Standalone TMAP 3.4.1 error

[skbrimer]

Good Morning gang,

I have had, for the first time TMAP fail to put together some PGM reads for me. I do not blame the algorithm the data is not the best, but it is weird.

Below is the code I use to run and in the stats output I get stats [0.00,-nan,-nan,-nan,-nan,-nan] which I assume means there is no data. However when I use bwa samse and bwa mem I get mapped reads AND when I use TMAP vsw option I get mapped reads but the mapall function I get nothing.

sean@LEN320:~/Desktop/IBV/D1456/tmap$ tmap mapall -f ~/Desktop/templates/IBV_RefSeq.fasta -r ../raw_data/all_reads_no_host.fastq -n4 -v stage1 map1 map2 map3 > aln.sam
[tmap mapall] running with 4 threads (user set).
[tmap mapall] map1 will be run in stage 1.
[tmap mapall] map2 will be run in stage 1.
[tmap mapall] map3 will be run in stage 1.
[tmap mapall] reading in reference data.
[tmap mapall] 0.01/0.08 sec: reference data read in.
[tmap mapall] calculating maximum differences in map1 for stage 1.
[tmap mapall] 17bp reads will have at most 2 differences.
[tmap mapall] 38bp reads will have at most 3 differences.
[tmap mapall] 64bp reads will have at most 4 differences.
[tmap mapall] 93bp reads will have at most 5 differences.
[tmap mapall] 124bp reads will have at most 6 differences.
[tmap mapall] 157bp reads will have at most 7 differences.
[tmap mapall] 190bp reads will have at most 8 differences.
[tmap mapall] 225bp reads will have at most 9 differences.
[tmap mapall] setting the seed length to 10 in map3.
[tmap mapall] loading reads.
[tmap mapall] 0.04/0.12 sec: loaded 11128 reads.
[tmap mapall] processing reads.
[tmap mapall] 1.28/1.13 sec: processed 11128 reads.
[tmap mapall] 1.28/1.13 sec: stats [0.00,-nan,-nan,-nan,-nan,-nan].
[tmap mapall] loading reads.
[tmap mapall] 1.28/1.13 sec: loaded 0 reads.
[tmap mapall] 1.28/1.13 sec: cleaning up.
[tmap mapall] 1.30/1.15 sec: terminating successfully.

I do not mind that the mapping failed I was just more usurious on why it failed so I can learn more about how to best work the different data sets. I have attached a screen shoot from IGV showing the 4 different mappings. from top to bottome it is TMAP mapall, TMAP mapvsw, BWA semse, BWA mem