VICUNA error: Contiger::update_rcMap SC failed

[Tamer Mansour]

Hi,

VICUNA is giving me this error

--------------------------------------------------------

Program runs with the following Parameter setting:

===== Trimmer =====

vectorFileName

trimLogFileName

minMSize 9

minInternalMSize 15

maxOverhangSize 2

minReadSize 25

===== Profiler =====

MSAFileName

binNumber 20

kmerLength 15 (encode using 4 bytes)

maxHD 1

minSpan 75

blockNumber 5

rMapFileName

===== Contiger =====

w1 12

w2 5

Divergence 8

max_read_overhang 2

min_profile_col_weight 5

min_consensus_base_ratio 85

max_contig_overhang 10

seed_kmer_len 12

min_contig_overlap 25

min_contig_links 3

min_identity 90

min_perc_polymorphism 5

max_variant_len 20

===== Assembly =====

pFqDir /mnt/lustre_scratch_2012/Tamer/AF227/bowtie_output/allTumorsVsAllViruses3/reads/

npFqDir /mnt/lustre_scratch_2012/Tamer/AF227/bowtie_output/allTumorsVsAllViruses3/reads_np/

batchSize 1000000

LibSizeLowerBound 100

LibSizeUpperBound 800

min_output_contig_len 200

outputDIR /mnt/lustre_scratch_2012/Tamer/AF227/bowtie_output/allTumorsVsAllViruses3/allGenomes/vincuna/

--------------------------------------------------------

Indexing ...

/mnt/lustre_scratch_2012/Tamer/AF227/bowtie_output/allTumorsVsAllViruses3/reads//s_2.fq

/mnt/lustre_scratch_2012/Tamer/AF227/bowtie_output/allTumorsVsAllViruses3/reads//s_1.fq

Indexing ...

/mnt/lustre_scratch_2012/Tamer/AF227/bowtie_output/allTumorsVsAllViruses3/reads_np//s_se.fq

s_2.fq #reads: 2109993

s_1.fq #reads: 2109993

s_se.fq #reads: 301626

Total # Input Reads: 4521612

Indexing done !!! *** 0.268952 mins ***

-----------------------------------------------------------

Trimming ...

no vector trimming applied.

Writing trim logs to file: /mnt/lustre_scratch_2012/Tamer/AF227/bowtie_output/allTumorsVsAllViruses3/allGenomes/vincuna/trim.log

Number of Reads Trimmed by Heads, Tails, Full, Total:

0(-nan%total) 0(-nan%total) 0(-nan%total) 0

Number of low complexity reads: 90743

Number of trimmed read-pairs: 474 ( inf %total)

Trimming done !!! *** 0.40754 mins ***

-----------------------------------------------------------

No MSA file specified, Profiler Skipped

Profiling done !!! *** 6.99361e-07 mins ***

-----------------------------------------------------------

Building Contigs ...

create super shingles for 4521612 reads

*** 0.724548 mins ***

Clustering via super-shingles

*** 0.0707701 mins ***

Init contigs

no. initial contigs: 139452

no. reads involved: 4359880

*** 1.76926 mins ***

seed_template = 1101101111100110000111111

STable size: 253523

no. contigs: 142506

no. reads involved: 4430513

*** 2.07856 mins ***

Validate contigs

no. resulting contigs: 110696

no. reads involved: 4412320

*** 6.64508 mins ***

Merge contigs via rID

*** 0.88919 mins ***

Validate contigs

no. resulting contigs: 6461

no. reads involved: 4404669

Extend contigs

no. contigs to be extended: 6461

[EXIT]: Contiger::update_rcMap SC failed

Thank you for help

Regards

Tamer Mansour

[Xiao Yang]

Hi Tamer,

Could you try disable the use of s_se.fq file and see if the problem remains ?

I have not thoroughly tested the use of singleton fq files. 

thanks,

Xiao

Tamer Mansour

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- Xiao

[Tamer Mansour]

Yes, this is the problem

Thank you