READS ARE NOT AT LEAST 75 BP LONG error about oyster_river_protocol HOT 2 OPEN

Hi,

Thanks for your reports - I will respond to each. In this case, the error message has been updated to 76bp, and I will add the part about odd numbers. I know SPAdes rec. is 50% of read length, but we with this second SPAdes assembly we are trying to to recover specifically higher expression transcripts.

Of note, you could have avoided editing the code by passing the SPADES2_KMER=INT flag, if I'm understanding your issue properly.

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I could be wrong, but I don't think the issue can be fixed by just passing the SPADES2_KMER=INT flag. I tried this, but couldn't get it to work. The reason is: if that if statement executes (which it does if your reads are 75 bp, regardless of what you set SPADES2_KMER as), it prints the error message and then calls $$(shell exit);\, ending the program. The if statement should check whether the read length is compatible with the current SPADES2_KMER setting, not whether it is > 75.

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