AntonBankevich/LJA

=== Stack Trace === Child process crashed

Oieswarya opened this issue · 0 comments

I am trying to run LJA with simulated HiFi reads of Human Chr 7 (mean length of reads=10kbp, coverage is 10x). But I am having child process crashed error.
This is my .o file:
00:00:00 2Mb INFO: Hello! You are running La Jolla Assembler (LJA), a tool for genome assembly from PacBio HiFi reads
00:00:00 2Mb INFO: LJA pipeline started
00:00:00 2Mb INFO: Performing initial correction with k = 501
00:00:00 0Mb INFO: Reading reads
00:00:00 0Mb INFO: Extracting minimizers
00:00:11 1.6Gb INFO: Finished read processing
00:00:11 1.6Gb INFO: 874644 hashs collected. Starting sorting.
00:00:11 1.6Gb INFO: Finished sorting. Total distinct minimizers: 117385
00:00:11 1.6Gb INFO: Starting construction of sparse de Bruijn graph
00:00:11 1.6Gb INFO: Vertex map constructed.
00:00:11 1.6Gb INFO: Filling edge sequences.
00:00:26 1.8Gb INFO: Finished sparse de Bruijn graph construction.
00:00:26 1.8Gb INFO: Collecting tips
00:00:26 1.8Gb INFO: Added 2331 artificial minimizers from tips.
00:00:26 1.8Gb INFO: Collected 252400 old edges.
00:00:26 1.8Gb INFO: New minimizers added to sparse graph.
00:00:26 1.8Gb INFO: Refilling graph with old edges.
00:00:29 1.8Gb INFO: Filling graph with new edges.
00:00:29 1.8Gb INFO: Finished fixing sparse de Bruijn graph.
00:00:29 1.8Gb INFO: Starting to extract disjointigs.
00:00:30 1.8Gb INFO: Finished extracting 29983 disjointigs of total size 131109972
00:00:32 0Mb INFO: Loading disjointigs from file "/home/LJA-main/Outputs/HM7/k501/disjointigs.fasta"
00:00:34 490Mb INFO: Filling bloom filter with k+1-mers.
00:00:45 492Mb INFO: Filled 534849159 bits out of 3714816128
00:00:45 492Mb INFO: Finished filling bloom filter. Selecting junctions.
00:00:55 0.5Gb INFO: Collected 69828 junctions.
00:00:56 0.5Gb INFO: Starting DBG construction.
00:00:56 0.5Gb INFO: Vertices created.
00:00:58 0.5Gb INFO: Filled dbg edges. Adding hanging vertices
00:00:58 0.5Gb INFO: Added 8 hanging vertices
00:00:58 0.5Gb INFO: Merging unbranching paths
00:00:59 0.5Gb INFO: Ended merging edges. Resulting size 26839
00:01:00 0.5Gb INFO: Cleaning edge coverages
00:01:00 0.5Gb INFO: Collecting alignments of sequences to the graph
No outgoing for middle

-68385489142965885844029488329806185330G 7129
=== Stack Trace ===
Child process crashed

My command to run is this:
/home/LJA-main/bin/lja -o /home/LJA-main/Outputs/HM7/ --reads /home/obhowmik/HM7.fa -t 32

And I am running this is 200 GB.

I ahve also emailed the dbg.log file to the given email address.