Assembly App Errors

This is a list of error messages found within the Job Log for Assembly App Jobs, what they mean and how to go about fixing them or if a job ticket needs to be submitted.

Types of Errors

• UE=User fixable or possible user error

• KE=KBase error

• UK=Unknown or multiple possibles causes

• TE=Temporary system problem

Use your Browser's search tool to paste in your error message to locate your error message, information about the error and next steps.

You can always submit a ticket for help, questions, or follow-up to the KBase Help Board.

Common errors across SPAdes Assembly Apps

Assemble Reads with SPAdes; Assemble Reads with HybridSPAdes; Assemble Reads with metaSPAdes; Filter Assembled Contigs by Length

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.

Error running SPAdes, return code: 1

UE: Potential explanations

• The coverage of your input is so uneven that everything is disconnected.

• The reads contain too many k-mers to fit into available memory.

• Incomplete write! Reason: No space left on device.

• Coverage not uniform hybridSPAdes ended abnormally

• Failed to align paired reads left paired reads is not equal to right paired reads cannot specify any data types except a single paired-end library (optionally accompanied by a single library of TSLR-contigs, or PacBio reads, or Nanopore reads) in metaSPAdes mode

• The program was terminated by segmentation fault

• Too many erroneous kmers, the estimates might be unreliable

Look for an explanation from SPAdes in the log. If possible, correct the error and try resubmitting the job.

Deinterleave failed - line count is not divisible by 8

UE: The interleaved file does not appear to be the correct format.

Recheck that the files are labeled properly and try resubmitting the job.

Reads object XXX is marked as containing metagenomic data but the assembly method was not specified as metagenomic

UE: The input object and the selected parameters disagree

Change the data input or the app parameters and try resubmitting the job.

Plasmid assembly requires that one and only one library as input.

UE: There is more than one input library.

Change the input to be just one library, change the library source, or merge the libraries and try resubmitting the job.

Invalid type for object 27459/32/1…..

UE: The user is allowed to enter an Assembly for the long reads (like in the MaSuRCA app) but this results in an error.

Ensure objects correspond with the object types listed and try resubmitting the job.

QUAST reported an error, return code was 4

UE: None of the assembly files contains correct contigs (none greater than the minimum contig filter).

Provide different files or decrease --min-contig threshold. Then try resubmitting the job.

Velvet Assembler

Error on Object #1: Illegal character in object name

UE: Velvet did not assemble any contigs longer than the minimum length.

Change the configuration and try resubmitting the job.

Assemble with HipMer

'list index out of range'

UE: There is no input data

Add data to the app and try resubmitting the job.

Error in HipMER execution

UE: Possible causes -

• The data was a metagenome, but the metagenome flag was not enabled

• The metagenome flag was enabled but the data was not a metagenome

• Exceeded time limit at NERSC

• Other data/parameter combinations that result in no returned assembly

Change the configuration and try resubmitting the job.

Using input parameters, you have filtered all contigs from the HipMer assembly. Decrease the minimum contig size and try again

UE: The minimum contig length is too large.

Lower the minimum contig length in the parameters and try resubmitting the job.

(2, No such file or directory)

TE: Hipmer was in the queue too long and did not run.

Try resubmitting the job.

MaSuRCA Assembler

Error running command: XXX/config.txt Exit Code: 1

UE: invalid file for PACBIO invalid file for NANOPORE.

Recheck the file and try resubmitting the job.

Assemble Transcripts using StringTie

Genome at 48203/40/2 does not have reference to the assembly object

UE: A previous step (e.g., HISAT) used an assembly instead of a genome as input.

Go back to the previous step and use a genome as input.

coercing to unicode: need string or buffer

KE: genome related issue with some of the NCBI RefSeq genomes.

Workaround: import the GFF-format genome with correct feature annotations and try resubmitting the job. See https://kbase-jira.atlassian.net/browse/PUBLIC-969

Merge Reads Libraries

incompatible read library types in ReadsSet

UE: Every library in the input to merge must be of the same type, either all Paired-End or Single-End.

Change the inputs and try resubmitting the job.

[Errno 28] No space left on device

UE/KE: Most likely case: The combined size of the libraries exceeds the current KBase hardware. Efforts are being made to increase capacity and to provide a cleaner more informative message. Workarounds should be considered.

The workarounds include:

1. Reduce the number of libraries in the merge

2. Run Kaiju to determine which samples have similar profiles. Then try the co-assemblies pairwise using two-at-a-time based on which profiles are most similar.