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shizhuoxing / BGI-Full-Length-RNA-Analysis-Pipeline

Full-Length RNA Analysis pipeline developted by BGI RD group.
https://github.com/shizhuoxing/BGI-Full-Length-RNA-Analysis-Pipeline
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unable to use the softwares (classify_by_primer,classify_by_primer.fullpa,flnc2sam) #4

Open geluanfeng opened 2 years ago

geluanfeng commented 2 years ago

hello！I`m geluanfeng.I have some problems.I have these software installed, but I am getting errors when running them. “ gelf2022@qmaster:/public252/gelf2022/datas/Zea_mays/Iso-Seq/BGI-Full-Length-RNA-Analysis-Pipeline/bin$ export PATH=$PATH:/public252/gelf2022/datas/Zea_mays/Iso-Seq/BGI-Full-Length-RNA-Analysis-Pipeline/bin/ gelf2022@qmaster:/public252/gelf2022/datas/Zea_mays/Iso-Seq/BGI-Full-Length-RNA-Analysis-Pipeline/bin$ classify_by_primer -h classify_by_primer: Operation not permitted 已杀死 gelf2022@qmaster:/public252/gelf2022/datas/Zea_mays/Iso-Seq/BGI-Full-Length-RNA-Analysis-Pipeline/bin$ classify_by_primer.fullpa classify_by_primer.fullpa: Operation not permitted 已杀死 gelf2022@qmaster:/public252/gelf2022/datas/Zea_mays/Iso-Seq/BGI-Full-Length-RNA-Analysis-Pipeline/bin$ flnc2sam flnc2sam: Operation not permitted 已杀死 gelf2022@qmaster:/public252/gelf2022/datas/Zea_mays/Iso-Seq/BGI-Full-Length-RNA-Analysis-Pipeline/bin$ ll 总用量 72 drwxrwxrwx 2 gelf2022 gelf2022 4096 9月 1 13:49 ./ drwxrwxr-x 7 gelf2022 gelf2022 4096 9月 1 13:49 ../ -rwxr-xr-x 1 gelf2022 gelf2022 17408 9月 1 13:49 classify_by_primer -rwxr-xr-x 1 gelf2022 gelf2022 17624 9月 1 13:49 classify_by_primer.fullpa -rwxr-xr-x 1 gelf2022 gelf2022 12376 9月 1 13:49 flnc2sam -rwxr-xr-x 1 gelf2022 gelf2022 2226 9月 1 13:49 PolymeraseReads.stat.pl -rwxr-xr-x 1 gelf2022 gelf2022 1631 9月 1 13:49 SubReads.stat.pl* ” Thank you!

shizhuoxing commented 2 years ago

Hi, this may be due to an issue with execute permissions. You can try: chmod 777 CLASSIFY_BY_primer CLASSIFY_by_primer.fullpa flNC2sam.

geluanfeng commented 2 years ago

Hi, this may be due to an issue with execute permissions. You can try: chmod 777 CLASSIFY_BY_primer CLASSIFY_by_primer.fullpa flNC2sam.

thanks for your answer I have tried doing this, but it still gives an error “ gelf2022@qmaster:/public252/gelf2022/datas/Zea_mays/Iso-Seq/BGI-Full-Length-RNA-Analysis-Pipeline/bin$ chmod 777 classify_by_primer gelf2022@qmaster:/public252/gelf2022/datas/Zea_mays/Iso-Seq/BGI-Full-Length-RNA-Analysis-Pipeline/bin$ classify_by_primer -h classify_by_primer: Operation not permitted 已杀死 gelf2022@qmaster:/public252/gelf2022/datas/Zea_mays/Iso-Seq/BGI-Full-Length-RNA-Analysis-Pipeline/bin$ chmod 777 classify_by_primer.fullpa gelf2022@qmaster:/public252/gelf2022/datas/Zea_mays/Iso-Seq/BGI-Full-Length-RNA-Analysis-Pipeline/bin$ chmod 777 flnc2sam gelf2022@qmaster:/public252/gelf2022/datas/Zea_mays/Iso-Seq/BGI-Full-Length-RNA-Analysis-Pipeline/bin$ flnc2sam flnc2sam: Operation not permitted 已杀死 gelf2022@qmaster:/public252/gelf2022/datas/Zea_mays/Iso-Seq/BGI-Full-Length-RNA-Analysis-Pipeline/bin$ classify_by_primer.fullpa classify_by_primer.fullpa: Operation not permitted 已杀死 ”

shizhuoxing commented 2 years ago

I just uploaded the source code of the program, you can try it to see if it works.

geluanfeng commented 2 years ago

I just uploaded the source code of the program, you can try it to see if it works.

