Cohort mode of GermlineCNVCaller: FileNotFoundError

Running GermlineCNVCaller in the cohort mode---FileNotFoundError: [Errno 2] No such file or directory: '/tmp/intervals2009046725159223001.tsv'

My code for calling CNV:

cgsdir=/paedwy/disk1/wma/old_samples/raw_data/read_cgs
gatk=/home/yangyxt/software/gatk-4.1.3.0/gatk
ref_gen=/paedwy/disk1/yangyxt/indexed_genome
hdfsamples=/paedwy/disk1/wma/old_samples/raw_data/read_cgs

gCNV_model=${hdfsamples}/cgsnoB9_gCNV_model
valid_ploidy_call=${hdfsamples}/cgsNOB9_ploidy_model/cgs_normal_cohort-calls


module load miniconda3
module load gcc/4.9.1
module load GenomeAnalysisTK/4.1.3.0

source activate /software/GenomeAnalysisTK/4.1.3.0
$gatk GermlineCNVCaller \
--run-mode COHORT \
-L ${hdfsamples}/cgs.cohort.gc.filtered.interval_list \
--class-coherence-length 1000 \
--cnv-coherence-length 1000 \
--interval-merging-rule OVERLAPPING_ONLY \
--contig-ploidy-calls ${valid_ploidy_call} \
--verbosity DEBUG \
--annotated-intervals ${cgsdir}/cgs.annotated.tsv \
-I ${hdfsamples}/A100175.counts.hdf5 \
-I ${hdfsamples}/A100288B.counts.hdf5 \
-I ${hdfsamples}/A100308.counts.hdf5 \
-I ${hdfsamples}/A130042.counts.hdf5 \
-I ${hdfsamples}/A140135A.counts.hdf5 \
-I ${hdfsamples}/A140136A.counts.hdf5 \
-I ${hdfsamples}/A140347.counts.hdf5 \
-I ${hdfsamples}/A140348.counts.hdf5 \
-I ${hdfsamples}/A140417A.counts.hdf5 \
-I ${hdfsamples}/A140418A.counts.hdf5 \
-I ${hdfsamples}/A150123.counts.hdf5 \
-I ${hdfsamples}/A160134A.counts.hdf5 \
-I ${hdfsamples}/A160135A.counts.hdf5 \
-I ${hdfsamples}/A160149A.counts.hdf5 \
-I ${hdfsamples}/A160352A.counts.hdf5 \
-I ${hdfsamples}/A160353.counts.hdf5 \
-I ${hdfsamples}/A160354.counts.hdf5 \
-I ${hdfsamples}/A160355.counts.hdf5 \
-I ${hdfsamples}/A160627.counts.hdf5 \
-I ${hdfsamples}/A160788A.counts.hdf5 \
-I ${hdfsamples}/A160790B.counts.hdf5 \
-I ${hdfsamples}/A160792B.counts.hdf5 \
-I ${hdfsamples}/A170001.counts.hdf5 \
-I ${hdfsamples}/A170007.counts.hdf5 \
-I ${hdfsamples}/PID11-210.counts.hdf5 \
-I ${hdfsamples}/PID12-027.counts.hdf5 \
-I ${hdfsamples}/PID12-028.counts.hdf5 \
-I ${hdfsamples}/PID12-029.counts.hdf5 \
-I ${hdfsamples}/PID12-102.counts.hdf5 \
-I ${hdfsamples}/PID12-103.counts.hdf5 \
-I ${hdfsamples}/PID13-020.counts.hdf5 \
-I ${hdfsamples}/PID13-100.counts.hdf5 \
-I ${hdfsamples}/PID13-101.counts.hdf5 \
-I ${hdfsamples}/PID13-119.counts.hdf5 \
-I ${hdfsamples}/PID13-120.counts.hdf5 \
-I ${hdfsamples}/PID13-129.counts.hdf5 \
-I ${hdfsamples}/PID13-130.counts.hdf5 \
-I ${hdfsamples}/PID13-215.counts.hdf5 \
-I ${hdfsamples}/PID13-216.counts.hdf5 \
-I ${hdfsamples}/PID13-217.counts.hdf5 \
-I ${hdfsamples}/PID13-218.counts.hdf5 \
-I ${hdfsamples}/PID13-223.counts.hdf5 \
-I ${hdfsamples}/PID13-224.counts.hdf5 \
-I ${hdfsamples}/PID13-264.counts.hdf5 \
-I ${hdfsamples}/PID13-272.counts.hdf5 \
-I ${hdfsamples}/PID13-273.counts.hdf5 \
-I ${hdfsamples}/PID13-286.counts.hdf5 \
-I ${hdfsamples}/PID13-313.counts.hdf5 \
-I ${hdfsamples}/PID13-376.counts.hdf5 \
-I ${hdfsamples}/PID14-097.counts.hdf5 \
-I ${hdfsamples}/PID14-101.counts.hdf5 \
-I ${hdfsamples}/PID14-152A.counts.hdf5 \
-I ${hdfsamples}/PID14-191.counts.hdf5 \
-I ${hdfsamples}/PID14-192.counts.hdf5 \
-I ${hdfsamples}/PID14-200.counts.hdf5 \
-I ${hdfsamples}/PID14-203.counts.hdf5 \
-I ${hdfsamples}/PID14-205.counts.hdf5 \
-I ${hdfsamples}/PID14-208.counts.hdf5 \
-I ${hdfsamples}/PID14-209.counts.hdf5 \
-I ${hdfsamples}/PID14-210.counts.hdf5 \
-I ${hdfsamples}/PID14-211.counts.hdf5 \
-I ${hdfsamples}/PID14-229.counts.hdf5 \
-I ${hdfsamples}/PID14-230.counts.hdf5 \
-I ${hdfsamples}/PID14-325.counts.hdf5 \
-I ${hdfsamples}/PID14-360.counts.hdf5 \
-I ${hdfsamples}/PID14-361.counts.hdf5 \
-I ${hdfsamples}/PID14-362.counts.hdf5 \
-I ${hdfsamples}/PID15-017.counts.hdf5 \
-I ${hdfsamples}/PID15-018.counts.hdf5 \
-I ${hdfsamples}/PID15-105.counts.hdf5 \
-I ${hdfsamples}/PID15-106.counts.hdf5 \
-I ${hdfsamples}/PID15-116A.counts.hdf5 \
-I ${hdfsamples}/PID15-119A.counts.hdf5 \
-I ${hdfsamples}/PID16-101.counts.hdf5 \
-I ${hdfsamples}/PID16-102.counts.hdf5 \
-I ${hdfsamples}/PID16-124B.counts.hdf5 \
-I ${hdfsamples}/PID16-125A.counts.hdf5 \
-I ${hdfsamples}/PID16-177.counts.hdf5 \
-I ${hdfsamples}/PID16-178.counts.hdf5 \
-I ${hdfsamples}/PID16-179.counts.hdf5 \
-I ${hdfsamples}/PID16-202A.counts.hdf5 \
-I ${hdfsamples}/PID16-203A.counts.hdf5 \
-I ${hdfsamples}/PID16-204A.counts.hdf5 \
-I ${hdfsamples}/PID16-205A.counts.hdf5 \
-I ${hdfsamples}/PID16-211.counts.hdf5 \
-I ${hdfsamples}/PID16-212.counts.hdf5 \
-I ${hdfsamples}/PID16-213.counts.hdf5 \
-I ${hdfsamples}/XLA-016A.counts.hdf5 \
--output ${gCNV_model} \
--output-prefix cgsnoB9_gCNV_normal_cohort

source deactivate