Error: Cannot cast array data from dtype('O') to dtype('int64') according to the rule 'safe'

[DanBeaton]

Error: Cannot cast array data from dtype('O') to dtype('int64') according to the rule 'safe'

[DanBeaton]

Hello -- I have done more digging. The error described above appears to follow from the conversion of the krkinput.fastq file to the krakenreport.txt file.

kraken_report_annotated_otu.txt has otu information from kingdom to species.
kraken_report_annotated.txt only has information to the level of kingdom.

The diversity analysis in kraken_push.py starts that the level of class so the report files have no data to analyze and create the the diversity files.

The seqid for the first taxon id in the list is shown in the file to be on row 2 rather than row 1.

Any suggestions on how to fix or workaround and see if it occurs in other qced.fastq files in the sequencing run?

[DanBeaton]

After much looking, the issue here is with the fats5 conversion to fastq.