Posting for future users:
I ran into the below error in my phyloflash.bbmap.out while running phyloflash. I installed with conda and downloaded the pre-formatted databases with wget and used --dbhome following the instructions.
Exception in thread "SamLineWriter-Worker-5" java.lang.AssertionError: This program requires bases or a cigar string for every sam line. Problem line:
LH00526:351:22WHVMLT4:2:1154:14919:16325 1:N:0:TGATAGGC+ACTCAGAC 337 GBIZ01041476.5342.6799 Bacteria;Cyanobacteria;Cyanobacteriia;Chloroplast;Arachis hypogaea var. vulgaris 495 32 * GEEU01029790.14.1484 Bacteria;Cyanobacteria;Cyanobacteriia;Chloroplast;Ettlia oleoabundans 139 0 * * AM:i:32 NH:i:3
at stream.SamLine.length(SamLine.java:2019)
at stream.SamWriter$ProcessThread.processJobs(SamWriter.java:367)
at stream.SamWriter$ProcessThread.run(SamWriter.java:302)
Phyloflash installed with bbmap=39.79 for me, and switching version to 39.01 with conda install bbmap=39.01 fixed the problem and it ran to completion. Thanks for making a great program!
Mike
Posting for future users:
I ran into the below error in my
phyloflash.bbmap.outwhile running phyloflash. I installed with conda and downloaded the pre-formatted databases with wget and used --dbhome following the instructions.Phyloflash installed with bbmap=39.79 for me, and switching version to 39.01 with
conda install bbmap=39.01fixed the problem and it ran to completion. Thanks for making a great program!Mike