Import Job Errors
UE=User fixable or possible user error
KE=KBase error
Use your Browser's search tool to paste in the error to locate possible fixes or next steps.
You can always submit a ticket for help, questions, or follow-up to the KBase Help Board.
UE: The provided URL cannot be accessed from within KBase.
Recheck the URL and permissions. Then try resubmitting the job.
UE: The provided URL cannot be accessed from within KBase. Perhaps the option for ‘Direct’ download should be specified instead of ‘FTP’ (e.g., when downloading from the SRA)
Recheck the URL and permissions. Then try resubmitting the job.
UE: The provided URL cannot be accessed from within KBase.
Recheck the URL and its permission. Then try resubmitting the job.
UE: The file is not in the Staging Area.
Verify that the name is correct and upload is complete. Then try resubmitting the job.
KE: The fastqdump ran but the file names are not the expected names.
Use the long workaround here.
UE: The format of the file is not recognized.
Recheck the file and try resubmitting the job.
KE/UE: Sometimes the user has specified the file name wrong. It can also happen because the importer has problems with file names that end in ".1"
Use the long workaround here.
UE: The file does not appear to be in the expected SRA format.
Recheck the file and try resubmitting the job.
UE: The file could not be unzipped by KBase and most likely couldn’t be unzipped by the user either.
Verify the file is can be unzipped locally.
UE: The inputs should be either all fastq/a or all SRA.
Modify the inputs, then try resubmitting the job.
UE: There are names for both a forward and reverse strand and they are identical.
A Single-end read library only needs one name. A Paired-end read library needs two files with different names.
UE: Either the file is not in fastq format or the file extension is not recognized.
Recheck that the file is in the right format. Change the extension to .fastq if needed, then try resubmitting the job.
UE: Possible issues
The fastq file includes one or more sequences that are less than 10 bases. Short reads are a problem for some tools.
The fastq file doesn't have the right number of lines. For example, the lines in a single-end file needs to be a multiple of four and interleaved paired-end library should be a multiple of eight.
The options haven't been selected correctly. For example, using an interleaved fastq file but failing to check the Interleaved box. The documentation on FASTQ/SRA Reads may be helpful.
The file might not have the right filename to be recognized.
The file is an SRA file and not FASTQ.
DOS-style carriage-return line files along with new-lines. Our fasta validation doesn't handle this properly. To remove the carriage return characters use this unix command:
tr -d '\015' < 1.fastq >cleaned_1.fastq
UE: The number of lines in the FASTQ file are not a multiple of four.
Recheck the file and try resubmitting the job.
UE: Something went wrong trying to interleave the Paired-end files.
Recheck the line count of the files. Hidden carriage returns or linefeeds in the file could contribute to the problem.
UE: The interleaved file does not appear to be the correct format.
Recheck the file and try resubmitting the job.
UE: The name of the output reads object can’t have spaces or special characters.
Rename the output file and then try resubmitting the job.
UE: There are no contigs that passed the minimum contig size.
Adjust the minimum contig size or other optional parameters. Then try resubmitting the job.
UE: The FASTA header lines may not be unique.
Recheck the format of the header lines and try resubmitting the job.
UE: The file appears to be proteins or special characters instead of DNA.
Recheck the file contents, and then try resubmitting the job.
UE: The file appears to be proteins instead of DNA.
Recheck the file contents, and then try resubmitting the job.
UE: Selected file does not match the import selected.
Select a valid combination and try resubmitting the job.
UE: Attempt to import a zip file with multiple files as a single data object.
Run the App ' Unpack a Compressed File in Staging Area' on the file and retry resubmitting the job.
UE: Gene IDs within the input file are not unique.
Edit gene IDs and try resubmitting the job.
UE: The app only recognizes the listed file extensions as valid GenBank files.
Change the file extension and try resubmitting the job.
UE: The Taxonomy ID in the advanced parameters is optional and needs to be an integer when specified. The user provided the text string ‘XXX’.
Use an integer taxon ID or leave it blank. The information will be picked up from the GenBank file or from the scientific name.
UE: The IDs in the ‘sequence source’ lines must match the header lines in the FASTA file in the GFF format.
Correct the GFF format and try resubmitting the job.
UE: The file may not be in GFF format.
Recheck the file format and try resubmitting the job.
UE: The coordinates for the feature are outside the bounds of the contig.
Recheck the file where indicated and try resubmitting the job. In rare instances, the GFF file contains a feature that wraps around the 0 position and the coordinates look like the feature goes off the end of the sequence. The options are to 1) remove the feature from the GFF file, 2) edit the feature so that it is in two parts, or 3) find a GenBank formatted version of the file and resubmit.
UE: File format is not recognized.
Recheck the file format and try resubmitting the job.
UE: File format is not recognized.
Recheck the file format and try resubmitting the job.
UE: The genome does not exist in the narrative
Fix the genome name and try resubmitting the job.
UE: The file could not be unzipped by KBase and most likely couldn’t be unzipped by the user either.
Verify the file can be unzipped locally.
