scotty323

[lzc@localhost lotusbam]$ ../rascaf-join -r WT2.out -o WT2join -ms 20 Found raw assembly file: /home/lzc/CJM_reseq/rascaf/lotusbam/Lotus_mega_gap1M.fa Segmentation fault (core dumped) [lzc@localhost lotusbam]$ ls Lotus_mega_gap1M.fa Lotus_mega_gap1M.fa.header Lotus_mega_gap1Munix.fa.header nohup.out SRR2052526_0.out SRR2052526.bam SRR2052526raslog WT2_0.out WT2.bam...

Hi Li, Rascalf ran Ok. See bellow. The error occurred when I ran rascaf-join. [lzc@localhost lotusbam]$ ../rascaf -b WT2.bam -f Lotus_mega_gap1M.fa.header.fa -o WT2 -ms 20 Found 443702 exon blocks. Found...

[lzc@localhost lotusbam]$ ../rascaf -b WT2.bam -f Lotus_mega_gap1M.fa.header.fa -o WT2 -ms 20 Found 443702 exon blocks. Found 175543 gene blocks. Found 5247 non-trivial gene block components. [lzc@localhost lotusbam]$ [lzc@localhost lotusbam]$ ../rascaf-join...

The bam file was sorted. error still occur [lzc@localhost lotusbam]$ samtools sort WT2.bam -o WT2sort [bam_sort_core] merging from 17 files... [lzc@localhost lotusbam]$ ../rascaf -b WT2sort.bam -f Lotus_mega_gap1M.fa.header.fa -o WT2sort Found...

60553785 + 0 in total (QC-passed reads + QC-failed reads) 4961784 + 0 secondary 0 + 0 supplementary 0 + 0 duplicates 60553785 + 0 mapped (100.00% : N/A) 55592001...

it is aligned by Tophat