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DaehwanKimLab / hisat2

Graph-based alignment (Hierarchical Graph FM index)
GNU General Public License v3.0
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ERROR while aligning with HISAT2 #242

Open sekhwal opened 4 years ago

sekhwal commented 4 years ago

Hi, I am getting following ERROR message while aligning my data.

command: ./hisat2 -f -x ../hisat-trt/PEDV -U ../clean_trt.fasta -S ../trt.sam

ERROR: File "/home/kumarm/allan-work/hisat2-2.2.0/hisat2_read_statistics.py", line 182 length_map = sorted(length_map.iteritems(), key=lambda (k,v):(v,k), reverse=True) SyntaxError: invalid syntax 15065158 reads; of these: 15065158 (100.00%) were unpaired; of these: 15065081 (100.00%) aligned 0 times 77 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate

parkchanhee commented 4 years ago

Hi @sekhwal Python script in hisat2 only works on python2. We are converting these scripts to python3. Could you run it again in the python2 environment?

Actually, this error doesn't affect the alignment result.

sekhwal commented 4 years ago

Ok! Sounds good. Thanks!

sekhwal commented 4 years ago

However, if I am using the alignment .sam file further for variant calling with GATK. I am not getting any output vcf file.

parkchanhee commented 4 years ago

@sekhwal The alignment rate of the result is too low. Most of the reads are not aligned. Before calling variant, reads must be properly aligned.

sekhwal commented 4 years ago

How I can increase the alignment rate......

sekhwal commented 4 years ago

I tried with other files and used HISAT2 this time I am getting enough data in vcf file using GATK.