Error: make: *** No targets. Stop.

[Juergen Tomasch]

Hi Nicholas

I installed HiC-Pro succesfully.

However, when I start HiC-Pro with

/usr/local/bin/HiC-Pro_2.11.4/bin/HiC-Pro -i /data2/hic/20201110/input -o /data2/hic/20201110/output -c /data2/hic/config-hicpro_proximo.txt

I get this strange error:

make: *** No targets.  Stop.

I tried to track down where the error occurs by introducing errors in the command input and see if i get a different error message. 

When I provide a wrong configuration file I get the error:

Error - Hi-C config file '/data2/hic/config-hicpro_proximo2.txt' not found

produced in hic.inc.sh in line 69

When I provide input files in the wrong format or a wrong input folder, I again get the make no targets error. So my best guess is that the error is produced by the make command within the read_config()-function in hic.inc.sh line 39 but I have no idea what exactly went wrong.

Any help is much appreciated.

Thanks, Jürgen

[nservant]

Hi,

That's weird ! I do not understand why the error mentioned 'config-hicpro-poximo2.txt', while you provide 'config-hicpro-proximo.txt'

Any idea ?

Otherwise, could you show me the content of the input folder please ?

Best

[Juergen Tomasch]

Thanks for the quick response.

Sorry, I think I was imprecise here:

When running:

/usr/local/bin/HiC-Pro_2.11.4/bin/HiC-Pro -i /data2/hic/20201110/input -o /data2/hic/20201110/output -c /data2/hic/config-hicpro_proximo.txt

the error is: 

make: *** No targets.  Stop. 

In order to find out where in the skript the error occurs I systematically introduced errors in the command

When running: 

/usr/local/bin/HiC-Pro_2.11.4/bin/HiC-Pro -i /data2/hic/20201110/input -o /data2/hic/20201110/output -c /data2/hic/config-hicpro_proximo2.txt

I get:

Error - Hi-C config file '/data2/hic/config-hicpro_proximo2.txt' not found

because this file does not exist

However when running 

/usr/local/bin/HiC-Pro_2.11.4/bin/HiC-Pro -i /data2/hic/20201110/input2 -o /data2/hic/20201110/output -c /data2/hic/config-hicpro_proximo2.txt 

I get:

make: *** No targets.  Stop.  

If the script would have continued to the line in which it checks the input files, I would have expected the error 

Inputs '$INPUT' not found. Exit. 

because this folder with the input data does not exist

 

The input folder contains one subfolder with the data:

drwxrwxrwx 2 jto07 moba 4096 Nov 29 17:43 sample1/

The content of sample1/

drwxrwxrwx 2 jto07 moba      4096 Nov 29 17:43 ./

drwxr-xr-x 3 jto07 moba      4096 Nov 29 17:43 ../

-rwxrwxrwx 1 jto07 moba 230584350 Nov 29 13:21 HiC_PA14_C3_S95_c1.fastq.gz*

-rwxrwxrwx 1 jto07 moba 240436190 Nov 29 13:21 HiC_PA14_C3_S95_c2.fastq.gz*

[nservant]

I do not see anything wrong in your  message or conf :(

To me, it seems that the `make` command does not find the Makefile ...

Did you have any trouble during the installation ? do you the script /usr/local/bin/HiC-Pro_2.11.4/script/Makefile ?

Would be great if you could add some trace for instance at the end of the bin/HiC-Pro script, there is the make command ... could you print it to check how it looks like ?

[Juergen Tomasch]

  The installation messages indicate no error but there are warnings:

(python2.7) root@hzi-bsmoba:/home/jto07/HiC-Pro# make configure

make -f ./scripts/install/Makefile CONFIG_SYS=./config-install.txt

make[1]: Entering directory '/home/jto07/HiC-Pro'

./scripts/install/install_dependencies.sh -c ./config-install.txt -o  /usr/local/bin/HiC-Pro_2.11.4 -q

Make sure internet connection works for your shell prompt under current user's privilege ...

Starting HiC-Pro installation ...

Checking dependencies ...

Checking Python libraries ...

The required Python libraries appear to be already installed.

Checking R installation ...

The required R packages appear to be already installed.

Bowtie2 Aligner appears to be already installed.

Samtools appears to be already installed.

Dependencies checked !

Check HiC-Pro configuration ...

