Always failed to install BinPack my Ubuntu system. Could you please upload a...
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Always failed to install BinPack on my Ubuntu system. But I tried BinPack_binary version directly without installation and it works. But it seems this binary is the 1.0 version of BinPack and some of my data can not finish (quit with errors). Since I have tried many times to install 1.1 verion without any success (seems boost can not be installed correctly on my system with mutiple errors), could you please upload a binary version for BinPack 1.1 directly? Thanks very much.
Also, in ./BinPacker_binary/src/ folder, the binarys of the programs: packing, read_result, change_fasta, and Find_errors, etc. were missing (since I can not build them, could you include the binarys of them in the BinPack 1.1 binary package?) Thanks!
Processing data...
cat ./saved/left.fa ./saved/right.fa >both.fa
Processing completele!
Constructing Splicing Graph...
/media/windupzs/NGS/othertools/BinPacker/BinPacker_binary/src/Assemble --reads both.fa -k 25 --pair_end --double_stranded_mode --pair_gap_length 200 --min_seed_coverage 2 --min_seed_entropy 1.5 --min_kmer_coverage 1 --min_kmer_entropy 0.0 --min_junction_coverage 2 --debug
Assembling Transtripts...
rm: cannot remove '/media/windupzs/NGS/Data/Hamster-Hydrocephalus/Denovo/RawGraphs/raw_graph.list': No such file or directory
Processing Splicing Graph: Assemble.log BinPacker-All BinPacker-All.sh BinPacker-All.sh~ Denovo-Assembly_All.sh Denovo-Assembly_All.sh~ LDBB3_R1-paired-clean.fq.gz.readcount LDBB3_R2-paired-clean.fq.gz.readcount LDNB2_R1-paired-clean.fq.gz.readcount LDNB2_R2-paired-clean.fq.gz.readcount LDNN1_R1-paired-clean.fq.gz.readcount LDNN1_R2-paired-clean.fq.gz.readcount LLBB9_R1-paired-clean.fq.gz.readcount LLBB9_R2-paired-clean.fq.gz.readcount LLNB8_R1-paired-clean.fq.gz.readcount LLNB8_R2-paired-clean.fq.gz.readcount LLNN7_R1-paired-clean.fq.gz.readcount LLNN7_R2-paired-clean.fq.gz.readcount LNBB6_R1-paired-clean.fq.gz.readcount LNBB6_R2-paired-clean.fq.gz.readcount LNNB5_R1-paired-clean.fq.gz.readcount LNNB5_R2-paired-clean.fq.gz.readcount LNNN4_R1-paired-clean.fq.gz.readcount LNNN4_R2-paired-clean.fq.gz.readcount log_temp RawGraphs RDBB12_R1-paired-clean.fq.gz.readcount RDBB12_R2-paired-clean.fq.gz.readcount RDNB11_R1-paired-clean.fq.gz.readcount RDNB11_R2-paired-clean.fq.gz.readcount RDNN10_R1-paired-clean.fq.gz.readcount RDNN10_R2-paired-clean.fq.gz.readcount RLBB18_R1-paired-clean.fq.gz.readcount RLBB18_R2-paired-clean.fq.gz.readcount RLNB17_R1-paired-clean.fq.gz.readcount RLNB17_R2-paired-clean.fq.gz.readcount RLNN16_R1-paired-clean.fq.gz.readcount RLNN16_R2-paired-clean.fq.gz.readcount rnaSPAdes rnaSPAdes.sh rnaSPAdes.yaml RNBB15_R1-paired-clean.fq.gz.readcount RNBB15_R2-paired-clean.fq.gz.readcount RNNB14_R1-paired-clean.fq.gz.readcount RNNB14_R2-paired-clean.fq.gz.readcount RNNN13_R1-paired-clean.fq.gz.readcount RNNN13_R2-paired-clean.fq.gz.readcount saved SOAPdenovo_conf SOAPdenovo_conf_All SOAPdenovo-Trans SOAPdenovo-Trans.sh Trinity-All.sh Trinity-All.sh~ Trinity-Groups.sh Trinity-Groups.sh~ Trinity-LNs-OK Trinity-RDs-OK ...
/media/windupzs/NGS/othertools/BinPacker/BinPacker_binary/BinPacker: line 275: /media/windupzs/NGS/othertools/BinPacker/BinPacker_binary/src/packing: No such file or directory
cp: cannot stat 'New_Splicing_Graph.txt': No such file or directory
cp: cannot stat 'Line_Graph.txt': No such file or directory
/media/windupzs/NGS/othertools/BinPacker/BinPacker_binary/BinPacker: line 316: /media/windupzs/NGS/othertools/BinPacker/BinPacker_binary/src/read_result: No such file or directory
/media/windupzs/NGS/othertools/BinPacker/BinPacker_binary/BinPacker: line 320: /media/windupzs/NGS/othertools/BinPacker/BinPacker_binary/src/packing: No such file or directory
cp: cannot stat 'Line_Graph.txt': No such file or directory
/media/windupzs/NGS/othertools/BinPacker/BinPacker_binary/BinPacker: line 360: /media/windupzs/NGS/othertools/BinPacker/BinPacker_binary/src/read_result: No such file or directory
awk: cannot open BinPacker_temp.fa (No such file or directory)
/media/windupzs/NGS/othertools/BinPacker/BinPacker_binary/BinPacker: line 365: /media/windupzs/NGS/othertools/BinPacker/BinPacker_binary/src/change_fasta: No such file or directory
/media/windupzs/NGS/othertools/BinPacker/BinPacker_binary/BinPacker: line 366: /media/windupzs/NGS/othertools/BinPacker/BinPacker_binary/src/Find_errors: No such file or directory
rm: cannot remove 'Temp.fa': No such file or directory
rm: cannot remove 'Raw_New_Splicing_Graph.txt': No such file or directory
mv: cannot stat 'BinPacker.fa': No such file or directory
mv: cannot move 'BinPacker_Out_Dir' to './BinPacker-All/BinPacker_Out_Dir': Directory not empty
Congratulations! Your job is finished!