Hello,
I have been trying to de novo assemble a transcriptome from Illumina paired end reads using IDBA-TRAN. Following the input requirement for interlaced fastA file, I first interlaced fastq file, then trimmed the ends based on quality score, and then converted fastq to fasta and used that as short read input for IDBA-TRAN.
After 6 and a half hours, the job finished without errors (green), but the output is 0 bytes. There are no output files, also not hidden. stderr is empty, and stdout says:
number of threads 1
reads 39947710
long reads 0
reads 35990640
long reads 0
read_length 60
kmer 20
kmers 61114274 61358568
merge bubble 64508
contigs: 2860843 n50: 39 max: 2135 mean: 39 total length: 111904454 n80: 22
contigs: 479802 n50: 218 max: 5846 mean: 107 total length: 51719613 n80: 63
contigs: 56207 n50: 779 max: 5846 mean: 682 total length: 38382589 n80: 440
aligned 14342471 reads
confirmed bases: 21420332 correct reads: 10271584 bases: 1869872
distance mean 117.682 sd 13.2224
seed contigs 60342 local contigs 959604
kmer 30
kmers 58216282 58094590
merge bubble 3521
contigs: 2176161 n50: 57 max: 3356 mean: 54 total length: 119061165 n80: 32
contigs: 346235 n50: 252 max: 8510 mean: 158 total length: 54876331 n80: 89
contigs: 64352 n50: 1016 max: 10697 mean: 818 total length: 52689690 n80: 513
aligned 19083034 reads
confirmed bases: 24375021 correct reads: 13940231 bases: 838227
distance mean 117.779 sd 13.2481
seed contigs 62230 local contigs 692470
kmer 40
kmers 54776504 54539913
merge bubble 1186
contigs: 1587800 n50: 72 max: 3356 mean: 71 total length: 113399504 n80: 42
contigs: 273653 n50: 286 max: 9584 mean: 197 total length: 53921293 n80: 114
contigs: 64630 n50: 1034 max: 10694 mean: 829 total length: 53614987 n80: 520
aligned 21303172 reads
confirmed bases: 25661370 correct reads: 15801920 bases: 425639
distance mean 117.871 sd 13.2686
seed contigs 65220 local contigs 547306
kmer 50
kmers 49860512 49600886
merge bubble 602
contigs: 1142951 n50: 95 max: 3437 mean: 89 total length: 102612799 n80: 53
contigs: 221570 n50: 335 max: 9831 mean: 235 total length: 52174887 n80: 132
contigs: 60226 n50: 1025 max: 16280 mean: 822 total length: 49525736 n80: 515
aligned 23208851 reads
confirmed bases: 26991623 correct reads: 17178702 bases: 314873
distance mean 117.878 sd 13.3256
seed contigs 66651 local contigs 443140
kmer 60
kmers 44861387 44655122
merge bubble 295
contigs: 785451 n50: 124 max: 4086 mean: 111 total length: 87783277 n80: 63
contigs: 229351 n50: 349 max: 8750 mean: 229 total length: 52549323 n80: 138
contigs: 58836 n50: 996 max: 14065 mean: 808 total length: 47550068 n80: 507
aligned 21889836 reads
confirmed bases: 27616209 correct reads: 16067435 bases: 76623
distance mean 117.852 sd 13.2698
seed contigs 67611 local contigs 458702
What could the reason be?
Best,
Milan