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aquaskyline / SOAPdenovo2

Next generation sequencing reads de novo assembler.
GNU General Public License v3.0
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reading too few reads? Not supporting gz format?! #63

Closed bitcometz closed 4 years ago

bitcometz commented 5 years ago

Hello, I try to run SOAPdenovo with around 10g data, however, It seems cannot properly reads the raw reads:

Pregraph

Parameters: pregraph -s config_file -d 1 -p 24 -K 37 -R -o s_1

In config_file, 1 lib(s), maximum read length 150, maximum name length 256.

24 thread(s) initialized. Import reads from file: path/s_1_HHMYJDSXX_L3_1.fq.gz Import reads from file: path/s_1_HHMYJDSXX_L3_2.fq.gz Time spent on hashing reads: 1s, 356 read(s) processed. LIB(s) information: [LIB] 0, avg_ins 350, reverse 0. 37344 node(s) allocated, 39516 kmer(s) in reads, 39516 kmer(s) processed. done hashing nodes 35172 kmer(s) removed. Time spent on delowcvgNode: 0s. 2098 linear node(s) marked. Time spent on marking linear nodes: 0s. Time spent on pre-graph construction: 1s.

Does it not support the gz format? I try to unzip the fq and it works well again.

Thanks!

aquaskyline commented 4 years ago

mostly likely due to a version problem of the gzip library you are linking to.

NiuNiuguohao commented 1 year ago

I met the same problem. Could you please tell me how did you fix it? Thanks!

HZAU-Wss commented 8 months ago

I had the same problem. 2 gigabytes of clean date can be run with ”spades“, but “soap” can only read 20,000 reads.