Troubleshooting

1 Runtime Errors

1.1 “Unable to read from/write to …”

Arises when either the input or output file/stream can’t be opened. This may occur for a variety of reasons, including missing input files, incorrectly named files, hard disk space that is too small to open the output file, or a lack of permissions to write to a directory.

1.2 “Please provide a reference”

dupsifter needs a reference FASTA in order to infer the bisulfite strand if a strand tag is not found in the read. Add a reference to your command line invocation and try again. See the Usage page for help with running dupsifter.

1.3 “Reference must end in .fa/.fa.gz/.fasta/.fasta.gz”

This serves as a basic check that the correct file type is being used as the reference input. Check you have your inputs in the correct order and that any reference FASTA files have the proper extensions.

1.4 “Read with length (number) is longer than max read length”

Arises when dupsifter encounters a read that is longer than the specified max read length. This ensures that no reads would run beyond the specified padding around the chromosome lengths. Rerunning dupsifter with a longer max read length (the --max-read-length option) should resolve this issue.

1.5 “Can’t find read 1 and/or read 2 with read ID …”

Arises when input that isn’t read-name grouped is provided to dupsifter. This can be resolved by name sorting or collating your SAM/BAM with samtools sort -n or samtools collate and then providing the sorted input to dupsifter.

1.6 “No reads found in …”

The input file has no reads. This may be either from a completely empty file or a SAM/BAM file that has a header, but no reads. Double check the contents of your input.

1.7 “Read information is missing”

Can either occur for single/mate-unmapped reads or paired-end reads. Arises from an error reading a SAM entry. Check your input file to ensure it is not corrupted.

1.8 “Unknown cigar operation”

Arises when dupsifter encounters a CIGAR operation that it doesn’t recognize. This error is most likely to occur in versions 1.2.0 and earlier when you use input from tools that make use of extended CIGAR operations (= and X). If this is your issue, upgrading to at least version 1.2.1 should resolve your problem.

1.9 “Unknown orientation found”

Arises when a read orientation (see the Methodology page for details on read orientation) is encountered that dupsifter does not recognize. Please open an issue if you encounter this error.

1.10 “Unable to create argument list for PG string”

dupsifter failed to collect all command line arguments and form the PG SAM tag string. Try running dupsifter again.

1.11 “Failed to add PG tag to output header”

dupsifter could not write PG SAM tag to the SAM header for output. Likely due to a corruption in the SAM header of the input file itself or a lack of sufficient memory to add the PG tag contents to the header.

1.12 “Header writing failed”

dupsifter could not write the SAM header for output. May occur due to an inability to write to the output file or a corrupt SAM header.