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过滤完、建立索引后 无法进行sRNA的比对和注释 #5

Closed wydsqgg closed 1 month ago

wydsqgg commented 1 month ago

您好，我在进行如下命令后 image sRNAminer One_step_sRNAminer -g /data1/jfhe/HJF_240918_sRNA_seq/ZmNAM/ZmB73-NAM5.0_genomic.fa -i /data1/jfhe/HJF_240918_sRNA_seq/clean_data/OE_1.fq -p 60 --nd /data1/jfhe/HJF_240918_sRNA_seq/ncRNA_filter/Rfam_ncRNA.fa --od /data1/jfhe/HJF_240918_sRNA_seq/Organelle/Organelle.fa --miRNA --PHAS21 --PHAS24 --hc_siRNA -o ./ 在建立文件夹和索引后，过滤后，没有进行sRNA的比对和注释，请您帮我解答一下。 image OE_1.fq.trimmed.mc.no_rRNA.fa.rfam.log One_Step_sRNAminer.log

kli28 commented 1 month ago

您好，我在进行如下命令后 image sRNAminer One_step_sRNAminer -g /data1/jfhe/HJF_240918_sRNA_seq/ZmNAM/ZmB73-NAM5.0_genomic.fa -i /data1/jfhe/HJF_240918_sRNA_seq/clean_data/OE_1.fq -p 60 --nd /data1/jfhe/HJF_240918_sRNA_seq/ncRNA_filter/Rfam_ncRNA.fa --od /data1/jfhe/HJF_240918_sRNA_seq/Organelle/Organelle.fa --miRNA --PHAS21 --PHAS24 --hc_siRNA -o ./ 在建立文件夹和索引后，过滤后，没有进行sRNA的比对和注释，请您帮我解答一下。 image OE_1.fq.trimmed.mc.no_rRNA.fa.rfam.log One_Step_sRNAminer.log

This question might be caused by the blast version, you can change to 2.12.

wydsqgg commented 1 month ago

This problem might be caused by the blast version, and please change to 2.12

您好，可以青柠说的具体一下吗？具体要怎么操作执行呢，是要重新指定一个blast吗，我下载了一个blast 2.12

kli28 commented 1 month ago

This problem might be caused by the blast version, and please change to 2.12

您好，可以青柠说的具体一下吗？具体要怎么操作执行呢，是要重新指定一个blast吗，我下载了一个blast 2.12

Just install the blast version 2.12 in your sRNAminer environment. Then done.

wydsqgg commented 1 month ago

我按照您的建议，在conda环境下安装了blast，结果还是一样，没有进行比对。

kli28 commented 1 month ago

我按照您的建议，在conda环境下安装了blast，结果还是一样，没有进行比对。

I checked your [OE_1.fq.trimmed.mc.no_rRNA.fa.rfam.log and found that you didn't put your bowtie index of your data cleaning database sequence file(Rfam*.fa and Organelle.fa) together with your database sequence files. please put them in the same directory.

wydsqgg commented 1 month ago

我按照您的建议，在conda环境下安装了blast，结果还是一样，没有进行比对。

I checked your [OE_1.fq.trimmed.mc.no_rRNA.fa.rfam.log and found that you didn't put your bowtie index of your data cleaning database sequence file(Rfam*.fa and Organelle.fa) together with your database sequence files. please put them in the same directory.

很抱歉再次打扰您，我将所有文件放在一个文件夹下运行，还是出现了一样的问题。 image image

kli28 commented 1 month ago

我按照您的建议，在conda环境下安装了blast，结果还是一样，没有进行比对。

I checked your [OE_1.fq.trimmed.mc.no_rRNA.fa.rfam.log and found that you didn't put your bowtie index of your data cleaning database sequence file(Rfam*.fa and Organelle.fa) together with your database sequence files. please put them in the same directory.

很抱歉再次打扰您，我将所有文件放在一个文件夹下运行，还是出现了一样的问题。 image image

Looks like you building the data_cleaning_database by yourself. Your error showed that the basename is error. You need to construct your index using your sequence file name, such as "Rfam_ncRNA.fa".

wydsqgg commented 1 month ago

我按照您的建议，在conda环境下安装了blast，结果还是一样，没有进行比对。

I checked your [OE_1.fq.trimmed.mc.no_rRNA.fa.rfam.log and found that you didn't put your bowtie index of your data cleaning database sequence file(Rfam*.fa and Organelle.fa) together with your database sequence files. please put them in the same directory.

很抱歉再次打扰您，我将所有文件放在一个文件夹下运行，还是出现了一样的问题。 image image

Looks like you building the data_cleaning_database by yourself. Your error showed that the basename is error. You need to construct your index using your sequence file name, such as "Rfam_ncRNA.fa".

OK，这个问题已经解决，已经可以成功运行并输出结果，十分感谢作者，非常有耐心的解答，sRNAMiner 是一款十分好用的sRNA分析工具。