hsnguyen
commented
6 years ago Thanks for reporting the bug! I have changed the code back to its previous working state, please update and re-compile the package and see if it works. Cheers,
Open wingwingWY opened 6 years ago
hsnguyen
commented
6 years ago Thanks for reporting the bug! I have changed the code back to its previous working state, please update and re-compile the package and see if it works. Cheers,
Hello, I run npScarf with nanopore reads for scaffolding spades assembly result. my shell is:
$myexe/jsa.seq.sort -r -n --input $inputfa --output sort_spades.fasta &> $outfile bwa index sort_spades.fasta &>> $outfile bwa mem -t 20 -x ont2d -a -Y sort_spades.fasta $reads >sort_spades.fasta.sam $myexe/jsa.np.npscarf --input sort_spades.fasta.sam --seqFile sort_spades.fasta --format sam --spadesDir ../output_spades_rmLong/ --verbose --prefix=npScarf &>> $outfile
It crashes with error:
Sort list of bridges
Starting scaffolding....... Extending 0 to the rear Last of scaffold 0 extention is on contig 0 (1-NODE_1_length_44147_cov_8.432349): iterating among 57 bridges ...10-NODE_10_length_15495_cov_30.258980 Exception in thread "main" java.lang.NullPointerException at japsa.bio.hts.scaffold.ContigBridge.display(ContigBridge.java:777) at japsa.bio.hts.scaffold.ScaffoldGraphDFS.walk2(ScaffoldGraphDFS.java:378) at japsa.bio.hts.scaffold.ScaffoldGraphDFS.connectBridges(ScaffoldGraphDFS.java:261) at japsa.tools.bio.np.NPScarfCmd.main(NPScarfCmd.java:286)