Perl script cannot access folder

Billebaars has asked for the wisdom of the Perl Monks concerning the following question:

I'm running a Perl script from the EMBL (found here https://github.com/EMBL-EBI-GCA/reseqtrack/blob/master/scripts/variation_data/calculate_allele_frq_from_vcf.pl) Under Ubuntu 16.10 I have installed Vcftools and Tabix as is required and both have been tested to work accordingly. I execute the script with the following command:

perl /home/[user]/calculate_allele_frq_from_vcf.pl \
-vcf /home/[user]/share/1000genomesPhase3VCFFiles/ALL.chr1.phase3_shap
+eit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz \
-sample_panel /home/[user]/share/1000genomesPhase3VCFFiles/integrated_
+call_samples_v3.20130502.ALL.panel \
-out_dir /home/[user]/Desktop/AlleleFrequency \
-tabix  /home/[user]/tabix-0.2.6 \
-vcftools_dir /home/[user]/vcftools_0.1.13 \
-region 1:1-10000 \
-pop CEU,FIN \
[download]

This returns the following error

Smartmatch is experimental at /home/[user]/calculate_allele_frq_from_v
+cf.pl line 133.
Smartmatch is experimental at /home/[user]/calculate_allele_frq_from_v
+cf.pl line 144.
sh: 1: /home/[user]/tabix-0.2.6: Permission denied
Broken VCF header, no column names?
 at /home/[user]/vcftools_0.1.13/perl/Vcf.pm line 172.
    Vcf::throw(Vcf4_2=HASH(0x55761601d320), "Broken VCF header, no col
+umn names?") called at /home/[user]/vcftools_0.1.13/perl/Vcf.pm line 
+866
    VcfReader::_read_column_names(Vcf4_2=HASH(0x55761601d320)) called 
+at /home/[user]/vcftools_0.1.13/perl/Vcf.pm line 601
    VcfReader::parse_header(Vcf4_2=HASH(0x55761601d320)) called at /ho
+me/[user]/vcftools_0.1.13/perl/vcf-subset line 121
    main::vcf_subset(HASH(0x557615b24558)) called at /home/[user]/vcft
+ools_0.1.13/perl/vcf-subset line 12
Broken VCF header, no column names?
 at /home/[user]/vcftools_0.1.13/perl/Vcf.pm line 172.
    Vcf::throw(Vcf4_2=HASH(0x55fa53436f60), "Broken VCF header, no col
+umn names?") called at /home/[user]/vcftools_0.1.13/perl/Vcf.pm line 
+866
    VcfReader::_read_column_names(Vcf4_2=HASH(0x55fa53436f60)) called 
+at /home/[user]/vcftools_0.1.13/perl/Vcf.pm line 601
    VcfReader::parse_header(Vcf4_2=HASH(0x55fa53436f60)) called at /ho
+me/[user]/vcftools_0.1.13/perl/fill-an-ac line 45
    main::fill_an_ac(undef) called at /home/[user]/vcftools_0.1.13/per
+l/fill-an-ac line 9
sh: 1: /home/[user]/tabix-0.2.6: Permission denied
Broken VCF header, no column names?
 at /home/[user]/vcftools_0.1.13/perl/Vcf.pm line 172.
    Vcf::throw(Vcf4_2=HASH(0x5607d059a190), "Broken VCF header, no col
+umn names?") called at /home/[user]/vcftools_0.1.13/perl/Vcf.pm line 
+866
    VcfReader::_read_column_names(Vcf4_2=HASH(0x5607d059a190)) called 
+at /home/[user]/vcftools_0.1.13/perl/Vcf.pm line 601
    VcfReader::parse_header(Vcf4_2=HASH(0x5607d059a190)) called at /ho
+me/[user]/vcftools_0.1.13/perl/vcf-subset line 121
    main::vcf_subset(HASH(0x5607d00a1558)) called at /home/[user]/vcft
+ools_0.1.13/perl/vcf-subset line 12
Broken VCF header, no column names?
 at /home/[user]/vcftools_0.1.13/perl/Vcf.pm line 172.
    Vcf::throw(Vcf4_2=HASH(0x556b8e952110), "Broken VCF header, no col
+umn names?") called at /home/[user]/vcftools_0.1.13/perl/Vcf.pm line 
+866
    VcfReader::_read_column_names(Vcf4_2=HASH(0x556b8e952110)) called 
+at /home/[user]/vcftools_0.1.13/perl/Vcf.pm line 601
    VcfReader::parse_header(Vcf4_2=HASH(0x556b8e952110)) called at /ho
+me/[user]/vcftools_0.1.13/perl/fill-an-ac line 45
    main::fill_an_ac(undef) called at /home/[user]/vcftools_0.1.13/per
+l/fill-an-ac line 9
/home/[user]/Desktop/AlleleFrequency/calculated_fra.process3085.1.1-10
+000.CEU_FIN
[download]

It appears that the script doesn't have permission to access Tabix for some reason. I've given the folder full read/write permission for the user executing the script (me). Any ideas?

Comment on Perl script cannot access folder Select or Download Code

Replies are listed 'Best First'.
Re: Perl script cannot access folder by choroba (Cardinal) on Feb 21, 2017 at 16:28 UTC
Crossposted to StackOverflow. It's considered polite to inform about crossposting to avoid duplicate work of people not attending both sites. Also, see my answer there. ($q=q:Sq=~/;[c](.)(.)/;chr(-\|\|-\|5+lengthSq)`"S\|oS2"`map{chr \|+ord }map{substrSq`S_+\|`\|}3E\|-\|`7**2-3:)=~y+S\|`+$1,++print+eval$q,q,a, [download]	[reply] [d/l]
Re^2: Perl script cannot access folder by Billebaars (Initiate) on Feb 21, 2017 at 18:03 UTC
Ah, thanks for letting me know, I was unaware of this. Also, many thanks for your answer. Stupidly, I indeed didn't include the executable in the path. It works now with the correct path: `/home/[user]/tabix-0.2.6/tabix`	[reply] [d/l]
Re: Perl script cannot access folder by stevieb (Canon) on Feb 21, 2017 at 16:52 UTC
Is the "tabix" an application that runs under its own user account (that may not have correct permissions)? Reason I ask is it looks like something has been shelled out: `sh: 1: /home/[user]/tabix-0.2.6` [download] To see if you have correct permissions: `perl -E 'open my $fh, ">", "/home/[user]/tabix-0.2.6/test.txt" or die +$!'` [download] If you don't get a permission denied error, the problem is elsewhere. Perhaps also show the perms you do have on the dir. The chunk of Perl code that wraps this work may be helpful to us to troubleshoot to help as well.	[reply] [d/l] [select]