It works !Thank you !

geluanfeng commented 2 years ago

您好，我是用conda来安装的isoseq3 （mamba install -y isoseq3）。现在运行isoseq3 cluster isoseq_flnc.bam unpolished.bam --split-bam 3这一步， 一直不出结果，查看后台，投递的这个任务一直处于休眠状态。服务器的资源是够的，500G内存，110个线程。 用您提供的示例数据（test.mtzl.ccs.bam），也是出现上面同样情况。“m64048_220820_021531/263906/448_1137_CCS 4 0 255 0 0 ATGGGGAATTCGGCAAATTATTTTTTACCTGTTTATTAAAAACATGTCTTTTTGTAAAAATATAAAGTCTAACCTGCCCTATGAAAATTTAAATGGCCGCGGTATATTAACCGTGCTAAGGTAGCATAATCATTAGTTTTTTAATTGAAAGCTGGAATGAAGGGTTGGATAAAAAAATAACTGTCTCTATAAAAATGATTGAATTTTATTTTTAAGTTAAAAAGCTTAAATTTTTTTAAAAGACGAGAAGACCCTATAGAGTTTAATATAAAATATAATTATTTTTTTTAGTATTTATTTAAATAATTAGATTTTATATTTAGTTGGGGTGATTGAAAAATTAAATAAACTTTTTTTGTATAAAAATATATTTTTATAAATTATTGATCCAAAAATTTTGATTATAAGATAAAATTACCTTAGGGATAACAGCGTAATTTTATTAGAGAGTTCTTATTGATAATAAAGATTGCGACCTCGATGTTGGATTAAAATTTATAATTGGTGCAGAAGCTATATTATTAAGTCTGTTCGACTTTTAAAATTTTACATGATCTGAGTTTAAACCGGTGTAAGCCAGGTTGGTTTCTATCTTTAATAAATTTATATATTTTAGTACGAAAGGACCAATTATATAAATAATATTTT !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! RG:Z:dca2ca1b ac:B:i,15,0,14,2 bc:B:S,7,7 bq:i:68 ec:f:15.5106 ma:i:0 np:i:15 rq:f:0.999418 sn:B:f,10.9128,16.2304,4.03405,7.14647 we:i:7840042 ws:i:5142358 zm:i:263906 m64048_220820_021531/263906/3204_3555_CCS 4 0 255 0 0 ATGGGGGCCGTCAAATCAGCTATTACCCAAGCATCACTAAACCAAATAGCCACTACTACTATCCCCAATCTAGAGAAACCACTGCTGCAGCCTATTACAATCGCCATCAGCCAGTTATCCTCGACGATTACGAGCCTGAAAGAATTGCGCCCTGCTATAAACACCTTAAACGATTCACTTGCCGCGTTCAGGCCCTCTCTGACATCGAGTATGTACGAACTATGTATCCTCCCGCTAAAAGAGACGCTTACCAACGTGTTCTATTAGATTTAAATAGTGGGGGCAAGGTATCATACGGAATAACACCATTCACT !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! RG:Z:dca2ca1b ac:B:i,15,0,14,2 bc:B:S,7,7 bq:i:68 ec:f:15.5106 ma:i:0 np:i:15 rq:f:0.999418 sn:B:f,10.9128,16.2304,4.03405,7.14647 we:i:7840042 ws:i:5142358 zm:i:263906 ”isoseq_flnc.bam文件中截图两条序列是这样的，能麻烦您看一下这个输出文件的格式及内容是准确的吗

geluanfeng commented 2 years ago

I just uploaded the source code of the program, you can try it to see if it works.

Sorry,I have another question.I replaced the "!" in the file with "~" and now I can run the next step, does this affect the accuracy of my results?

shizhuoxing commented 2 years ago

I guess you used the CCS parameter '--skip-polish', which only output the initial draft template (faster, less accurate). I have no similar experience, if you want to continue running through the next steps, it is recommended to strictly check the filtering criteria after mapping to the reference genome (coverage>=0.99 && identity>=0.95).