Error parsing track line key=value pairs
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There is an error for in the key values that are used in the track line. Example key value pairs are: track name="HSMv12.1" description="AmpliSeq Pool HSMv12.1" version="Ampliseq.com1.0" type="bedDetail".
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Review the BED file and ensure that the value pairs are correct.
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Error parsing track line, no closing quotes
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The closing quotes are missing from the key value pair in the first line (track line) of the BED file. For example: track name="HSMv12.1" description="AmpliSeq Pool HSMv12.1" version="Ampliseq.com1.0" type=bedDetail.
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Review the track line and add closing quotes.
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ionVersion track key is only valid with type=bedDetail
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A BED file that includes an IonVersion field must also have a type=bedDetail field.
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Review the first line (track line) of the BED file and ensure that the type=bedDetail and the ionVerison field are included.
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Field OBS cannot be the same as REF
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The strings used in the OBS and REF fields cannot be the same. Both fields cannot be ATC, for example.
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Change OBS=string so that it is not the same as the REF=string.
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Inconsistent number of columns
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Every line in the BED file must include the same number of columns.
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Review the BED file and ensure that every line in the file has the same number of columns.
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BED track line only allowed in the first line: All lines ignored after this one
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BED files allow only one track line in the first line of the header. An example track line is: track name="HSMv12.1" description="AmpliSeq Pool HSMv12.1" version="Ampliseq.com1.0" type=bedDetail".
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Remove the redundant track line.
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Line length exceeds 64K
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A line in the BED file exceeds 64K characters.
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Review the BED file and reduce the line length so that it is 64K or less.
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Unknown chromosome name
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A chromosome name in the BED file is not included in the FASTA file.
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Review the BED file and provide the correct chromosome name.
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Region start not in a valid range
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For hotspot BED file, the region start value is not in a targeted BED region.
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Remove this line.
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Region end not in a valid range
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For hotspots BED file, the region end value is not in a target bed region.
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Remove this line.
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Region start and end in reverse order
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The region end has a smaller value than the value for the start region.
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Ensure that the value for the region start has a smaller value than the value for the end region.
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Detail BED file with type=bedDetail must have between 5 and 14 columns
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The numbers of columns in a Detail BED file that includes type=bedDetail must have between 5 and 14 columns
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Review the number of columns in the BED file and ensure that there are between 5 and 14 columns.
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Hotspots BED file must have format type=bed
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Information is missing from the header of the BED file.
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Add format type=bedDetail to the file header of the hotspots BED file.
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BED file without type=bedDetail must have between 3 and 12 columns
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The number of columns for a BED file without type=bedDetail has the incorrect number of columns
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Review the number of columns in the BED file and ensure that there are between 3 and 12 columns.
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BED file contains no usable regions
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The BED file might be empty, or every line has at least one error.
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Ensure that you are using a BED file that is valid and correctly formatted.
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REF field contains characters other than ATCGatcg
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The alpha-numeric characters ATCG, or atcg, are not used in the REF field.
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Find the REF field in the custom BAM file. Ensure that the field is populated with characters that use the format ATCG or atcg.
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OBS field contains characters other than ATCGatcg
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The alpha-numeric characters ATCG, or atcg, are not used in the OBS field.
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Find the OBS field in the custom BAM file. Ensure that the field is populated with characters that use the format ATCG or atcg.
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ANCHOR field contains characters other than ATCGatcg
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The alpha-numeric characters ATCG, or atcg, are not used in the ANCHOR field.
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Find the ANCHOR field in the custom BAM file. Ensure that the field is populated with characters that use the format ATCG or atcg.
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REF field does not match content of reference fasta file
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The string for the REF sequence does not match the reference file.
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Look at the REF=string and ensure that string is the as the one at that position of the reference sequence from the FASTA file
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Mandatory OBS field not found |
A field is missing from the custom BED file.
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Add an OBS field to the custom BAM file. Ensure that the field is populated with characters that use the format ATCG or atcg.
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