Warning : Scheduler system not defined - Default is Torque/PBS

Configuration for TORQUE/PBS system.

make[1]: Leaving directory '/home/jto07/HiC-Pro'

(python2.7) root@hzi-bsmoba:/home/jto07/HiC-Pro# make install

(g++ -Wall -O2 -std=c++0x -o build_matrix /home/jto07/HiC-Pro/scripts/src/build_matrix.cpp; mv build_matrix /home/jto07/HiC-Pro/scripts)

(g++ -Wall -O2 -std=c++0x -o cutsite_trimming /home/jto07/HiC-Pro/scripts/src/cutsite_trimming.cpp; mv cutsite_trimming /home/jto07/HiC-Pro/scripts)

Installing the iced package as root

(cd /home/jto07/HiC-Pro/scripts/src/ice_mod/; /usr/bin/miniconda3/envs/python2.7/bin/python setup.py install;)

/usr/bin/miniconda3/envs/python2.7/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'include_package_data'

  warnings.warn(msg)

/usr/bin/miniconda3/envs/python2.7/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'zip_safe'

  warnings.warn(msg)

Warning: Assuming default configuration (iced/utils/{setup_utils,setup}.py was not found)Appending iced.utils configuration to iced

Ignoring attempt to set 'name' (from 'iced' to 'iced.utils')

Appending iced.datasets configuration to iced

Ignoring attempt to set 'name' (from 'iced' to 'iced.datasets')

non-existing path in 'iced/io': '../src/cblas'

non-existing path in 'iced/io': '../src/cblas'

Appending iced.io configuration to iced

Ignoring attempt to set 'name' (from 'iced' to 'iced.io')

non-existing path in 'iced': '../src/cblas'

non-existing path in 'iced': '../src/cblas'

Appending iced configuration to

Ignoring attempt to set 'name' (from '' to 'iced')

running install

running build

running config_cc

unifing config_cc, config, build_clib, build_ext, build commands --compiler options

running config_fc

unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options

running build_src

build_src

building extension "iced.io.fastio_" sources

building extension "iced.io.read" sources

building extension "iced._normalization_" sources

building extension "iced._filter_" sources

building data_files sources

build_src: building npy-pkg config files

running build_py

running build_ext

customize UnixCCompiler

customize UnixCCompiler using build_ext

running build_scripts

running install_lib

running install_scripts

changing mode of /usr/bin/miniconda3/envs/python2.7/bin/ice to 755

running install_data

running install_egg_info

Removing /usr/bin/miniconda3/envs/python2.7/lib/python2.7/site-packages/iced-0.4.2-py2.7.egg-info

Writing /usr/bin/miniconda3/envs/python2.7/lib/python2.7/site-packages/iced-0.4.2-py2.7.egg-info

running install_clib

customize UnixCCompiler

cp -Ri /home/jto07/HiC-Pro /usr/local/bin/HiC-Pro_2.11.4

HiC-Pro installed in /usr/local/bin/HiC-Pro_2.11.4 !

The Makefile is there.

The trace looks like this:

(python2.7) root@hzi-bsmoba:/home/jto07/HiC-Pro# bash -x /usr/local/bin/HiC-Pro_2.11.4/bin/HiC-Pro -i /data2/hic/20201110/input -o /data2/hic/20201110/output -c /data2/hic/config-hicpro_proximo.txt

+ SOFT=HiC-Pro

+ VERSION=2.11.4

++ dirname /usr/local/bin/HiC-Pro_2.11.4/bin/HiC-Pro

+ BIN_PATH=/usr/local/bin/HiC-Pro_2.11.4/bin

++ cd /usr/local/bin/HiC-Pro_2.11.4/bin

++ pwd

+ ABS_BIN_PATH=/usr/local/bin/HiC-Pro_2.11.4/bin

+ SCRIPTS_PATH=/usr/local/bin/HiC-Pro_2.11.4/bin/../scripts/

+ INSTALL_PATH=/usr/local/bin/HiC-Pro_2.11.4/bin/../

+ CUR_PATH=/home/jto07/HiC-Pro

+ CLUSTER=0

+ MAKE_OPTS=

+ INPUT=

+ OUTPUT=

+ CONF=

+ '[' 6 -lt 1 ']'

+ for arg in "$@"

+ shift

+ case "$arg" in

+ set -- /data2/hic/20201110/input -o /data2/hic/20201110/output -c /data2/hic/config-hicpro_proximo.txt -i

+ for arg in "$@"

+ shift

+ case "$arg" in

+ set -- -o /data2/hic/20201110/output -c /data2/hic/config-hicpro_proximo.txt -i /data2/hic/20201110/input

+ for arg in "$@"

+ shift

+ case "$arg" in

+ set -- /data2/hic/20201110/output -c /data2/hic/config-hicpro_proximo.txt -i /data2/hic/20201110/input -o

+ for arg in "$@"

+ shift

+ case "$arg" in

+ set -- -c /data2/hic/config-hicpro_proximo.txt -i /data2/hic/20201110/input -o /data2/hic/20201110/output

+ for arg in "$@"

+ shift

+ case "$arg" in

+ set -- /data2/hic/config-hicpro_proximo.txt -i /data2/hic/20201110/input -o /data2/hic/20201110/output -c

+ for arg in "$@"

