Assembling of 22 reads from D-LOOP failed

Question

[netsam]

Hi, I wondered why the assembling of 11 PE reads from D-LOOP of wolf failed. I tried both with Sapdes and Uncycler. I attach the IGB tracks.

[h.mon]

What do you mean by "failed"? What was the result? Two contigs? Three contigs? No contigs at all?

Best hypothesis you will get two contigs, as there is clearly a gap between ~630 to ~680bp.

[netsam]

There was no scaffold and no contigs. I used Spades embedded in Galaxy. Last rows of error log file:

=== Stack Trace === [0x5f9c32] [0x58ad81] [0x55d2c1] [0x408c19] [0x40123c] [0x87a73b] [0x407c01] Verification of expression 'cov_.size() > 10' failed in function 'void coverage_model::KMerCoverageModel::Fit()'. In file '/spades/src/common/modules/coverage_model/kmer_coverage_model.cpp' on line 187. Message 'Invalid kmer coverage histogram, make sure that the coverage is indeed uniform'. Verification of expression 'cov_.size() > 10' failed in function 'void coverage_model::KMerCoverageModel::Fit()'. In file '/spades/src/common/modules/coverage_model/kmer_coverage_model.cpp' on line 187. Message 'Invalid kmer coverage histogram, make sure that the coverage is indeed uniform'. spades-core: /spades/src/common/modules/coverage_model/kmer_coverage_model.cpp:187: void coverage_model::KMerCoverageModel::Fit(): Assertion `cov_.size()

10' failed.

== Error == system call for: "['/mnt/pulsar/server/dependencies/_conda/envs/__spades@3.12.0/share/spades-3.12.0-1/bin/spades-core', '/mnt/pulsar/files/staging/649831/working/K55/configs/config.info', '/mnt/pulsar/files/staging/649831/working/K55/configs/careful_mode.info']" finished abnormally, err code: -6

======= SPAdes pipeline finished abnormally and WITH WARNINGS!

=== Error correction and assembling warnings: * 0:00:01.344 8M / 1G WARN General (simplification.cpp : 479) The determined erroneous connection coverage threshold may be determined improperly ======= Warnings saved to /mnt/pulsar/files/staging/649831/working/warnings.log

=== ERRORs: * system call for: "['/mnt/pulsar/server/dependencies/_conda/envs/__spades@3.12.0/share/spades-3.12.0-1/bin/spades-core', '/mnt/pulsar/files/staging/649831/working/K55/configs/config.info', '/mnt/pulsar/files/staging/649831/working/K55/configs/careful_mode.info']" finished abnormally, err code: -6

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