Uchime error: This job was terminated because it ran longer than the maximum allowed job run time.

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1

Hello, I am new to bioinformatics analyses and trying to use Uchime for chimera removal. I’m guessing my job was terminated due to input error - Could I get help to see if the formatting for my input files are appropriate?

Tool used: Chimera.uchime

Input candiate Aligned Sequence

  • fasta file, converted from 77999 FASTQ reads
  • File size: 36 MB
  • Dataset peek:

SRR10525645.51 51 length=250
ACTCCTACGGGAGGCAGCAGTGGGGGATATTGCACAATGGGGGAAACCCTGATGCAGCGACGCCGCGTGAGTGAAGAAGTATTTCGGTATGTAAAGCTCTATCGGCAGGGAAGAAAAAAATGACAGTACCTGACTAAGAAGCCCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGGCGGCCATGCAAGTCAGAAGTGAAAACCCGGGGCTCAACCCTGGGAGTGCTTTTGAAACTGTGCGGCTAGAGTGTCGGAGGGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGATGACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGGATTAGAAACCCTGGTAGTCC

Input reference to align with

  • fasta file, 510508 sequences
  • File size: 784 MB
  • File manually downloaded from Silva database, and then gunzipped
  • Dataset peek:

AY846379.1.1791 Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Chlorophyceae;Sphaeropleales;Monoraphidium;Monoraphidium sp. Itas 9/21 14-6w
AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAACUGCUUAUACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUAUUUGAUGGUACCUCUACACGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCGUAAAUCCCGACUUCUGGAAGGGACGUAUUUAUUAGAUAAAAGGCCGACCGAGCUUUGCUCGACCCGCGGUGAAUCAUGAUAACUUCACGAAUCGCAUAGCCUUGUGCUGGCGAUGUUUCAUUCAAAUUUCUGCCCUAUCAACUUUCG

2

Hi @lyehui

Next time you run this, check the box for “Output logfile?”. Those are usually helpful whenever available.

That said, this job may actually be too large to process at UseGalaxy.org.
Understanding walltime error messages

Options:

  1. Consider splitting the query up into a dataset collection, running the tool in batch, then merging the output. (This isn’t appropriate for all tools). Using dataset collections
  2. Try at UseGalaxy.eu instead. Each server has different resources.