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.
Types of 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.
Common Import Job Error Messages
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.
Bulk or Batch Imports
(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.
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 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
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 8
UE: 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.
Every feature sequence id must match a fasta sequence id
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.
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.
