integrate not working

[Bontempogianpaolo1]

script:
./nextflow run pipeline.nf --outdir /nas/softechict-nas-2/gbontempo/ --rnareads "/homes/gbontempo/citarella/FusionFlow/tutorial/reads_{1,2}." --dnareads_tumor “/homes/gbontempo/citarella/FusionFlow/tutorial/reads_{3,4}.” --dnareads_normal “/homes/gbontempo/citarella/FusionFlow/tutorial/reads_{5,6}.*” --integrate

Error:
`
Error executing process > 'integrate_downloader (Downloading)'

Caused by:
Process integrate_downloader (Downloading) terminated with an error exit status (2)

Command executed:

#!/bin/bash

export PATH="/homes/gbontempo/.conda/envs/integrate/bin:$PATH"

mkdir files && cd "$_"

wget https://genome-idx.s3.amazonaws.com/bt/GRCh38_noalt_as.zip
unzip GRCh38_noalt_as.zip
rm GRCh38_noalt_as.zip

curl -O -J -L https://osf.io/dgvcx/download

curl -O -J -L https://osf.io/gv7sq/download
tar -xvf INTEGRATE.0.2.6.tar.gz
rm INTEGRATE.0.2.6.tar.gz

cd INTEGRATE_0_2_6 && mkdir INTEGRATE-build && cd "$_"
cmake ../Integrate/ -DCMAKE_BUILD_TYPE=release
make

Command exit status:
2

Command output:
[ 70%] Built target sasearch
Scanning dependencies of target mksary
[ 75%] Building C object examples/CMakeFiles/mksary.dir/mksary.o
[ 80%] Linking C executable mksary
[ 80%] Built target mksary
Scanning dependencies of target bwt
[ 85%] Building C object examples/CMakeFiles/bwt.dir/bwt.o
[ 90%] Linking C executable bwt
[ 90%] Built target bwt
Scanning dependencies of target suftest
[ 95%] Building C object examples/CMakeFiles/suftest.dir/suftest.o
[100%] Linking C executable suftest
[100%] Built target suftest
[ 14%] Performing install step for 'libdivsufsort-2.0.1'
[ 25%] Built target divsufsort64
[ 50%] Built target divsufsort
[ 60%] Built target unbwt
[ 70%] Built target sasearch
[ 80%] Built target mksary
[ 90%] Built target bwt
[100%] Built target suftest
Install the project...
-- Install configuration: "Release"
-- Installing: files/INTEGRATE_0_2_6/INTEGRATE-build/vendor/divsufsort/lib/pkgconfig/libdivsufsort.pc
-- Installing: files/INTEGRATE_0_2_6/INTEGRATE-build/vendor/divsufsort/lib/pkgconfig/libdivsufsort64.pc
-- Installing: files/INTEGRATE_0_2_6/INTEGRATE-build/vendor/divsufsort/include/divsufsort.h
-- Installing: files/INTEGRATE_0_2_6/INTEGRATE-build/vendor/divsufsort/include/divsufsort64.h
-- Installing: files/INTEGRATE_0_2_6/INTEGRATE-build/vendor/divsufsort/lib/libdivsufsort.so.3.0.1
-- Installing: files/INTEGRATE_0_2_6/INTEGRATE-build/vendor/divsufsort/lib/libdivsufsort.so.3
-- Installing: files/INTEGRATE_0_2_6/INTEGRATE-build/vendor/divsufsort/lib/libdivsufsort.so
-- Installing: files/INTEGRATE_0_2_6/INTEGRATE-build/vendor/divsufsort/lib/libdivsufsort64.so.3.0.1
-- Installing: files/INTEGRATE_0_2_6/INTEGRATE-build/vendor/divsufsort/lib/libdivsufsort64.so.3
-- Installing: files/INTEGRATE_0_2_6/INTEGRATE-build/vendor/divsufsort/lib/libdivsufsort64.so
[ 16%] Completed 'libdivsufsort-2.0.1'
[ 16%] Built target libdivsufsort-2.0.1
Scanning dependencies of target samtools-0.1.19
[ 18%] Creating directories for 'samtools-0.1.19'
[ 20%] Performing download step (verify and extract) for 'samtools-0.1.19'
-- extracting...
src='files/INTEGRATE_0_2_6/Integrate/vendor/samtools-0.1.19.tar.gz'
dst='files/INTEGRATE_0_2_6/INTEGRATE-build/vendor/samtools'
-- extracting... [tar xfz]
-- extracting... [analysis]
-- extracting... [rename]
-- extracting... [clean up]
-- extracting... done
[ 22%] No update step for 'samtools-0.1.19'
[ 25%] No patch step for 'samtools-0.1.19'
[ 27%] No configure step for 'samtools-0.1.19'
[ 29%] Performing build step for 'samtools-0.1.19'

Command error:
^~
ar: u' modifier ignored since D' is the default (see `U')
bam2bcf.c: In function ‘bcf_call2bcf’:
bam2bcf.c:428:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
if (bc->read_pos_bias != -1 )
^~
bam2bcf.c:430:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
kputc('\0', &s);
^~~~~
bam2bcf_indel.c: In function ‘bcf_call_add_rg’:
bam2bcf_indel.c:32:4: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
for (r = p; *r && *r != '\t' && *r != '\n'; ++r); lp = r - p;
^~~
bam2bcf_indel.c:32:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
for (r = p; *r && *r != '\t' && *r != '\n'; ++r); lp = r - p;
^~
bam2bcf_indel.c:33:4: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
for (r = q; *r && *r != '\t' && *r != '\n'; ++r); lq = r - q;
^~~
bam2bcf_indel.c:33:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
for (r = q; *r && *r != '\t' && r != '\n'; ++r); lq = r - q;
^~
errmod.c: In function ‘errmod_cal’:
errmod.c:79:8: warning: self-comparison always evaluates to false [-Wtautological-compare]
if (m > m) return -1;
^
cut_target.c: In function ‘main_cut_target’:
cut_target.c:137:36: warning: variable ‘lastpos’ set but not used [-Wunused-but-set-variable]
int c, tid, pos, n, lasttid = -1, lastpos = -1, l, max_l;
^~~~~~~
cut_target.c: In function ‘process_cns.isra.1’:
cut_target.c:96:2: warning: assuming signed overflow does not occur when assuming that (X + c) < X is always false [-Wstrict-overflow]
for (i = 0, s = -1; i <= l; ++i) {
^~~
bam2depth.c: In function ‘main_depth’:
bam2depth.c:85:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation]
else
^~~~
bam2depth.c:87:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’
data = calloc(n, sizeof(void)); // data[i] for the i-th input
^~~~
bam_tview_curses.c:5:10: fatal error: curses.h: No such file or directory
#include <curses.h>
^~~~~~~~~~
compilation terminated.
make[4]: *** [Makefile:24: bam_tview_curses.o] Error 1
make[3]: *** [Makefile:27: all-recur] Error 1
make[2]: *** [CMakeFiles/samtools-0.1.19.dir/build.make:132: vendor/src/samtools-0.1.19-stamp/samtools-0.1.19-build] Error 2
make[1]: *** [CMakeFiles/Makefile2:148: CMakeFiles/samtools-0.1.19.dir/all] Error 2
make: *** [Makefile:103: all] Error 2

Work dir:
/homes/gbontempo/citarella/FusionFlow/work/f2/4fde73474c8bf55146b8ce55832211

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh
`