Unexpected end of file and Malformed input error

[Rohit-Satyam]

While running KMA, I get the following (file name has been masked in error below)

# Reading inputfile:    /home/tuli15/scratch/B0#####_R1.fastq.gz /home/tuli15/scratch/B0#####_R2.fastq.gz
# Phred scale:  33
#
# Total time used for DB loading: 83.86 s.
#
# Finding k-mer ankers
#
# Total number of query fragment after trimming:        12795654
#
# Query converted
#
# Query ankered
#
# Score collection done
#
# Sort, output and select k-mer alignments.
# Total time for sorting and outputting KMA alignment   34.97 s.
#
# Doing local assemblies of found templates, and output results
# Total time used for local assembly: 694.54 s.
#
# Closing files
# Collecting k-mer scores.
# Reading inputfile:    /home/tuli15/scratch/B0#####_R1.fastq.gz /home/tuli15/scratch/B0#####_R2.fastq.gz
# Phred scale:  33
#
# Total time used for DB loading: 86.50 s.
#
# Finding k-mer ankers
Malformed input.
Malformed input.
Malformed input.
Malformed input.
Malformed input.

Also for some files I get the Unexpected end of file error

Finding k-mer ankers
Unexpected end of file
#
# Total number of query fragment after trimming:        10362034
#
# Query converted
#
# Query ankered
#
# Score collection done
#
# Sort, output and select k-mer alignments.
# Total time for sorting and outputting KMA alignment   22.75 s.

[vrmarcelino]

Hi,

Sorry for the late response. It might be better to post this in the KMA repository, but let's try: So KMA works with some of your files but not others? Is it possible that the input files that are not working have been corrupted by any chance? Do they have the same number of reads in the fwd and rev files?

Thanks!

[Rohit-Satyam]

Yes I think input files are corrupted because number of reads were different. I have removed those two corrupted samples and have put it on rerun. If I get the same error on the good files I will let u know.