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gjospin / PhyloSift

Phylogenetic and taxonomic analysis for genomes and metagenomes
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Use of uninitialized value $timestamp in scalar chomp at.. #500

Open ganiatgithub opened 5 years ago

ganiatgithub commented 5 years ago

Hi,

I'm using phylosift on a university server to taxonomically place MAGs. I'm using phylosift_v1.0.1, and have placed the markers.tgz as follows: /home/uqgni1/share/phylosift/markers ncbi..tgz at: /home/uqgni1/share/phylosift/ncbi

My code: /path_to_phylosift/phylosift all \ /path_to_MAGs/out.1.fa \ --output /path_to_output/out.1.fa_out \ --threads 12 --coverage --disable_updates

And I couldn't solve the following issue: Use of uninitialized value $timestamp in scalar chomp at /gpfs1/scratch/30days/uqgni1/tools/phylosift_v1.0.1/bin/../lib/Phylosift/Utilities.pm line 365, <$FH> line 1. Use of uninitialized value $timestamp in scalar chomp at /gpfs1/scratch/30days/uqgni1/tools/phylosift_v1.0.1/bin/../lib/Phylosift/Utilities.pm line 365, <$FH> line 1. Use of uninitialized value in join or string at /gpfs1/scratch/30days/uqgni1/tools/phylosift_v1.0.1/bin/../lib/Phylosift/Summarize.pm line 568. Unable to read from --disable_updates at /gpfs1/scratch/30days/uqgni1/tools/phylosift_v1.0.1/bin/../lib/Phylosift/Utilities.pm line 85. Phylosift::Utilities::ps_open("--disable_updates") called at /gpfs1/scratch/30days/uqgni1/tools/phylosift_v1.0.1/bin/../lib/Phylosift/Summarize.pm line 99 Phylosift::Summarize::read_coverage("file", "--disable_updates") called at /gpfs1/scratch/30days/uqgni1/tools/phylosift_v1.0.1/bin/../lib/Phylosift/pplacer.pm line 69 Phylosift::pplacer::pplacer("self", Phylosift::Phylosift=HASH(0x55643347acd8), "marker_reference", ARRAY(0x5564327e4cf8), "chunk", 1) called at /gpfs1/scratch/30days/uqgni1/tools/phylosift_v1.0.1/bin/../lib/Phylosift/MarkerAlign.pm line 137 Phylosift::MarkerAlign::MarkerAlign("self", Phylosift::Phylosift=HASH(0x55643347acd8), "marker_reference", ARRAY(0x5564332cc990), "chunk", 1) called at /gpfs1/scratch/30days/uqgni1/tools/phylosift_v1.0.1/bin/../lib/Phylosift/FastSearch.pm line 156 Phylosift::FastSearch::run_search("self", Phylosift::Phylosift=HASH(0x55643347acd8), "marker_reference", ARRAY(0x5564332cc990)) called at /gpfs1/scratch/30days/uqgni1/tools/phylosift_v1.0.1/bin/../lib/Phylosift/Phylosift.pm line 418 Phylosift::Phylosift::run_search("self", Phylosift::Phylosift=HASH(0x55643347acd8), "cont", 0, "marker", ARRAY(0x5564332cc990)) called at /gpfs1/scratch/30days/uqgni1/tools/phylosift_v1.0.1/bin/../lib/Phylosift/Phylosift.pm line 175 Phylosift::Phylosift::run(Phylosift::Phylosift=HASH(0x55643347acd8), "force", undef, "custom", undef, "cont", undef) called at /gpfs1/scratch/30days/uqgni1/tools/phylosift_v1.0.1/bin/../lib/Phylosift/Command/all.pm line 129 Phylosift::Command::all::execute(Phylosift::Command::all=HASH(0x556433560ed0), Getopt::Long::Descriptive::Opts::OPT::2=HASH(0x556433581e58), ARRAY(0x556431434b98)) called at /gpfs1/scratch/30days/uqgni1/tools/phylosift_v1.0.1/bin/../lib/App/Cmd.pm line 243 App::Cmd::execute_command(Phylosift=HASH(0x55643334ff88), Phylosift::Command::all=HASH(0x556433560ed0), Getopt::Long::Descriptive::Opts::OPT::2=HASH(0x556433581e58), "/30days/uqgni1/jiaoyang/phylosift/bins/out.1.fa") called at /gpfs1/scratch/30days/uqgni1/tools/phylosift_v1.0.1/bin/../lib/App/Cmd.pm line 171 App::Cmd::run("Phylosift") called at /30days/uqgni1/tools/phylosift_v1.0.1/bin/phylosift line 7

What would you suggest?

