Pregraph and contig modules work, but not map and scaff

[Kim]

I am using SOAPdenovo2 with 2x100 paired-end Illumina reads from a single lane, from both 200 and 800 bp insert libraries.  I am using the sparse pregraph module with the contig, map, and scaff assembler modules.  The sparse pregraph and contig modules seem to work fine, but nothing happens in the map and scaff modules.  The log file says that no reads were mapped to the contigs, and that no scaffolds were made.  But yet contigs were made.  It's weird how it dies after the contig step; maybe I left out an option during the pregraph that screwed up the later stages.  This happens to me with both the 63mer and the 127mer executable versions.  

My commands:

pregraph_sparse_127mer.v1.0.3 -s 200_800_reads.config -K 71 -z 378590000 -p 30 -o 71kmer 1>71kmer_pregraph.log 2>71kmer_pregraph.err

SOAPdenovo-127mer contig -g 71kmer -p 30 1>71kmer_contig.log 2>71kmer_contig.err

SOAPdenovo-127mer map -s 200_800_reads.config -g 71kmer -p 30 -k 71 1>71kmer_map.log 2>71kmer_map.err

SOAPdenovo-127mer scaff -g 71kmer -p 30 1>71kmer_scaff.log 2>71kmer_scaff.err

My config file:

max_rd_len=100

[LIB]

avg_ins=200

reverse_seq=0

asm_flags=3

rd_len_cutoff=3

rank=1

pair_num_cutoff=3

map_len=32

q1=/home/kdu224/sequences/N_lecontei_genome/filtered_fastq/200_R1_qfiltered.fastq

q2=/home/kdu224/sequences/N_lecontei_genome/filtered_fastq/200_R2_qfiltered.fastq

[LIB]

avg_ins=800

reverse_seq=0

asm_flags=3

rd_len_cutoff=3

rank=2

pair_num_cutoff=3

map_len=32

q1=/home/kdu224/sequences/N_lecontei_genome/filtered_fastq/800_R1_qfiltered.fastq

q2=/home/kdu224/sequences/N_lecontei_genome/filtered_fastq/800_R2_qfiltered.fastq

The first 10 lines of one of my fastq files (the quality scores are in phred+33): 

@HWI-ST354R:352:D11GRACXX:5:1101:1335:1949 1:N:0:ACTTGAA

CAAAAACTTCTATAAAACATAGATTTGAAATTTTTTACTAAAGCTAACTTAGTTGCAACCAAATAAAAACTGTGGTCTACATAGCACAGAAAAAAGTT

+

=DDDBBHFFFDIGIIIIIIIIEHIIEGIIGGEDGCGCHHHIIGHIHCDDBDGGFEFBGGIIIGGIGHHIEEHHHDFFFFFECEECECC?AC@<??=>A

@HWI-ST354R:352:D11GRACXX:5:1101:1445:1960 1:N:0:ACTTGAA

TACTCGGAGAGATTCGATTTTGGACGGCGAGTCGAGAACTCGGAGAATTGAAAAAAAAAAAAAAAAATAAACGGAAATTTGAAACGGGATTGATAA

+

=DFFFFGFHDHDHIIJJJJJJIJHGIJEGEIHGHIJCEE?EDFFDBDDDDCCDCDDDDBDDDD&5>B1@CC4<<?@<:AAC>@CA?B55-93::>C

@HWI-ST354R:352:D11GRACXX:5:1101:1325:1982 1:N:0:ACTTGAA

TTTTATTGCATACCTTTTTTTGTATAATACATTGTGCTCAACATGTTCTGCTGTGTCAACTTAACTGGACCACCTCATATAATGGGTTGTAAACTATAAA

The log files for each module are attached.  The same pattern of no mapped reads and no scaffolds made is also seen for 51, 61 and 81 kmer sizes (51 and 61 kmer were run with the 63mer executables).  

[黄伟华]

The rd_len_cutoff in the config file should be set to the length of read(e.g. 100).

 

---

Weihua Huang

BGI shenzhen

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