Xiangyang1984
commented
4 years ago Hi，APHA-AMR-VIR ， Thanks for your interete in Gcluster tool. The error is occurred due to that the .tbl files could not be rewritten. I suggested you should check the read-write permission for the Gcluster__output_direction.
Sincerely, Xiangyang Li
Hi, I came across your program and would like to use it to make nice alignments as in your paper. Installation via conda is fine and the test.pl works but when I try with my own data or your test data I get the error below. Can you please give me clue to resolve this problem. Many thanks Manal
(veiwing) [p170122@PC-228 Gcluster-master]$ Gcluster.pl -dir '/home/p170122/mnt/BactiPipes_MA2017/programs/Gcluster/Gcluster-master/test_data/gbk/' -gene '/home/p170122/mnt/BactiPipes_MA2017/programs/Gcluster/Gcluster-master/test_data/interested_gene_name.txt' -o ~/mnt/REHAB_OR1061/Data_analysis/Chr_AMR/Cattle/RHB12-C24/Gcluster/outputtest
Tue Jul 14 11:22:27 2020: Gcluster.pl start...
GenBank_extraction_percent: 11...22...33...44...55...66...77...88...100...done Step 1-1: Extract all predicted proteomic sequences of each genebank file in folder, and transformat protein sequence into a ID-sequence hash
Step 1-2: Extract all feature table of each genebank file in folder Can't do inplace edit on /home/p170122/mnt/REHAB_OR1061/Data_analysis/Chr_AMR/Cattle/RHB12-C24/Gcluster/outputtest/Sub_TFT.gbk/Thiomonas_arsenitoxydans_3As.tbl_2935.part: File exists. Can't do inplace edit on /home/p170122/mnt/REHAB_OR1061/Data_analysis/Chr_AMR/Cattle/RHB12-C24/Gcluster/outputtest/Sub_TFT.gbk/Thiomonas_delicata_DSM_16361.tbl_1215.part: File exists. Can't do inplace edit on /home/p170122/mnt/REHAB_OR1061/Data_analysis/Chr_AMR/Cattle/RHB12-C24/Gcluster/outputtest/Sub_TFT.gbk/Thiomonas_intermedia_ATCC_15466.tbl_248.part: File exists. Can't do inplace edit on /home/p170122/mnt/REHAB_OR1061/Data_analysis/Chr_AMR/Cattle/RHB12-C24/Gcluster/outputtest/Sub_TFT.gbk/Thiomonas_intermedia_K12.tbl_3085.part: File exists. Can't do inplace edit on /home/p170122/mnt/REHAB_OR1061/Data_analysis/Chr_AMR/Cattle/RHB12-C24/Gcluster/outputtest/Sub_TFT.gbk/Thiomonas_sp._ACO3.tbl_2878.part: File exists. Can't do inplace edit on /home/p170122/mnt/REHAB_OR1061/Data_analysis/Chr_AMR/Cattle/RHB12-C24/Gcluster/outputtest/Sub_TFT.gbk/Thiomonas_sp._ACO7.tbl_1889.part: File exists. Can't do inplace edit on /home/p170122/mnt/REHAB_OR1061/Data_analysis/Chr_AMR/Cattle/RHB12-C24/Gcluster/outputtest/Sub_TFT.gbk/Thiomonas_sp._B1.tbl_3573.part: File exists. Can't do inplace edit on /home/p170122/mnt/REHAB_OR1061/Data_analysis/Chr_AMR/Cattle/RHB12-C24/Gcluster/outputtest/Sub_TFT.gbk/Thiomonas_sp._FB-Cd.tbl_2821.part: File exists. Can't do inplace edit on /home/p170122/mnt/REHAB_OR1061/Data_analysis/Chr_AMR/Cattle/RHB12-C24/Gcluster/outputtest/Sub_TFT.gbk/Thiomonas_sp._X19.tbl_3231.part: File exists. Can't open /home/p170122/mnt/REHAB_OR1061/Data_analysis/Chr_AMR/Cattle/RHB12-C24/Gcluster/outputtest/Sub_TFT.gbk/Thiomonas_delicata_DSM_16361.tbl_1215.part: Device not a stream.
Step 2: Generate a sub-TFT table file containing the gene information flanking the interested gene Device not a stream at /home/p170122/anaconda2/envs/veiwing/share/Gcluster/lib/process.pm line 402, line 62704.