+ shift

+ case "$arg" in

+ set -- -i /data2/hic/20201110/input -o /data2/hic/20201110/output -c /data2/hic/config-hicpro_proximo.txt

+ getopts :i:o:c:s:pvh OPT

+ case $OPT in

+ INPUT=/data2/hic/20201110/input

+ getopts :i:o:c:s:pvh OPT

+ case $OPT in

+ OUTPUT=/data2/hic/20201110/output

+ getopts :i:o:c:s:pvh OPT

+ case $OPT in

+ CONF=/data2/hic/config-hicpro_proximo.txt

+ getopts :i:o:c:s:pvh OPT

+ [[ ! -e /usr/local/bin/HiC-Pro_2.11.4/bin/..//config-system.txt ]]

+ [[ -z /data2/hic/20201110/input ]]

+ [[ -z /data2/hic/20201110/output ]]

+ [[ -z /data2/hic/config-hicpro_proximo.txt ]]

+ [[ '' == '' ]]

+ which ice

+ '[' 0 '!=' 0 ']'

+ . /usr/local/bin/HiC-Pro_2.11.4/bin/../scripts//hic.inc.sh

++ set -o pipefail

++ set -o errexit

+++ dirname /usr/local/bin/HiC-Pro_2.11.4/bin/HiC-Pro

++ CURRENT_PATH=/usr/local/bin/HiC-Pro_2.11.4/bin

++ tmpfile1=/tmp/hic1.3315346

++ tmpfile2=/tmp/hic2.3315346

++ tmpmkfile=/tmp/hicmk.3315346

++ trap 'rm -f /tmp/hic1.3315346 /tmp/hic2.3315346 /tmp/hicmk.3315346' 0 1 2 3

++ SYS_CONF=/usr/local/bin/HiC-Pro_2.11.4/bin/../config-system.txt

++ '[' -e /usr/local/bin/HiC-Pro_2.11.4/bin/../config-system.txt ']'

++ read_config /usr/local/bin/HiC-Pro_2.11.4/bin/../config-system.txt

++ local conf=/usr/local/bin/HiC-Pro_2.11.4/bin/../config-system.txt

++ cat /usr/local/bin/HiC-Pro_2.11.4/bin/../config-system.txt

++ echo _dummy_target_:

++ make -f /tmp/hicmk.3315346 -p -n

++ filter_config

++ sed -e 's/#.*//'

++ egrep '^[ \t]*[a-zA-Z_][a-zA-Z0-9_]*[ \t]*:?='

++ sed -e 's/[ \t]*:=[ \t]*/ :=/' -e 's/[ \t][^:]*=[ \t]*/ =/' -e 's/\([^ \t]*\)=/\1 =/' -e 's/ *$//g'

++ sort -u -k 1b,1

++ cat /usr/local/bin/HiC-Pro_2.11.4/bin/../config-system.txt

++ filter_config

++ sed -e 's/#.*//'

++ egrep '^[ \t]*[a-zA-Z_][a-zA-Z0-9_]*[ \t]*:?='

++ sed -e 's/[ \t]*:=[ \t]*/ :=/' -e 's/[ \t][^:]*=[ \t]*/ =/' -e 's/\([^ \t]*\)=/\1 =/' -e 's/ *$//g'

++ sort -u -k 1b,1

+++ join /tmp/hic1.3315346 /tmp/hic2.3315346

+++ awk '-F =' '{printf("%s=\"%s\"; export %s;\n", $1, $2, $1)}'

++ eval 'ANNOT_DIR="/usr/local/bin/HiC-Pro_2.11.4/annotation"; export ANNOT_DIR;

BOWTIE2_PATH="/usr/bin/miniconda3/envs/python2.7/bin"; export BOWTIE2_PATH;

CLUSTER_SCRIPT="/usr/local/bin/HiC-Pro_2.11.4/scripts/make_torque_script.sh"; export CLUSTER_SCRIPT;

INSTALL_PATH="/usr/local/bin/HiC-Pro_2.11.4"; export INSTALL_PATH;

PYTHON_PATH="/usr/bin/miniconda3/envs/python2.7/bin"; export PYTHON_PATH;

R_PATH="/usr/bin"; export R_PATH;

SAMTOOLS_PATH="/usr/bin/miniconda3/bin"; export SAMTOOLS_PATH;

SCRIPTS="/usr/local/bin/HiC-Pro_2.11.4/scripts"; export SCRIPTS;

SOURCES="/usr/local/bin/HiC-Pro_2.11.4/scripts/src"; export SOURCES;'

