTO_1 1 3023783 ...
0.19user 0.02syst...*Created by: keiranmraine*
Hi,
It looks like there is a mem leak in the Faidx.pm/xs module:
```
$ /usr/bin/time perl snpPanelGcCorrections.pl genome.fa SnpPositions.tsv
Chr Position ...
AUTO_1 1 3023783 ...
0.19user 0.02system 0:00.22elapsed 97%CPU (0avgtext+0avgdata 129104maxresident)k
0inputs+0outputs (0major+10915minor)pagefaults 0swaps
$ /usr/bin/time perl snpPanelGcCorrections.pl genome.fa SnpPositions.tsv
Chr Position ...
AUTO_1 1 3023783 ...
AUTO_2 1 3036178 ...
0.36user 0.03system 0:00.40elapsed 97%CPU (0avgtext+0avgdata 237648maxresident)k
0inputs+0outputs (0major+18918minor)pagefaults 0swaps
$ /usr/bin/time perl snpPanelGcCorrections.pl genome.fa SnpPositions.tsv
Chr Position ...
AUTO_1 1 3023783 ...
AUTO_2 1 3036178 ...
AUTO_3 1 3050521 ...
0.52user 0.06system 0:00.60elapsed 95%CPU (0avgtext+0avgdata 308112maxresident)k
0inputs+0outputs (0major+25291minor)pagefaults 0swaps
```
Each line is the result of 16 requests against faidx around a position increasing up to 10mb