[error] Failed to extract reads from the specified region

[katerinaoleynikova]

Hello!

I have a problem while executing the main command. Option --locus as far as I understood requires an appropriate string of LocusID from the EH's outfile. For instance, as it follows in my result file (.json) (a fragment):
.. }, "ATXN10": { "AlleleCount": 2, "Coverage": 0.32432432432432434, "FragmentLength": 215, "LocusId": "ATXN10", "ReadLength": 150, "Variants": { "ATXN10": { "CountsOfFlankingReads": "()", "CountsOfInrepeatReads": "()", "CountsOfSpanningReads": "()", "ReferenceRegion": "chr22:46191234-46191304", "RepeatUnit": "ATTCT", "VariantId": "ATXN10", "VariantSubtype": "Repeat", "VariantType": "Repeat" } } ..
I tried to paste ATXN10 as an argument of --locus option, but have not gotten any success.

*btw, I have looked at Issue #2, particularly at the type of command from bw2. In his/her case, he/she got the EH's outfile with specified contig name and coordinates in LocusID:
"LocusId": "FXN-chr9-69037286-69037304-GAA". That makes me worried about that: possibly my outfile from EH is wrong?

Thank you so much!

[egor-dolzhenko]

Thank you for reporting the issue! It looks like you are doing everything correctly. EH was just unable to analyze this locus due to very low coverage ("Coverage": 0.32) and lack of informative reads ("CountsOfFlankingReads": "()", "CountsOfInrepeatReads": "()", "CountsOfSpanningReads": "()"). This repeat should be marked as "LowDepth" in the corresponding VCF file. EH requires that the read depth is at least 10.

The next version of REViewer will produce a better error message in such cases.

[katerinaoleynikova]

It sounds great! Thanks a lot, Egor!

[egor-dolzhenko]

Great! Happy to help!

[katerinaoleynikova]

Sorry, it's me again. I have checked another one:
}, "ATXN3": { "AlleleCount": 2, "Coverage": 11.837837837837837, "FragmentLength": 334, "LocusId": "ATXN3", "ReadLength": 150, "Variants": { "ATXN3": { "CountsOfFlankingReads": "()", "CountsOfInrepeatReads": "()", "CountsOfSpanningReads": "()", "Genotype": "0/0", "GenotypeConfidenceInterval": "0-714/0-714", "ReferenceRegion": "chr14:92537353-92537386", "RepeatUnit": "GCT", "VariantId": "ATXN3", "VariantSubtype": "Repeat", "VariantType": "Repeat" }
Here the coverage seems good, doesn't it? However, I have the same error(.

[Jolleboll]

I have this problem too, although my coverage is over 30:

"LocusResults": {
    "AFF2": {
      "AlleleCount": 2,
      "Coverage": 31.54054054054054,
      "FragmentLength": 352,
      "LocusId": "AFF2",
      "ReadLength": 150,
      "Variants": {
        "AFF2": {
          "CountsOfFlankingReads": "()",
          "CountsOfInrepeatReads": "()",
          "CountsOfSpanningReads": "()",
          "Genotype": "0/0",
          "GenotypeConfidenceInterval": "0-714/0-714",
          "ReferenceRegion": "X:147582151-147582211",
          "RepeatUnit": "GCC",
          "VariantId": "AFF2",
          "VariantSubtype": "Repeat",
          "VariantType": "Repeat"
        }
      }
    },

Not sure what's going on. I removed the entry from the catalog but got the same error still, at this one (the first one):

"AR": {
      "AlleleCount": 2,
      "Coverage": 41.91891891891891,
      "FragmentLength": 350,
      "LocusId": "AR",
      "ReadLength": 150,
      "Variants": {
        "AR": {
          "CountsOfFlankingReads": "(1, 2), (2, 2), (3, 3), (4, 1), (5, 1), (6, 2), (8, 6), (9, 1), (10, 3), (15, 3), (17, 1), (18, 3), (19, 5), (20, 2), (23, 1), (24, 1), (26, 1), (28, 1)",
          "CountsOfInrepeatReads": "()",
          "CountsOfSpanningReads": "(27, 16), (28, 9)",
          "Genotype": "27/28",
          "GenotypeConfidenceInterval": "27-27/28-28",
          "ReferenceRegion": "X:66765158-66765227",
          "RepeatUnit": "GCA",
          "VariantId": "AR",
          "VariantSubtype": "Repeat",
          "VariantType": "Repeat"
        }
      }
    },

I thought maybe the problem was that there are no InrepeatReads, but the problem remains if I only include catalog entries where all three read categories have members, e.g:

"LocusResults": {
    "RFC1": {
      "AlleleCount": 2,
      "Coverage": 41.513513513513516,
      "FragmentLength": 351,
      "LocusId": "RFC1",
      "ReadLength": 150,
      "Variants": {
        "RFC1": {
          "CountsOfFlankingReads": "(1, 2), (2, 2), (3, 3), (4, 2), (5, 2), (7, 2), (8, 5), (10, 2), (11, 1), (15, 1), (16, 1), (17, 2), (20, 1), (21, 1), (22, 1), (25, 1), (29, 4)",
          "CountsOfInrepeatReads": "(30, 15), (31, 1), (32, 1)",
          "CountsOfSpanningReads": "(10, 11), (15, 1)",
          "Genotype": "10/65",
          "GenotypeConfidenceInterval": "10-10/53-102",
          "ReferenceRegion": "4:39350044-39350099",
          "RepeatUnit": "AARRG",
          "VariantId": "RFC1",
          "VariantSubtype": "Repeat",
          "VariantType": "Repeat"
        }
      }
    }
  }

[2022-03-25 14:42:00.258] [info] Loading specification of locus RFC1
[2022-03-25 14:42:00.260] [error] Failed to extract reads from the specified region

What to do? :-(

REViewer-v0.2.7-linux_x86_64\
	--reads "$out"/exphout_"${sample}"_realigned.sorted.bam\
	--reference "$genome"\
	--catalog "$catalog"\
	--vcf exphout_"${sample}".vcf\
	--locus "RFC1"\
	--output-prefix "$out"/reviewerout_"${sample}"

Grateful for help with this! Am excited to see the pretty diagrams...