kevsilva / strainflair Goto Github PK

Thank you for developing a great tool.

What do the columns in strains_profile.csv mean?

detected_genes,mean_abund,mean_abund_nz,median_abund,median_abund_nz

What does "_nz" mean above?
Thank you.

Hi,

I am trying out StrainFLAIR at the moment, and noticed a huge, repeating stream of errors during the graph construction phase:

Stack trace path: /tmp/vg_crash_1XXwg5/stacktrace.txt
Please include the stack trace file in your bug report!
error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph
error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathMutableHandleGraph
ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug.
Stack trace path: /tmp/vg_crash_IkwoiT/stacktrace.txt
Please include the stack trace file in your bug report!
error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph
error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathMutableHandleGraph
seqwish: error while loading shared libraries: libatomic.so.1: cannot open shared object file: No such file or directory
seqwish: error while loading shared libraries: libatomic.so.1: cannot open shared object file: No such file or directory
ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug.
Stack trace path: /tmp/vg_crash_XPeI58/stacktrace.txt
Please include the stack trace file in your bug report!
vg: /home/erik/vg-release/vg/include/gfakluge.hpp:569: size_t gfak::mmap_open(const string&, char*&, int&): Assertion false' failed. error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathMutableHandleGraph ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_jSkxpb/stacktrace.txt Please include the stack trace file in your bug report! vg: /home/erik/vg-release/vg/include/gfakluge.hpp:569: size_t gfak::mmap_open(const string&, char*&, int&): Assertion false' failed.
error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph
vg: /home/erik/vg-release/vg/include/gfakluge.hpp:569: size_t gfak::mmap_open(const string&, char*&, int&): Assertion false' failed. error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathMutableHandleGraph ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_eE7vxo/stacktrace.txt Please include the stack trace file in your bug report! vg: /home/erik/vg-release/vg/include/gfakluge.hpp:569: size_t gfak::mmap_open(const string&, char*&, int&): Assertion false' failed.
error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph
error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathMutableHandleGraph
vg: /home/erik/vg-release/vg/include/gfakluge.hpp:569: size_t gfak::mmap_open(const string&, char*&, int&): Assertion false' failed. ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_WtvH71/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_SBiDqw/stacktrace.txt Please include the stack trace file in your bug report! seqwish: error while loading shared libraries: libatomic.so.1: cannot open shared object file: No such file or directory error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathMutableHandleGraph vg: /home/erik/vg-release/vg/include/gfakluge.hpp:569: size_t gfak::mmap_open(const string&, char*&, int&): Assertion false' failed.
vg: /home/erik/vg-release/vg/include/gfakluge.hpp:569: size_t gfak::mmap_open(const string&, char*&, int&): Assertion false' failed. error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathMutableHandleGraph seqwish: error while loading shared libraries: libatomic.so.1: cannot open shared object file: No such file or directory vg: /home/erik/vg-release/vg/include/gfakluge.hpp:569: size_t gfak::mmap_open(const string&, char*&, int&): Assertion false' failed.
vg: /home/erik/vg-release/vg/include/gfakluge.hpp:569: size_t gfak::mmap_open(const string&, char*&, int&): Assertion false' failed. vg: /home/erik/vg-release/vg/include/gfakluge.hpp:569: size_t gfak::mmap_open(const string&, char*&, int&): Assertion false' failed.
vg: /home/erik/vg-release/vg/include/gfakluge.hpp:569: size_t gfak::mmap_open(const string&, char*&, int&): Assertion `false' failed.
ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug.
Stack trace path: /tmp/vg_crash_sDZ3Kf/stacktrace.txt
Please include the stack trace file in your bug report!
ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug.
Stack trace path: /tmp/vg_crash_GRUTMm/stacktrace.txt

I assume I need to install the missing shared libraries, but any help beyond that would be appreciated!

StrainFLAIR is compared on the real datasets (PRJEB42498) which is available for download. Can you please provide the ground truth information of this data set to which your tool was compared, or provide the source where the ground truth information is available.

Could you please tag a release? It is needed to add strainflair to bioconda.

Hi,

I followed the install instructions exactly, which ran without error, yet seqwish cannot be found.

It has been created and exists under the StrainFLAIR/seqwish/bin directory.

Should it actually be copied somewhere else or added to path ?

StrainFLAIR$ ls seqwish/bin
seqwish

The conda env Strain is still activated

After installing StrainFLAIR as required on your github website and installing seqwish using conda, I tried to run StrainFLAIR on your minimal dataset using the command:
StrainFLAIR.sh index -i data/list_fasta_min.txt -o myproject

Unfortunately, I get the following error, although there is no problem with disk space or permissions and other dependency tools such as prodigal and cd-hit use the same /tmp directory without any problem:

GRAPHS CONSTRUCTION
mkdir myproject/graphs
graphs_construction -s myproject/all_genes_extended.fasta -c myproject/clusters/all_genes_clusters.clstr -o myproject/graphs
[seqwish::tempfile]: couldn't create temp directory: /tmp/tmph647__ej/cluster_temp.work/seqwish-z7WwsM
[seqwish::tempfile]: couldn't create temp directory: /tmp/tmpiungev29/cluster_temp.work/seqwish-ZHeMAX
[seqwish::tempfile]: couldn't create temp directory: /tmp/tmpdlx6kgou/cluster_temp.work/seqwish-ko0LE2

Could you please tell me where the problem is and how to solve it?

I am validating this using multiple datasets generated by a read simulator for metagenomics. Each data set contains a total of 500,000 reads. It is running on a Docker container with StrainFLAIR installed on a Linux machine with 120 GB of memory. Some of the data sets succeed and some fail with the following error, so I don't think it is due to lack of memory on the machine.

I can share these test data with you. Any further help would be appreciated!

Percent: [##################################################] 100% Done...
/opt/conda/envs/StrainFLAIR/bin/StrainFLAIR.sh: line 639: 49 Killed $cmd

GENE-LEVEL ABUNDANCES
json2csv -g out_Lm3_Pf_Sh/graphs/all_graphs.gfa -m out_Lm3_Pf_Sh/mapping/mapping_mix_Pf-Sh-Lm1e-1_1M.json -p out_Lm3_Pf_Sh/graphs/dict_clusters.pickle -o out_Lm3_Pf_Sh/results/mix_Pf-Sh-Lm1e-1_1M
 there was a problem with the gene-level table generation