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5.9 years ago
zeynep
▴
10
I am trying to run HLAScan but so far I failed to get results, it always says "HLAscan cannot determine proper types".
I am getting results with every other tool I tried, only HLAScan fails to report a result!
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1671-3
Please double check that you are doing everything as per the manual. Paste your commands here, if you wish, and tell us from where your reads originate.
Have you find the solution to deal with this question? If you have ahcieve it,can you supply your solution, Thank you
Which error are you receiving, 438410826?
It's always pritn "can't determine type".May be I don't uncompress my fastq file.It cause software can't read it. But thank for you reply. My name is Shiqi Li,from China
Hello Shiqi Li. What is the command that you used?
The follow is my command: ./hla_scan_r_v2.1.2 -t 6 -l R1.fastq.gz.paired.fq -r R2.fastq.gz.paired.fq -d data-set/db/HLA-ALL.IMGT -g HLA-A HLA-B HLA-C &>>eo & I have solved problem that "can't determine type",But when I run this command,It will Exit and in the file eo I found there print "===================================================== HLAscan v2.1 Report created
2018. 8. 15. 8:56:41
HLA gene : HLA-A
of considered types : 3182
----------- HLA-Types ----------- [Type 1] 02:03:06 EX3_232.286_100 EX2_99.2556_100 EX4_89.8623_85 EX5_246.248_100 [Type 2] 02:07:05 EX3_222.725_100 EX2_99.2667_100 EX4_11.5906_56.6667 EX5_246.248_100 " I don't know if you met this situation! Best regards.
It seems that the program identified that your samples are HLA-A. Is this correct?
But I don't know why I can't get relatively output? And have you met similar problem?
What do you mean by 'relatively output'?
It means that I can't get corresponding result.May be I made a mistake expression.I'm so sorry
Do not worry, my friend. Perhaps you can contact the developers of the program: https://omictools.com/hlascan-tool
From what I can see, the program result is HLA-A, that is, the program identified that your sample sequence data contained HLA Class A.
I used new data for run this software,But it needs time is too long.In fact I have contact with author,But can't solve problem that I met
The execution time of HLAscan is too long when input fastq data is too large, because HLAscan self-align all reads in fastq with IMGT/HLA database. In this case, firstly, make bam file using alignments tools (ex: BWA-MEM), and then execute HLAscan. The execution time of HLAscan is fast (<2min for HLA-A,B,C and <30sec for others).
I met the similar problem.When I input fastq files for running, I got the EXIT and KILLED.The log is below: HLAscan v5.0 Report created
2019. 3. 29. 19:41:7
HLA gene : HLA-E
of considered types : 17
----------- HLA-Types ----------- [Type 1] 01:03:02:01 EX3_497.134_100 EX2_280.156_100 EX4_681.949_100 EX5_306.479_100 [Type 2] 01:03:01:01 EX3_497.134_100 EX2_264.293_100 EX4_681.949_100 EX5_306.479_100
My command is "./hla_scan_r_v2.0 -l normal_wes_R1.fq -r normal_wes_R2.fq -d ./db/HLA-ALL.IMGT -v 37 -g HLA-E -t 2 > HLA-E.log ".
So I want to know what's wrong ?And if I need to input bam file ,do I run FixMateInformation,Markdupliates,RealignerTargetCreator and IndelRealigner after runing bwa-mem ? And is the reference genome IMGT/HLA database or hg19 fasta?
thx~
Hopefully the author can help. She / He will know their program better than anybody here.
Yes,you are right.Thank for your answer my questions.Best regards
Did you get any answer? I have the exactly same problem. In the Mac terminal I was not able to run it and after changing to Ubuntu, I always end up with the 'HLAscan cannot determine proper types' message
Were you able to solve this problem? 'HLAscan cannot determine proper types' message I am having the same problem.
Did you try to contact the developer of HLAscan?
Yes, no answer yet.
I will contact them.
Hello. For each gene, HLAscan is executed independently. In command, just type a gene after "-g" option.
Hi. This is very basic question but I am trying to run HLAscan and getting error.
I was trying to get DB for HLA-A. The documentation shows that I need DB like this.
(1) DB HLA-ALL.IMGT : IMGT/HLA database
But I don't really understand how to input the correct database. But how do I combine all the HLA database like you did from the IMGT ftp? -d data-set/db/HLA-ALL.IMGT
Thanks in advance.
Maybe you can get DB from this url:
You can find this url from HLAScan website.
Inside the zipped file from the url provided by @airexpend inside of data-set/db/ folders named HLA-ALL.IMGT. just addd it in front of -d command.
Thanks I was able to download the data-set/db/HLA-ALL.IMGT.
Have you solved the problem?I used fastq files to run HLAscan, and the result returned EXIT.I don't know what the problem is, could you please answer it ~ thank you