Issue in running cnvkit.py batch command

[Donatella93]

Hello!
I am facing an issue while I am running the cnvkit.py batch command:

cnvkit.py batch /mnt/illumina/PROGETTO/CNVkit/SAMPLES/TUMOR/.bam -n /mnt/illumina/PROGETTO/CNVkit/SAMPLES/NORMAL/.bam -t /mnt/illumina/PROGETTO/CNVkit/BED/CAPTURE/MUT-CNV_capture_targets.bed --annotate /mnt/illumina/PROGETTO/CNVkit/refFlat.txt -f /mnt/illumina/PROGETTO/ucsc.hg19.fasta --access /mnt/illumina/PROGETTO/CNVkit/BED/access-5k-mappable.hg19.bed --output-reference /mnt/illumina/PROGETTO/CNVkit/cnvkit_output/autobin_filtered_ref/my_reference.cnn -d /mnt/illumina/PROGETTO/CNVkit/cnvkit_output/autobin_filtered_ref/ --drop-low-coverage -p 0 --diagram --scatter

When I run the script, it stops after this message:

Targets: 51 (4.412%) bins failed filters (log2 < -5.0, log2 > 5.0, spread > 1.0)
TPRG1L chr1:3541617-3541856 log2=-1.444 spread=0.170 rmask=nan
GIPC2 chr1:78511759-78512036 log2=-0.066 spread=0.088 rmask=nan
CD58 chr1:117057379-117057498 log2=-0.666 spread=0.193 rmask=nan
" chr1:117113499-117113618 log2=-1.218 spread=0.162 rmask=nan
NOTCH2NLC,NOTCH2,NOTCH2NLR chr1:120611925-120612044 log2=-6.004 spread=0.197 rmask=nan
PAPOLG chr2:60997559-60997678 log2=0.266 spread=0.023 rmask=nan
SF3B1 chr2:198269781-198269997 log2=0.162 spread=0.048 rmask=nan
SUMF1 chr3:4508641-4508948 log2=-0.313 spread=0.144 rmask=nan
CSPG5 chr3:47619153-47619436 log2=-0.064 spread=0.084 rmask=nan
" chr3:47620075-47620194 log2=-3.219 spread=0.229 rmask=nan
TBL1XR1 chr3:176751907-176752192 log2=-0.342 spread=0.086 rmask=nan
HCN1 chr5:45695983-45696213 log2=-1.163 spread=0.220 rmask=nan
CLTB chr5:175843158-175843383 log2=-0.654 spread=0.091 rmask=nan
LTB chr6:31548713-31548958 log2=-2.840 spread=0.276 rmask=nan
PIM1 chr6:37138333-37138570 log2=0.025 spread=0.116 rmask=nan
NFKBIE chr6:44232972-44233244 log2=-0.002 spread=0.117 rmask=nan
DLL1 chr6:170598581-170598914 log2=-0.296 spread=0.081 rmask=nan
" chr6:170599141-170599260 log2=-1.153 spread=0.115 rmask=nan
ACTB chr7:5569097-5569356 log2=-1.903 spread=0.244 rmask=nan
BRAF chr7:140624346-140624521 log2=-4.774 spread=0.303 rmask=nan
CDKN2A chr9:21974657-21974844 log2=0.557 spread=0.144 rmask=nan
PTEN chr10:89685247-89685366 log2=-0.906 spread=0.052 rmask=nan
" chr10:89690765-89690884 log2=0.135 spread=0.113 rmask=nan
IL10RA chr11:117857157-117857276 log2=-0.076 spread=0.170 rmask=nan
NFKBIA chr14:35873605-35873868 log2=-0.508 spread=0.205 rmask=nan
ANKRD9 chr14:102973253-102973500 log2=-0.178 spread=0.199 rmask=nan
" chr14:102973501-102973748 log2=-3.710 spread=0.469 rmask=nan
" chr14:102973749-102973996 log2=-1.329 spread=0.308 rmask=nan
" chr14:102973997-102974244 log2=-2.075 spread=0.277 rmask=nan
CREBBP chr16:3778801-3779091 log2=0.210 spread=0.091 rmask=nan
" chr16:3779092-3779382 log2=-0.468 spread=0.155 rmask=nan
" chr16:3799597-3799716 log2=-0.002 spread=0.061 rmask=nan
ABCA5 chr17:67244371-67244490 log2=-1.147 spread=0.097 rmask=nan
" chr17:67246025-67246144 log2=0.298 spread=0.094 rmask=nan
" chr17:67257773-67257892 log2=-0.265 spread=0.108 rmask=nan
" chr17:67309337-67309456 log2=-0.652 spread=0.076 rmask=nan
ZNF519 chr18:14105920-14106177 log2=0.118 spread=0.004 rmask=nan
ZCCHC2 chr18:60190639-60190882 log2=-5.566 spread=0.297 rmask=nan
" chr18:60190883-60191126 log2=-0.653 spread=0.088 rmask=nan
" chr18:60191127-60191370 log2=-0.543 spread=0.176 rmask=nan
" chr18:60191371-60191614 log2=0.263 spread=0.094 rmask=nan
BCL2 chr18:60985607-60985918 log2=0.560 spread=0.062 rmask=nan
ZNF516 chr18:74153446-74153709 log2=0.338 spread=0.146 rmask=nan
" chr18:74153710-74153973 log2=1.131 spread=0.058 rmask=nan
" chr18:74154502-74154765 log2=-0.179 spread=0.116 rmask=nan
MEF2B,BORCS8-MEF2B chr19:19256587-19256850 log2=-4.924 spread=0.239 rmask=nan
" chr19:19257077-19257196 log2=-3.700 spread=0.185 rmask=nan
RELB chr19:45504831-45504950 log2=-5.739 spread=0.177 rmask=nan
" chr19:45515165-45515562 log2=-1.725 spread=0.105 rmask=nan
ZNF416 chr19:58089997-58090116 log2=0.045 spread=0.082 rmask=nan
UBE2A chrX:118708637-118708756 log2=-0.891 spread=0.275 rmask=nan
Antitargets: 814 (4.256%) bins failed filters
Wrote /mnt/illumina/PROGETTO/CNVkit/cnvkit_output/autobin_filtered_ref/my_reference.cnn with 20281 regions
Running 23 samples in 12 processes (that's 1 processes per bam)

and in my output folder I get only the .cnn files (target/antitarget) related my NORMAL BAMs. the target/antitarget of my bed and the reference.cnn

Is there anyone could help clarifying why the issue?

Thanks