+++ ANNOT_DIR=/usr/local/bin/HiC-Pro_2.11.4/annotation

+++ export ANNOT_DIR

+++ BOWTIE2_PATH=/usr/bin/miniconda3/envs/python2.7/bin

+++ export BOWTIE2_PATH

+++ CLUSTER_SCRIPT=/usr/local/bin/HiC-Pro_2.11.4/scripts/make_torque_script.sh

+++ export CLUSTER_SCRIPT

+++ INSTALL_PATH=/usr/local/bin/HiC-Pro_2.11.4

+++ export INSTALL_PATH

+++ PYTHON_PATH=/usr/bin/miniconda3/envs/python2.7/bin

+++ export PYTHON_PATH

+++ R_PATH=/usr/bin

+++ export R_PATH

+++ SAMTOOLS_PATH=/usr/bin/miniconda3/bin

+++ export SAMTOOLS_PATH

+++ SCRIPTS=/usr/local/bin/HiC-Pro_2.11.4/scripts

+++ export SCRIPTS

+++ SOURCES=/usr/local/bin/HiC-Pro_2.11.4/scripts/src

+++ export SOURCES

++ BOWTIE2_IDX=/

++ export BOWTIE2_IDX

++ BOWTIE2_GLOBAL_OUTPUT_DIR=/bwt2_global

++ export BOWTIE2_GLOBAL_OUTPUT_DIR

++ BOWTIE2_LOCAL_OUTPUT_DIR=/bwt2_local

++ export BOWTIE2_LOCAL_OUTPUT_DIR

++ BOWTIE2_FINAL_OUTPUT_DIR=/bwt2

++ export BOWTIE2_FINAL_OUTPUT_DIR

+++ echo

+++ sed -e 's|^\./||'

++ RAW_DIR=

++ '[' '!' -z /data2/hic/config-hicpro_proximo.txt ']'

+++ abspath /data2/hic/config-hicpro_proximo.txt

+++ [[ /data2/hic/config-hicpro_proximo.txt = /* ]]

+++ echo /data2/hic/config-hicpro_proximo.txt

++ CONF=/data2/hic/config-hicpro_proximo.txt

++ '[' -e /data2/hic/config-hicpro_proximo.txt ']'

++ read_config /data2/hic/config-hicpro_proximo.txt

++ local conf=/data2/hic/config-hicpro_proximo.txt

++ cat /data2/hic/config-hicpro_proximo.txt

++ echo _dummy_target_:

++ make -f /tmp/hicmk.3315346 -p -n

++ filter_config

++ sed -e 's/#.*//'

++ egrep '^[ \t]*[a-zA-Z_][a-zA-Z0-9_]*[ \t]*:?='

++ sed -e 's/[ \t]*:=[ \t]*/ :=/' -e 's/[ \t][^:]*=[ \t]*/ =/' -e 's/\([^ \t]*\)=/\1 =/' -e 's/ *$//g'

++ sort -u -k 1b,1

make: *** No targets.  Stop.

+ rm -f /tmp/hic1.3315346 /tmp/hic2.3315346 /tmp/hicmk.3315346

Thanks!

[nservant]

Thanks for the details.

I'm almost sure that it crashes when it try to read the config file ... but I do not see anything special there !

To make it short, when HiC-pro read a config file, it makes a copy in /tmp/ and run ;

```

filter_config()                                                                                                                                                                                              

{                                                                                                                                                                                                            

    sed -e 's/#.*//' | egrep '^[ \t]*[a-zA-Z_][a-zA-Z0-9_]*[ \t]*:?=' | sed -e 's/[ \t]*:=[ \t]*/ :=/' -e 's/[ \t][^:]*=[ \t]*/ =/' -e 's/\([^ \t]*\)=/\1 =/' -e 's/ *$//g' | sort -u -k 1b,1                

}

 cat $conf > /tmp/hicpro00000                                                                                                                                                                                   

 echo "_dummy_target_:" >> /tmp/hicpro00000                                                                                                                                                                     

 make -f /tmp/hicpro00000 -p -n | filter_config                                                                                                                                                     

```

If you remove the line

```

 echo "_dummy_target_:" >> /tmp/hicpro00000                                                                                                                                                                     

```

Then, you have your error. Because there is no "Make target" in the config file.

On your logs, we see that it crashes at the 'make' command, a bit as if the "dummy_target" was not written in the /tmp/ file.

```

++ cat /data2/hic/config-hicpro_proximo.txt

++ echo _dummy_target_:

++ make -f /tmp/hicmk.3315346 -p -n

++ filter_config

```

And honestly, I do not know why. That's the first time I see this.

Maybe you could comment the line 21 in scripts/hic.inc.sh to not delete the tmp file.

```

trap "rm -f $tmpfile1 $tmpfile2 $tmpmkfile" 0 1 2 3                                                                                                                                                          

```

And check what it looks like ? and especially if you do see this `_dummy_tagert_` line ?

Otherwise, I'm wondering if it cannot be link to a make version ...

Which system are you using ? make version ?

Best