Import Job Errors
This is a list of error messages found within the Job Log for Import Jobs, what they mean and how to go about fixing them or if a job ticket needs to be submitted.
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This is a list of error messages found within the Job Log for Import Jobs, what they mean and how to go about fixing them or if a job ticket needs to be submitted.
Last updated
Was this helpful?
UE=User fixable or possible user error
KE=KBase error
You can always submit a ticket for help, questions, or follow-up to the .
Cannot connect to URL: ftp://ftp.imicrobe.us. ... UE: The provided URL cannot be accessed from within KBase.
Recheck the URL and permissions. Then try resubmitting the job.
Invalid FTP Link: ... 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.
Invalid Google Drive Link ... UE: The provided URL cannot be accessed from within KBase.
Recheck the URL and its permission. Then try resubmitting the job.
(2, No such file or directory) UE: The file is not in the Staging Area.
Verify that the name is correct and upload is complete. Then try resubmitting the job.
(2, No such file or directory) KE: The fastqdump ran but the file names are not the expected names.
SRA input file type selected. But missing SRA file UE: The format of the file is not recognized.
Recheck the file and try resubmitting the job.
Invalid FASTQ file ... 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"
Error running command: /kb/deployment/bin/fastq-dump ... UE: The file does not appear to be in the expected SRA format.
Recheck the file and try resubmitting the job.
Error running command:pigz ... 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.
Both SRA and FASTQ/FASTA file given. UE: The inputs should be either all fastq/a or all SRA.
Modify the inputs, then try resubmitting the job.
Same file [XXX.XXXX.gz] is used for forward and reverse. Please select different files and try again. 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.
File /kb/XXX.fasta is not a FASTQ file 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.
Invalid FASTQ file 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 file might not have the right filename to be recognized.
The file is an SRA file and not FASTQ.
Reading FASTQ record failed - non-blank lines are not a multiple of four.UE: The number of lines in the FASTQ file are not a multiple of four.
Recheck the file and try resubmitting the job.
Interleave failed - reads files do not have an equal number of records….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.
Deinterleave failed - line count is not divisible by 8UE: The interleaved file does not appear to be the correct format.
Recheck the file and try resubmitting the job.
Object 1: Illegal character in object name 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.
There are no contigs to save, thus there is no valid assembly.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.
The FASTA header key XXX appears more than once in the fileUE: The FASTA header lines may not be unique.
Recheck the format of the header lines and try resubmitting the job.
This FASTA file has non nucleic acid charactersUE: The file appears to be proteins or special characters instead of DNA.
Recheck the file contents, and then try resubmitting the job.
This FASTA file may have amino acids in it instead of the required nucleotides.UE: The file appears to be proteins instead of DNA.
Recheck the file contents, and then try resubmitting the job.
FASTQ/FASTA input file type selected. But missing FASTQ/FASTA fileUE: Selected file does not match the import selected.
Select a valid combination and try resubmitting the job.
(\utf-8\, b\PK\x03\x04\x14\x00\x08…….UE: Attempt to import a zip file with multiple files as a single data object.
Duplicate gene ID: XXXX_xxxxUE: Gene IDs within the input file are not unique.
Edit gene IDs and try resubmitting the job.
The input directory does not have any files with one of the following extensions .gbff,.gbk,.gb,.genbank,.dat,.gbfUE: The app only recognizes the listed file extensions as valid GenBank files.
Change the file extension and try resubmitting the job.
XXX is not a valid KBase taxon IDUE: 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.
Every feature sequence id must match a fasta sequence idUE: 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.
unable to parse >.....UE: The file may not be in GFF format.
Recheck the file format and try resubmitting the job.
Features must be completely contained within the Contig in the Fasta file.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.
Starch.csv" is not a valid EXCEL nor TSV fileUE: File format is not recognized.
Recheck the file format and try resubmitting the job.
data file 4.xml either does not use commas or tabs as a separatorUE: File format is not recognized.
Recheck the file format and try resubmitting the job.
No object with name _Nostoc_azollae__0708UE: The genome does not exist in the narrative
Fix the genome name and try resubmitting the job.
Error running command:pigz ... 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.
Use the long workaround .
Use the long workaround .
The options haven't been selected correctly. For example, using an interleaved fastq file but failing to check the Interleaved box. The documentation on may be helpful.
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 tr -d '\015' < 1.fastq >cleaned_1.fastq
Run the App ' ' on the file and retry resubmitting the job.