/var/spool/sge/scc-kb7/job_scripts/9374098: line 30: [: missing `]' /var/spool/sge/scc-kb7/job_scripts/9374098: line 30: 9: command not found ------------------------------------------------------------------------------- ERROR: deeptools/3.1.3 requires several additional modules. Run the following commands to load all of the dependencies (including this module): module load python2 module load deeptools/3.1.3 ------------------------------------------------------------------------------- cp: cannot stat '/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/WT_1/fastq/tophat2/WT_1_primary_unique.bam': No such file or directory cp: cannot stat '/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/WT_1/fastq/tophat2/WT_1_primary_unique.bam.bai': No such file or directory cp: cannot stat '/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/WT_2/fastq/tophat2/WT_2_primary_unique.bam': No such file or directory cp: cannot stat '/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/WT_2/fastq/tophat2/WT_2_primary_unique.bam.bai': No such file or directory cp: cannot stat '/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/WT_3/fastq/tophat2/WT_3_primary_unique.bam': No such file or directory cp: cannot stat '/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/WT_3/fastq/tophat2/WT_3_primary_unique.bam.bai': No such file or directory cp: cannot stat '/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/WT_4/fastq/tophat2/WT_4_primary_unique.bam': No such file or directory cp: cannot stat '/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/WT_4/fastq/tophat2/WT_4_primary_unique.bam.bai': No such file or directory cp: cannot stat '/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/MANFHet_1/fastq/tophat2/MANFHet_1_primary_unique.bam': No such file or directory cp: cannot stat '/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/MANFHet_1/fastq/tophat2/MANFHet_1_primary_unique.bam.bai': No such file or directory cp: cannot stat '/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/MANFHet_2/fastq/tophat2/MANFHet_2_primary_unique.bam': No such file or directory cp: cannot stat '/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/MANFHet_2/fastq/tophat2/MANFHet_2_primary_unique.bam.bai': No such file or directory cp: cannot stat '/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/MANFHet_3/fastq/tophat2/MANFHet_3_primary_unique.bam': No such file or directory cp: cannot stat '/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/MANFHet_3/fastq/tophat2/MANFHet_3_primary_unique.bam.bai': No such file or directory cp: cannot stat '/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/MANFHet_4/fastq/tophat2/MANFHet_4_primary_unique.bam': No such file or directory cp: cannot stat '/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/MANFHet_4/fastq/tophat2/MANFHet_4_primary_unique.bam.bai': No such file or directory ls: cannot access *.bam: No such file or directory ls: cannot access *.bam: No such file or directory mv: cannot stat '*.bam': No such file or directory mv: cannot stat '*.bam.bai': No such file or directory /var/spool/sge/scc-kb7/job_scripts/9374098: line 378: bamCorrelate: command not found Traceback (most recent call last): File "/restricted/projectnb/waxmanlab/environment/.conda/envs/new_env1/bin/plotCorrelation", line 5, in from deeptools.plotCorrelation import main File "/restricted/projectnb/waxmanlab/environment/.conda/envs/new_env1/lib/python2.7/site-packages/deeptools/plotCorrelation.py", line 13, in from deeptools.correlation import Correlation File "/restricted/projectnb/waxmanlab/environment/.conda/envs/new_env1/lib/python2.7/site-packages/deeptools/correlation.py", line 5, in import scipy.stats File "/restricted/projectnb/waxmanlab/environment/.conda/envs/new_env1/lib/python2.7/site-packages/scipy/stats/__init__.py", line 345, in from .stats import * File "/restricted/projectnb/waxmanlab/environment/.conda/envs/new_env1/lib/python2.7/site-packages/scipy/stats/stats.py", line 169, in import scipy.special as special File "/restricted/projectnb/waxmanlab/environment/.conda/envs/new_env1/lib/python2.7/site-packages/scipy/special/__init__.py", line 640, in from ._ufuncs import * ImportError: libgfortran.so.4: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/restricted/projectnb/waxmanlab/environment/.conda/envs/new_env1/bin/plotCorrelation", line 5, in from deeptools.plotCorrelation import main File "/restricted/projectnb/waxmanlab/environment/.conda/envs/new_env1/lib/python2.7/site-packages/deeptools/plotCorrelation.py", line 13, in from deeptools.correlation import Correlation File "/restricted/projectnb/waxmanlab/environment/.conda/envs/new_env1/lib/python2.7/site-packages/deeptools/correlation.py", line 5, in import scipy.stats File "/restricted/projectnb/waxmanlab/environment/.conda/envs/new_env1/lib/python2.7/site-packages/scipy/stats/__init__.py", line 345, in from .stats import * File "/restricted/projectnb/waxmanlab/environment/.conda/envs/new_env1/lib/python2.7/site-packages/scipy/stats/stats.py", line 169, in import scipy.special as special File "/restricted/projectnb/waxmanlab/environment/.conda/envs/new_env1/lib/python2.7/site-packages/scipy/special/__init__.py", line 640, in from ._ufuncs import * ImportError: libgfortran.so.4: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/restricted/projectnb/waxmanlab/environment/.conda/envs/new_env1/bin/plotCorrelation", line 5, in from deeptools.plotCorrelation import main File "/restricted/projectnb/waxmanlab/environment/.conda/envs/new_env1/lib/python2.7/site-packages/deeptools/plotCorrelation.py", line 13, in from deeptools.correlation import Correlation File "/restricted/projectnb/waxmanlab/environment/.conda/envs/new_env1/lib/python2.7/site-packages/deeptools/correlation.py", line 5, in import scipy.stats File "/restricted/projectnb/waxmanlab/environment/.conda/envs/new_env1/lib/python2.7/site-packages/scipy/stats/__init__.py", line 345, in from .stats import * File "/restricted/projectnb/waxmanlab/environment/.conda/envs/new_env1/lib/python2.7/site-packages/scipy/stats/stats.py", line 169, in import scipy.special as special File "/restricted/projectnb/waxmanlab/environment/.conda/envs/new_env1/lib/python2.7/site-packages/scipy/special/__init__.py", line 640, in from ._ufuncs import * ImportError: libgfortran.so.4: cannot open shared object file: No such file or directory cp: cannot stat '*.png': No such file or directory