When running tulipbulb, at the last step of outputting scaffolds, it seems to output most of the scaffolds, but stops a few hundred scaffolds short.
Here's the contents of the bundle_log file:
dvera@host$ cat ~/tulipbulb/try1bulb.bundle_log
TULIP bundling 0.4 late 2016 (European eel)
Command line
/home/cgpm/dvera/software/TULIP/tulipbulb.perl --seeds ../tulipseed/allBfcMrg20_cov20-200_lgt459_first450_renamed.fa --reads ../tulipseed/pacbio_renamed.fa --sam ../tulipseed/pacbio_bwaK16_allBfcMrg20_cov20-200_lgt459_first450_renamed.sam --input ../tulipseed/try1 --memory 10000000 --diploid --out try1bulb
Directory
/home/cgpm/dvera/tulipbulb
19:07:47 Run started
19:07:47 Seed length is 450
19:07:47 Retrieving graph from ../tulipseed/try1.graph_tmp
19:08:00 Retrieving scaffolds from ../tulipseed/try1.scaffolds_tmp
19:08:00 Retrieving scaffold seeds from ../tulipseed/try1.seeds_tmp
19:08:17 2387981 seeds in the graph
19:08:18 Bundling sam coordinates from ../tulipseed/pacbio_bwaK16_allBfcMrg20_cov20-200_lgt459_first450_renamed.sam with reads from ../tulipseed/pacbio_renamed.fa
21:00:01 4612747 long reads bundled for scaffold correction
21:00:01 Adding seed sequences from ../tulipseed/allBfcMrg20_cov20-200_lgt459_first450_renamed.fa
21:00:17 Sequences found for 2387981 seeds
21:00:17 Writing scaffold sequences to try1bulb_scaffold_nr.fasta
21:04:34 1487887540 nt written to 10277 scaffolds
21:04:34 Run ended
Here's what it outputs to the terminal:
dvera@host$ ~/software/TULIP/tulipbulb.perl --seeds ../tulipseed/allBfcMrg20_cov20-200_lgt459_first450_renamed.fa --reads ../tulipseed/pacbio_renamed.fa --sam ../tulipseed/pacbio_bwaK16_allBfcMrg20_cov20-200_l[8/1894]
rst450_renamed.sam --input ../tulipseed/try1 --memory 10000000 --diploid --out try1bulb 2>&1 > stdouterr
Unknown option: diploid
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Negative repeat count does nothing at /home/cgpm/dvera/software/TULIP/tulipbulb.perl line 313, <FASTA> line 5359550.
Hello,
When running tulipbulb, at the last step of outputting scaffolds, it seems to output most of the scaffolds, but stops a few hundred scaffolds short.
Here's the contents of the bundle_log file:
Here's what it outputs to the terminal: