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voutcn / megahit

Ultra-fast and memory-efficient (meta-)genome assembler
http://www.ncbi.nlm.nih.gov/pubmed/25609793
GNU General Public License v3.0
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Running into error "172 - Invalid format. Expect field k, got" #282

Closed tdido closed 4 years ago

tdido commented 4 years ago

Hello.

I'm trying to assembly a ~1.5Gb genome and am running into an error.

This is the original command line:

megahit -t 96 --k-min 25 -1 r1.fq -2 r2.fq -o megahit

I've also tried to resume with megahit --continue -o megahit and get the same.

Here's the error:

2020-08-04 06:52:27 - MEGAHIT v1.2.9
2020-08-04 06:52:27 - Using megahit_core with POPCNT and BMI2 support
2020-08-04 06:52:27 - passing check point 0
2020-08-04 06:52:27 - passing check point 1
2020-08-04 06:52:27 - Start assembly. Number of CPU threads 96 
2020-08-04 06:52:27 - k list: 25,35,45,55,65,75,85,95,105,115,125,135,141 
2020-08-04 06:52:27 - Memory used: 593496225792
2020-08-04 06:52:27 - passing check point 2
2020-08-04 06:52:27 - passing check point 3
2020-08-04 06:52:27 - passing check point 4
2020-08-04 06:52:27 - passing check point 5
2020-08-04 06:52:27 - passing check point 6
2020-08-04 06:52:27 - passing check point 7
2020-08-04 06:52:27 - passing check point 8
2020-08-04 06:52:27 - passing check point 9
2020-08-04 06:52:27 - passing check point 10
2020-08-04 06:52:27 - passing check point 11
2020-08-04 06:52:27 - passing check point 12
2020-08-04 06:52:27 - passing check point 13
2020-08-04 06:52:27 - passing check point 14
2020-08-04 06:52:27 - passing check point 15
2020-08-04 06:52:27 - passing check point 16
2020-08-04 06:52:27 - passing check point 17
2020-08-04 06:52:27 - passing check point 18
2020-08-04 06:52:27 - passing check point 19
2020-08-04 06:52:27 - passing check point 20
2020-08-04 06:52:27 - passing check point 21
2020-08-04 06:52:27 - passing check point 22
2020-08-04 06:52:27 - passing check point 23
2020-08-04 06:52:27 - Assemble contigs from SdBG for k = 75 
2020-08-04 06:52:27 - command conda/2b731b54/bin/megahit_core assemble -s megahit/tmp/k75/75 -o megahit/intermediate_contigs/k75 -t 96 --min_standalone 300 --prune_level 2 --merge_len 20 --merge_similar 0.95 --cleaning_rounds 5 --disconnect_ratio 0.1 --low_local_ratio 0.2 --cleaning_rounds 5 --min_depth 2 --bubble_level 2 --max_tip_len -1 --careful_bubble
2020-08-04 06:52:27 - b'INFO  main_assemble.cpp             :  129 - Loading succinct de Bruijn graph: megahit/tmp/k75/75FATAL utils/utils.h                 :  172 - Invalid format. Expect field k, got'
2020-08-04 06:52:27 - Error occurs, please refer to megahit/log for detail
2020-08-04 06:52:27 - Command: conda/2b731b54/bin/megahit_core assemble -s megahit/tmp/k75/75 -o megahit/intermediate_contigs/k75 -t 96 --min_standalone 300 --prune_level 2 --merge_len 20 --merge_similar 0.95 --cleaning_rounds 5 --disconnect_ratio 0.1 --low_local_ratio 0.2 --cleaning_rounds 5 --min_depth 2 --bubble_level 2 --max_tip_len -1 --careful_bubble; Exit code 1

Any help wold be appreciated.

tdido commented 4 years ago

For the record: I ran the exact same process with much more memory and the problem didn't happen.