Hi, fusioncatcher fails when it is run in Tower eg:
Traceback (most recent call last):
File "/opt/fusioncatcher/v1.33/bin/remove-adapter.py", line 1272, in
main()
File "/opt/fusioncatcher/v1.33/bin/remove-adapter.py", line 1268, in main
options.processes)
File "/opt/fusioncatcher/v1.33/bin/remove-adapter.py", line 1079, in trim_adapter
linkit(input_file_1,output_file_1,kind=link)
File "/opt/fusioncatcher/v1.33/bin/remove-adapter.py", line 104, in linkit
print >>sys.stderr,"WARNING: Cannot do hard links ('%s' and '%s')!" % (linkto,file_output)
UnboundLocalError: local variable 'linkto' referenced before assignment
Could be possible to change the
remove-adapter.py \
1146 --processes 12 \
1147 --input_1 //work/scratch/5HyTfJeqqZ8kAX/27/012aeab7afbbef5f1d4c0ca79e4b36/init-f-0_blox-0_1.fq \
1148 --input_2 /work/scratch/5HyTfJeqqZ8kAX/27/012aeab7afbbef5f1d4c0ca79e4b36/init-r-1_blox-0_2.fq \
1149 --output_1 /work/scratch/5HyTfJeqqZ8kAX/27/012aeab7afbbef5f1d4c0ca79e4b36/init-noadapt-0_blox-0_1.fq \
1150 --output_2 /work/scratch/5HyTfJeqqZ8kAX/27/012aeab7afbbef5f1d4c0ca79e4b36/init-noadapt-1_blox-0_2.fq \
1151 --trim-n 3 \
1152 --link hard \
1153 > /work/scratch/5HyTfJeqqZ8kAX/27/012aeab7afbbef5f1d4c0ca79e4b36/log_adapters_0.txt \
Hi, fusioncatcher fails when it is run in Tower eg:
Traceback (most recent call last): File "/opt/fusioncatcher/v1.33/bin/remove-adapter.py", line 1272, in
main()
File "/opt/fusioncatcher/v1.33/bin/remove-adapter.py", line 1268, in main
options.processes)
File "/opt/fusioncatcher/v1.33/bin/remove-adapter.py", line 1079, in trim_adapter
linkit(input_file_1,output_file_1,kind=link)
File "/opt/fusioncatcher/v1.33/bin/remove-adapter.py", line 104, in linkit
print >>sys.stderr,"WARNING: Cannot do hard links ('%s' and '%s')!" % (linkto,file_output)
UnboundLocalError: local variable 'linkto' referenced before assignment
Could be possible to change the remove-adapter.py \ 1146 --processes 12 \ 1147 --input_1 //work/scratch/5HyTfJeqqZ8kAX/27/012aeab7afbbef5f1d4c0ca79e4b36/init-f-0_blox-0_1.fq \ 1148 --input_2 /work/scratch/5HyTfJeqqZ8kAX/27/012aeab7afbbef5f1d4c0ca79e4b36/init-r-1_blox-0_2.fq \ 1149 --output_1 /work/scratch/5HyTfJeqqZ8kAX/27/012aeab7afbbef5f1d4c0ca79e4b36/init-noadapt-0_blox-0_1.fq \ 1150 --output_2 /work/scratch/5HyTfJeqqZ8kAX/27/012aeab7afbbef5f1d4c0ca79e4b36/init-noadapt-1_blox-0_2.fq \ 1151 --trim-n 3 \ 1152 --link hard \ 1153 > /work/scratch/5HyTfJeqqZ8kAX/27/012aeab7afbbef5f1d4c0ca79e4b36/log_adapters_0.txt \
for --link soft ?