No output for low-coverage bam files

[Npaffen]

The tools seems to have trouble to output the fastq file correctly if the bam file has low-coverage. In my case it is :

#rname  startpos        endpos  numreads        covbases        coverage        meandepth       meanbaseq       meanmapq
chr1    1       249250621       11282   1049594 0.4211  0.00476702      26.9    63.4
chr2    1       243199373       12504   1133407 0.46604 0.00542827      26.9    62.9
chr3    1       198022430       9977    937568  0.473466        0.00534363      26.9    66.5
chr4    1       191154276       9223    857623  0.448655        0.00510673      26.9    62.4
chr5    1       180915260       8553    800982  0.442739        0.00499967      26.9    64.1
chr6    1       171115067       8724    816399  0.477105        0.00540157      26.9    66.1
chr7    1       159138663       7785    709773  0.446009        0.0051798       27      61.1
chr8    1       146364022       7599    705045  0.481706        0.00549357      27      64.8
chr9    1       141213431       6267    572471  0.405394        0.00468613      26.8    59.1
chr10   1       135534747       6815    636626  0.469714        0.00529091      26.9    64.2
chr11   1       135006516       6577    597143  0.442307        0.00513988      26.9    63.5
chr12   1       133851895       6635    612528  0.457616        0.00519541      26.9    65.3
chr13   1       115169878       4682    441733  0.383549        0.00429756      26.9    66.8
chr14   1       107349540       4414    412879  0.384612        0.00432871      26.9    63.9
chr15   1       102531392       3974    372428  0.363233        0.00407474      27      63.1
chr16   1       90354753        3946    359844  0.398257        0.00454397      27      61.4
chr17   1       81195210        3562    330014  0.406445        0.00457848      27      62.6
chr18   1       78077248        3998    357124  0.457398        0.00544089      26.9    64
chr19   1       59128983        2285    209688  0.354628        0.00399973      26.9    59.1
chr20   1       63025520        3107    289886  0.45995 0.00514412      26.9    67.1
chr21   1       48129895        1750    160523  0.33352 0.00379575      26.8    57.2
chr22   1       51304566        1511    136987  0.267007        0.00300574      26.7    56.7
chrX    1       155270560       4612    428987  0.276284        0.00307974      26.7    55.9
chrY    1       59373566        803     70312   0.118423        0.00139485      26.8    23.8
chrM    1       16569   213     3224    19.458  1.37884 27.2    65.9

which leads to the following output of bazam :

================================================================================

Bazam

================================================================================

bazam.Bazam	[1]	INFO	|1:53:59 Extracting read pairs from some.bam
bazam.Bazam	[1]	INFO	|1:53:59 Initialising regions to scan from false 
gngs.pair.PairScanner	[1]	INFO	|1:53:59 Beginning scan of some.bam
gngs.pair.PairScanner	[1]	INFO	|1:53:59 Created 4 read pair locators 
gngs.pair.PairScanner	[1]	INFO	|1:54:00 Stopping parallel threads ... 
gngs.pair.PairScanner	[1]	INFO	|1:54:00 Stopping Locator 0 
gngs.pair.PairScanner	[1]	INFO	|1:54:00 Stopping Locator 1 
gngs.pair.PairScanner	[1]	INFO	|1:54:00 Stopping Locator 2 
gngs.pair.PairScanner	[1]	INFO	|1:54:00 Stopping Locator 3 
gngs.pair.PairScanner	[1]	INFO	|1:54:00 Stopping Chimeric Locator 
gngs.pair.PairScanner	[1]	INFO	|1:54:00 Stopping Formatter 
gngs.pair.PairScanner	[1]	INFO	|1:54:00 Stopping Writer 
gngs.pair.PairScanner	[1]	INFO	|1:54:00 Processed 142615 in 0.767 seconds  @ 185455.14/s   (*:0, loc: 142.6k,0,142.6k chimeric: 140.8k formatted: 0, written: 0)