Dataset ganges

• To run the ganges sample via the pipeline
• Paths:
  • lr: /scratch/users/sbusi/ONT/ganges/data/lr/SO_6051_metagenome
  • sr: /scratch/users/sbusi/ONT/ganges/data/sr/ERR2612536/ERR2612536_1.fastq.gz
• updated config file: commit ID 92935da4

added Analysis label

changed milestone to %Manuscript - initial version

changed title from Ganges sample - ONT run to Dataset ganges

changed the description

marked this issue as related to #39 (closed)

Issue w/ flye

[2020-07-14 07:41:36] INFO: Starting Flye 2.7.1-b1590
[2020-07-14 07:41:36] INFO: >>>STAGE: configure
[2020-07-14 07:41:36] INFO: Configuring run
[2020-07-14 07:41:39] INFO: Total read length: 104069305
[2020-07-14 07:41:39] INFO: Input genome size: 1000000000
[2020-07-14 07:41:39] INFO: Estimated coverage: 0
[2020-07-14 07:41:39] WARNING: Expected read coverage is 0, the assembly is not guaranteed to be optimal in this setting. Are you sure that the genome size was entered correctly?
[2020-07-14 07:41:39] INFO: Reads N50/N90: 2641 / 1152
[2020-07-14 07:41:39] INFO: Minimum overlap set to 1000
[2020-07-14 07:41:39] INFO: Selected k-mer size: 17
[2020-07-14 07:41:39] INFO: >>>STAGE: assembly
[2020-07-14 07:41:39] INFO: Assembling disjointigs
[2020-07-14 07:41:39] INFO: Reading sequences
[2020-07-14 07:41:41] INFO: Generating solid k-mer index
[2020-07-14 07:45:32] INFO: Counting k-mers (1/2):
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 
[2020-07-14 07:45:34] INFO: Counting k-mers (2/2):
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 
[2020-07-14 07:45:39] WARNING: Unable to separate erroneous k-mers from solid k-mers. Possible reasons: 
        (1) Incorrect expected assembly size parameter 
        (2) Highly uneven coverage of the assembly 
        (3) Running with error-corrected reads in raw reads mode
        Assembly will continue, but results might not be optimal
[2020-07-14 07:45:39] INFO: Filling index table (1/2)
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 
[2020-07-14 07:45:48] INFO: Filling index table (2/2)
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 
[2020-07-14 07:45:57] INFO: Extending reads
[2020-07-14 07:45:59] INFO: Overlap-based coverage: 0
[2020-07-14 07:45:59] INFO: Median overlap divergence: 0.397452
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 
[2020-07-14 07:46:10] INFO: Assembled 0 disjointigs
[2020-07-14 07:46:11] INFO: Generating sequence
[2020-07-14 07:46:11] ERROR: No disjointigs were assembled - please check if the read type and genome size parameters are correct
[2020-07-14 07:46:11] ERROR: Pipeline aborted

Issue w/ metaSPAdes (hybrid)

Out of memory using the following settings:

metaspades:
    threads: 10

assembly_hy_metaspades:
    time: "01-12:00:00"
    partition: "bigmem"
    qos: "qos-bigmem"
    nodes: 1
    n: 1
    explicit: ""

The reads contain too many k-mers to fit into available memory. You need approx. 486.432GB of free RAM to assemble your dataset

mentioned in commit 6a052006

Closing as we have decided not to use this sample

• not assembled in the paper
• issue w/ flye

closed

added Data label