ERROR : no pa file and Error no information for 0

[HLHsieh]

Hi there,

I followed the instructions you provided in #53 and ran each loci one-by-one instead using 'all' option for Fastq input, but I encountered an error message regarding the lack of gene/repeat information.

python /home/bin/RepeatHMM/bin/repeatHMM.py FASTQinput --fastq /home/C9ORF72_c3_stimulated/C9ORF72_c3_NanoSim_2x/C9ORF72_c3_NanoSim_2x.fasta --hg hg38 --hgfile --Patternfile /home/reference/myDefinedRepeat_chr9.bed --outFolder /home/C9ORF72_c3_stimulated/C9ORF72_c3_NanoSim_2x/repeatHMM_logfq

Error message:

('No pa file ', '/home//miniconda3/envs/repeathmmenv/lib/python2.7/site-packages/RepeatHMM/reference_sts//hg38/hg38.predefined.pa')
!!!Error: !!!!!! 
        None gene/repeat information is given. 

As suggested in #43, I could proceed with using only the bed file, so I ignore this message. However, for gene/repeat information, I am using a bed file that contains only one target of interest as follows, and I am unsure how to provide the corresponding gene/repeat information for this target. I would appreciate any suggestions you may have on this matter.

chr9    27573494        27573708        GGCCCC

I tried to fix this problem by specifying the repeatName as C9ORF72, since the target tandem repeat is located in that gene. However, I received an error message as follows:

python /home/bin/RepeatHMM/bin/repeatHMM.py FASTQinput --fastq /home/C9ORF72_c3_stimulated/C9ORF72_c3_NanoSim_2x/C9ORF72_c3_NanoSim_2x.fasta --hg hg38 --hgfile --Patternfile /home/reference/myDefinedRepeat_chr9.bed --outFolder /home/C9ORF72_c3_stimulated/C9ORF72_c3_NanoSim_2x/repeatHMM_logfq --repeatName C9ORF72

Error message:

('Error no information for 0\nError no information for 1\nError no information for 2\nError no information for 3\nError no information for 4\n', ['', '', '', '', '', '', ''], 'c9orf72')

Additionally, I noticed that the algorithm in Usage.md is designed for trinucleotide repeats. I was wondering if RepeatHMM is applicable to other types of repeats and if there are any length limits.

Thank you very much for your time and assistance.

Best,
Hsin

[liuqianhn]

@HLHsieh Please try to use --Patternfile with a .pa file. RepeatHMM can be used for any types of repeats, although we previously tested trinucleotide repeats.

[HLHsieh]

Hi @liuqianhn ,

Thank you for your quick reply. I just wanted to confirm whether it is still possible to use a .bed file with BAMinput and FASTQinput. Additionally, I was hoping you could provide more information on how to define my .pa file, especially for the last three columns (5.strand, 6.range, 7.others).

Thank you in advance for your assistance.

Best regards,
Hsin

[liuqianhn]

5.strand: + with a number for a repeat pattern as the reference genome, - with a number for a repeat as the complement of the reference number. But usually only +/- are used in the program. 
6.range : not used but for users' reference
7.others: not used but for users' reference

Additional, you can also specify repeat pattern using --UserDefinedRepeat. Also, use --Patternfile /Users/xxxxxxxxxxxxxxxxxxxxxxxxxx/RepeatHMM/bin/reference_sts/hg38/hg38.predefined.pa can avoid the issue caused by the existence of .pa file.

I membered that .bed file is support for FASTQinput but not for BAMinput.