NGS Whole genome pipeline hang at run.assembly.realign.sh

[NTNguyen13]

Hi, I am trying out SpecHLA using example data.
I have installed and indexed the tool according with some modification, because the shared library is missing when using bowtie2 from bin directory => I installed bowtie2 by conda, and changed the path in index.sh

(the error when using direct bowtie2 SpecHLA/bin/bowtie2/bowtie2-align-s: error while loading shared libraries: libtbb.so.2: cannot open shared object file: No such file or directory)

When I used the script: bash SpecHLA.sh -n test_wgs -1 HG00118_1.filter.fastq.gz -2 HG00118_2.filter.fastq.gz -p Caucasian -o output
it hanged at run.assembly.realign.sh. I checked the log file (test_wgs.local_assem.log), the last 5 lines are:

SpecHLA/script/../bin/fermikit/fermi.kit/bfc -1s 1k -k 10 -t 5 output/test_wgs/prefix2.ec.fq.gz 2> output/test_wgs/prefix2.flt.fq.gz.log | gzip -1 > output/test_wgs/prefix2.flt.fq.gz
SpecHLA/script/../bin/fermikit/fermi.kit/ropebwt2 -dNCr output/test_wgs/prefix2.flt.fq.gz > output/test_wgs/prefix2.flt.fmd 2> output/test_wgs/prefix2.flt.fmd.log
SpecHLA/script/../bin/fermikit/fermi.kit/fermi2 assemble -l 40 -m 53 -t 5 output/test_wgs/prefix2.flt.fmd 2> output/test_wgs/prefix2.pre.gz.log | gzip -1 > output/test_wgs/prefix2.pre.gz
SpecHLA/script/../bin/fermikit/fermi.kit/fermi2 simplify -CSo 45 -m 53 -T 40 output/test_wgs/prefix2.pre.gz 2> output/test_wgs/prefix2.mag.gz.log | gzip -1 > output/test_wgs/prefix2.mag.gz
"output/test_wgs/prefix2.mag.gz" may be a binary file.  See it anyway? 

the file output/test_wgs/prefix2.mag.gz is empty

Could you please help me debug this issue please?

[wshuai294]

Hello, we have solved this bug which is caused by the confusion of the Linus orders less and zless.