RNAseq demo (hisat2, stringtie) error at GBitVec: index 7 out of bounds (size 7) (osX and linux)

Data and codes are downloaded from ftp://ftp.ccb.jhu.edu/pub/RNAseq_protocol/ 

Byte-5:sva hqin$ ps

  PID TTY           TIME CMD

49035 ttys000    0:00.08 -bash

51361 ttys000    0:00.01 bash ./rnaseq_pipeline.sh out

51377 ttys000    0:00.03 bash ./rnaseq_pipeline.sh out

51378 ttys000    0:00.00 tee ./run.log

52036 ttys000    0:00.07 perl /Users/hqin/bin/hisat2 -p 8 --dta -x /Users/hqin/demo.lgf/RNAseq.hisat2/chrX_data/indexes/

52044 ttys000    0:00.49 perl /Users/hqin/bin/hisat2 -p 8 --dta -x /Users/hqin/demo.lgf/RNAseq.hisat2/chrX_data/indexes/

52045 ttys000    0:00.49 perl /Users/hqin/bin/hisat2 -p 8 --dta -x /Users/hqin/demo.lgf/RNAseq.hisat2/chrX_data/indexes/

52046 ttys000    3:02.29 /Users/hqin/bin/hisat2-align-s --wrapper basic-0 -p 8 --dta -x /Users/hqin/demo.lgf/RNAseq.hisa

52047 ttys000    0:00.31 gzip -dc /Users/hqin/demo.lgf/RNAseq.hisat2/chrX_data/samples/ERR188401_chrX_2.fastq.gz

52048 ttys000    0:00.31 gzip -dc /Users/hqin/demo.lgf/RNAseq.hisat2/chrX_data/samples/ERR188401_chrX_1.fastq.gz

  492 ttys001    0:00.21 -bash

51812 ttys002    0:00.02 -bash

51867 ttys002    0:11.01 tar xvfz hg38_tran.tar.gz

Byte-5:samtools hqin$ cd

Byte-5:~ hqin$ cd demo.lgf/

Byte-5:demo.lgf hqin$ cd RNAseq.hisat2/

Byte-5:RNAseq.hisat2 hqin$ ./rnaseq_pipeline.sh out

ERROR: samtools program not found, please edit the configuration script.

Byte-5:RNAseq.hisat2 hqin$ source /Users/hqin/.bash_profile

Byte-5:RNAseq.hisat2 hqin$ ./rnaseq_pipeline.sh out

[2016-11-14 15:07:24] #> START:  ./rnaseq_pipeline.sh out

[2016-11-14 15:07:24] Processing sample: ERR188044_chrX

[2016-11-14 15:07:24]    * Alignment of reads to genome (HISAT2)

[2016-11-14 15:07:56]    * Alignments conversion (SAMTools)

[2016-11-14 15:08:40]    * Assemble transcripts (StringTie)

[2016-11-14 15:08:51] Processing sample: ERR188104_chrX

[2016-11-14 15:08:51]    * Alignment of reads to genome (HISAT2)

[2016-11-14 15:09:37]    * Alignments conversion (SAMTools)

[2016-11-14 15:10:24]    * Assemble transcripts (StringTie)

[2016-11-14 15:10:36] Processing sample: ERR188234_chrX

[2016-11-14 15:10:36]    * Alignment of reads to genome (HISAT2)

[2016-11-14 15:11:11]    * Alignments conversion (SAMTools)

[2016-11-14 15:12:23]    * Assemble transcripts (StringTie)

[2016-11-14 15:12:45] Processing sample: ERR188245_chrX

[2016-11-14 15:12:45]    * Alignment of reads to genome (HISAT2)

[2016-11-14 15:13:45]    * Alignments conversion (SAMTools)

[2016-11-14 15:14:40]    * Assemble transcripts (StringTie)

[2016-11-14 15:14:51] Processing sample: ERR188257_chrX

[2016-11-14 15:14:51]    * Alignment of reads to genome (HISAT2)

