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Repo info
Hirak Sarkar
Hi I am relatively new to mccortex, and want to use it as a gfa constructor for our tool pufferfish https://github.com/COMBINE-lab/pufferfish
I tried to run mccortex with human transcriptome to do some testing with pufferfish
but failed to produce a gfa file
these are the commands I used
bin/mccortex31 build -m 70G -k 31 --sample human_transcript --seq /mnt/scratch7/pufferfish_data/gencode.v25.pc_transcripts_fixed.fa /mnt/scratch7/pufferfish_data/gencode.v25.pc_ transcripts_fixed.ctx
which worked well
followed by
bin/mccortex31 unitigs --gfa /mnt/scratch7/pufferfish_data/gencode.v25.pc_transcripts_fixed.ctx > /mnt/scratch7/pufferfish_data/gencode.v25.pc_transcripts_fixed.mccortex.gfa
which failed with the error
[03 Oct 2017 16:15:35-TiM][cmd] bin/mccortex31 unitigs --gfa /mnt/scratch7/pufferfish_data/gencode.v25.pc_transcripts_fixed.ctx
[03 Oct 2017 16:15:35-TiM][cwd] /home/hirak/Projects/mccortex
[03 Oct 2017 16:15:35-TiM][version] mccortex=v0.0.3-554-ga7d6f3b zlib=1.2.11 htslib=1.3.2-208-gd8d0323 ASSERTS=ON hash=Lookup3 CHECKS=ON k=3..31
[03 Oct 2017 16:15:35-TiM][memory] 137 bits per kmer
[03 Oct 2017 16:15:35-TiM][cmd_mem.c:98] Fatal Error: Not enough kmers in hash: require at least 79,334,030 kmers (min memory: 1.3GB)
can you please help me finding out what might have gone wrong
Winni Kretzschmar
Hiya Hirka, this is a bit late, but did you try specifying the memory flag again for the unitigs command?
Winni Kretzschmar
@hiraksarkar ^