Cheers, Gaofeng

gjospin commented 5 years ago

So it's trying to read the file labeled as the next option. So I would try giving it a coverage file for the contigs you are trying to place. so your command might look like the following:

path_to_phylosift/phylosift all /path_to_MAGs/out.1.fa --output /path_to_output/out.1.fa_out --threads 12 --coverage /path/to/coverage/file --disable_updates

I have rarely used coverage myself so I may be fuzzy on the details.

On Mon, May 13, 2019 at 2:57 PM ganiatgithub notifications@github.com wrote:

Hi,

I'm using phylosift on a university server to taxonomically place MAGs. I'm using phylosift_v1.0.1, and have placed the markers.tgz as follows: /home/uqgni1/share/phylosift/markers ncbi..tgz at: /home/uqgni1/share/phylosift/ncbi

My code: /path_to_phylosift/phylosift all /path_to_MAGs/out.1.fa --output /path_to_output/out.1.fa_out --threads 12 --coverage --disable_updates

And I couldn't solve the following issue: Use of uninitialized value $timestamp in scalar chomp at /gpfs1/scratch/30days/uqgni1/tools/phylosift_v1.0.1/bin/../lib/Phylosift/Utilities.pm line 365, <$FH> line 1. Use of uninitialized value $timestamp in scalar chomp at /gpfs1/scratch/30days/uqgni1/tools/phylosift_v1.0.1/bin/../lib/Phylosift/Utilities.pm line 365, <$FH> line 1. Use of uninitialized value in join or string at /gpfs1/scratch/30days/uqgni1/tools/phylosift_v1.0.1/bin/../lib/Phylosift/Summarize.pm line 568. Unable to read from --disable_updates at /gpfs1/scratch/30days/uqgni1/tools/phylosift_v1.0.1/bin/../lib/Phylosift/Utilities.pm line 85. Phylosift::Utilities::ps_open("--disable_updates") called at /gpfs1/scratch/30days/uqgni1/tools/phylosift_v1.0.1/bin/../lib/Phylosift/Summarize.pm line 99 Phylosift::Summarize::read_coverage("file", "--disable_updates") called at /gpfs1/scratch/30days/uqgni1/tools/phylosift_v1.0.1/bin/../lib/Phylosift/ pplacer.pm line 69 Phylosift::pplacer::pplacer("self", Phylosift::Phylosift=HASH(0x55643347acd8), "marker_reference", ARRAY(0x5564327e4cf8), "chunk", 1) called at /gpfs1/scratch/30days/uqgni1/tools/phylosift_v1.0.1/bin/../lib/Phylosift/MarkerAlign.pm line 137 Phylosift::MarkerAlign::MarkerAlign("self", Phylosift::Phylosift=HASH(0x55643347acd8), "marker_reference", ARRAY(0x5564332cc990), "chunk", 1) called at /gpfs1/scratch/30days/uqgni1/tools/phylosift_v1.0.1/bin/../lib/Phylosift/FastSearch.pm line 156 Phylosift::FastSearch::run_search("self", Phylosift::Phylosift=HASH(0x55643347acd8), "marker_reference", ARRAY(0x5564332cc990)) called at /gpfs1/scratch/30days/uqgni1/tools/phylosift_v1.0.1/bin/../lib/Phylosift/Phylosift.pm line 418 Phylosift::Phylosift::run_search("self", Phylosift::Phylosift=HASH(0x55643347acd8), "cont", 0, "marker", ARRAY(0x5564332cc990)) called at /gpfs1/scratch/30days/uqgni1/tools/phylosift_v1.0.1/bin/../lib/Phylosift/Phylosift.pm line 175 Phylosift::Phylosift::run(Phylosift::Phylosift=HASH(0x55643347acd8), "force", undef, "custom", undef, "cont", undef) called at /gpfs1/scratch/30days/uqgni1/tools/phylosift_v1.0.1/bin/../lib/Phylosift/Command/ all.pm line 129 Phylosift::Command::all::execute(Phylosift::Command::all=HASH(0x556433560ed0), Getopt::Long::Descriptive::Opts::OPT::2=HASH(0x556433581e58), ARRAY(0x556431434b98)) called at /gpfs1/scratch/30days/uqgni1/tools/phylosift_v1.0.1/bin/../lib/App/Cmd.pm line 243 App::Cmd::execute_command(Phylosift=HASH(0x55643334ff88), Phylosift::Command::all=HASH(0x556433560ed0), Getopt::Long::Descriptive::Opts::OPT::2=HASH(0x556433581e58), "/30days/uqgni1/jiaoyang/phylosift/bins/out.1.fa") called at /gpfs1/scratch/30days/uqgni1/tools/phylosift_v1.0.1/bin/../lib/App/Cmd.pm line 171 App::Cmd::run("Phylosift") called at /30days/uqgni1/tools/phylosift_v1.0.1/bin/phylosift line 7

What would you suggest?

Cheers, Gaofeng

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