Did anyone manage to successfully run HLAScan and get results?
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4.3 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

HLA-Typing NGS • 4.2k views
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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.

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Have you find the solution to deal with this question? If you have ahcieve it,can you supply your solution, Thank you

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Which error are you receiving, 438410826?

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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

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Hello Shiqi Li. What is the command that you used?

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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.

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It seems that the program identified that your samples are HLA-A. Is this correct?

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But I don't know why I can't get relatively output? And have you met similar problem?

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What do you mean by 'relatively output'?

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It means that I can't get corresponding result.May be I made a mistake expression.I'm so sorry

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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.

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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

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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).

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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~

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Hopefully the author can help. She / He will know their program better than anybody here.

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Yes,you are right.Thank for your answer my questions.Best regards

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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

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Were you able to solve this problem? 'HLAscan cannot determine proper types' message I am having the same problem.

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Did you try to contact the developer of HLAscan?

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Yes, no answer yet.

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I will contact them.

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Hello. For each gene, HLAscan is executed independently. In command, just type a gene after "-g" option.

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Hi. This is very basic question but I am trying to run HLAscan and getting error.

$ ./hla_scan -l NS_L001_R1_001.fastq.gz -d A_gen.fasta
HLA-A
ERROR: wrong HLA gene

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.

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Maybe you can get DB from this url:

http://www.genomekorea.com/download/attachments/8192004/data-set.zip?version=2&modificationDate=1520919371000&api=v2

You can find this url from HLAScan website.

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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.

$ ./hla_scan -l NS_L001_R1_001.fastq.gz -d data-set/db/HLA-ALL.IMGT
-g HLA-A
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Thanks I was able to download the data-set/db/HLA-ALL.IMGT.

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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

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