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nvalimak / fsm-lite

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Empty output file #7

Open myoungblom opened 5 years ago

myoungblom commented 5 years ago

I am using the following command (after making the input file as instructed) and am ending up with an empty output file. Any ideas? Installation went well and I can run 'fsm-lite -h' without issue.

fsm-lite -l fsmLite_input.list -t tmp -v > fsmLite_output.txt Reading input files... Read 108 input files and 216 sequences of total length 108178632 (includes rev.compl. sequences) Constructing the data structures... Construction complete, the main index requires 256.157 MiB plus 134.154 MiB for labels. All done.

TomLawrence1000 commented 4 years ago

I've also had this issue and was wondering if you managed to resolve it?

EDIT: So I had this issue with the tutorial dataset from pyseer but have not encountered the issue when running my own data. No idea why.

emmyneutron commented 4 years ago

I have same issue while running pyseer tutorial on S. pneumoniae genomes with "k-mer association mixed-effects model" when I ran this command: fsm-lite -l fsm_file_list.txt -s 6 -S 610 -v -t fsm_kmers

I got this result with empty k-mer file: Read 616 input files and 76132 sequences of total length 2528829918 (includes rev.compl. sequences) Constructing the data structures... Killed

huoww07 commented 3 years ago

Similar issue here: running this code fsm-lite -v -l genome_list_474.list -t genomes_474 > fsm_kmers_genomes_474.txt generated below error message:

Reading input files... Read 474 input files and 90624 sequences of total length 3759518196 (includes rev.compl. sequences) Constructing the data structures... Killed

Is it because not enough memory allocation (I have 32G mem for this run)?

Srividhya-Sainath commented 3 years ago

Facing the same issue here. I run fsm-lite -v -l input.txt -t tmp > fsm_kmers_output.txt and I get an output file that is empty. Has anyone solved this issue, or know why this is happening?

Manophab-L commented 1 month ago

Hi, I also faced the same thing, it gave the output of 20 bytes of fsm_kmers.txt.gz file.

fsm-lite` -l ../fsm_file_list.txt -s 6 -S 610 -v -t fsm_kmers | gzip -c - > ../fsm_kmers.txt.gz
Reading input files...
Read 616 input files and 76132 sequences of total length 2528829918 (includes rev.compl. sequences)
Constructing the data structures...
terminate called after throwing an instance of 'std::bad_alloc'
  what():  std::bad_alloc

Any recommendations to solve this?