[2016-11-14 15:15:42]    * Alignments conversion (SAMTools)

[2016-11-14 15:16:50]    * Assemble transcripts (StringTie)

[2016-11-14 15:17:04] Processing sample: ERR188273_chrX

[2016-11-14 15:17:04]    * Alignment of reads to genome (HISAT2)

[2016-11-14 15:17:50]    * Alignments conversion (SAMTools)

[2016-11-14 15:18:34]    * Assemble transcripts (StringTie)

[2016-11-14 15:18:44] Processing sample: ERR188337_chrX

[2016-11-14 15:18:44]    * Alignment of reads to genome (HISAT2)

[2016-11-14 15:21:18]    * Alignments conversion (SAMTools)

[2016-11-14 15:22:44]    * Assemble transcripts (StringTie)

[2016-11-14 15:23:09] Processing sample: ERR188383_chrX

[2016-11-14 15:23:09]    * Alignment of reads to genome (HISAT2)

[2016-11-14 15:25:31]    * Alignments conversion (SAMTools)

[2016-11-14 15:27:13]    * Assemble transcripts (StringTie)

[2016-11-14 15:27:36] Processing sample: ERR188401_chrX

[2016-11-14 15:27:36]    * Alignment of reads to genome (HISAT2)

[2016-11-14 15:31:58]    * Alignments conversion (SAMTools)

[2016-11-14 15:33:53]    * Assemble transcripts (StringTie)

[2016-11-14 15:34:12] Processing sample: ERR188428_chrX

[2016-11-14 15:34:12]    * Alignment of reads to genome (HISAT2)

[2016-11-14 15:35:46]    * Alignments conversion (SAMTools)

[2016-11-14 15:36:44]    * Assemble transcripts (StringTie)

[2016-11-14 15:36:59] Processing sample: ERR188454_chrX

[2016-11-14 15:36:59]    * Alignment of reads to genome (HISAT2)

[2016-11-14 15:39:12]    * Alignments conversion (SAMTools)

[2016-11-14 15:40:34]    * Assemble transcripts (StringTie)

[2016-11-14 15:40:50] Processing sample: ERR204916_chrX

[2016-11-14 15:40:50]    * Alignment of reads to genome (HISAT2)

[2016-11-14 15:41:50]    * Alignments conversion (SAMTools)

[2016-11-14 15:43:03]    * Assemble transcripts (StringTie)

[2016-11-14 15:43:18] #> Merge all transcripts (StringTie)

[2016-11-14 15:43:29] #> Estimate abundance for each sample (StringTie)

Error at GBitVec: index 7 out of bounds (size 7)

Byte-5:RNAseq.hisat2 hqin$ 

Rerun the shell at Linux (ridgeside) same error:
Error at GBitVec: index 7 out of bounds (size 7)
./rnaseq_pipeline.sh: line 82:  7126 Segmentation fault      (core dumped) $STRINGTIE -e -B -p $
NUMCPUS -G ${BALLGOWNLOC}/stringtie_merged.gtf -o ${BALLGOWNLOC}/${dsample}/${dsample}.gtf ${ALI
GNLOC}/${sample}.bam


Download v.1.3.1b, rerun the shell script at osX
... ... 

[2016-11-15 14:04:53] #> Merge all transcripts (StringTie)

[2016-11-15 14:04:57] #> Estimate abundance for each sample (StringTie)

Error at GBitVec: index 9 out of bounds (size 9)

./rnaseq_pipeline.sh: line 82:  2422 Abort trap: 6           $STRINGTIE -e -B -p $NUMCPUS -G ${BALLGOWNLOC}/stringtie_merged.gtf -o ${BALLGOWNLOC}/${dsample}/${dsample}.gtf ${ALIGNLOC}/${sample}.bam

Byte-5:RNAseq.hisat2 hqin$ stringtie -v

Command line was:

stringtie -v

StringTie v1.3.1b usage: