unable to run PlantClusterFinder

[amit4mchiba]

Hi,

I am trying to use PlantClusterFinder. I am working on plant genome and wanted to use this tool to search gene clusters of my interest.

Therefore, I downloaded the lattest release of PlantClusterFinder. I do not have matlab, and as instructed, I downloaded matlab runtime (2016b), installed it (I installed it locally, and then added path in ~/.bashrc as follows-export PATH="/home/amit8chiba/software/v91/runtime/glnxa64:/home/amit8chiba/software/v91/bin/glnxa64:/home/amit8chiba/software/v91/sys/os/glnxa64:/home/amit8chiba/software/v91/extern/bin/glnxa64:$PATH")

After this, I tried to perform test run using this command-
/mnt/md0/Gene_cluster_analysis/test/PlantClusterFinder/run_PlantClusterFinder.sh /home/amit8chiba/software/v91 -pgdb /mnt/md0/Gene_cluster_analysis/test/PlantClusterFinder/csubellipsoidea/pgdb/csubellipsoideacyc/1.0/data/ -rmdf /mnt/md0/Gene_cluster_analysis/test/PlantClusterFinder/Inputs/ReactionMetabolicDomainClassification.txt -md "{'Amines and Polyamines Metabolism'; 'Amino Acids Metabolism'; 'Carbohydrates Metabolism'; 'Cofactors Metabolism'; 'Detoxification Metabolism'; 'Energy Metabolism'; 'Fatty Acids and Lipids Metabolism'; 'Hormones Metabolism'; 'Inorganic Nutrients Metabolism'; 'Nitrogen-Containing Compounds'; 'Nucleotides Metabolism'; 'Phenylpropanoid Derivatives'; 'Polyketides'; 'Primary-Specialized Interface Metabolism'; 'Redox Metabolism'; 'Specialized Metabolism'; 'Sugar Derivatives'; 'Terpenoids'}" -psf /mnt/md0/Gene_cluster_analysis/test/PlantClusterFinder/csubellipsoidea/CsubellipsoideaC_169_227_v2.0.protein.pcf13.fa -gtpf /mnt/md0/Gene_cluster_analysis/test/PlantClusterFinder/csubellipsoidea/gtpf_CsubellipsoideaC_169_227_v2.0.annotation_info.txt.txt -glof /mnt/md0/Gene_cluster_analysis/test/PlantClusterFinder/csubellipsoidea/glof_CsubellipsoideaC_169_227_v2.0.gene.gff3.txt -dnaf /mnt/md0/Gene_cluster_analysis/test/PlantClusterFinder/csubellipsoidea/CsubellipsoideaC_169_227_v2.0.hardmasked.fa -sitf /mnt/md0/Gene_cluster_analysis/test/PlantClusterFinder/Inputs/scaffold-tailoring-reactions-05082016.tab -gout /mnt/md0/Gene_cluster_analysis/test/PlantClusterFinder/csubellipsoidea/ARAGene1_3_amit_memex.txt -cout /mnt/md0/Gene_cluster_analysis/test/PlantClusterFinder/csubellipsoidea/ARAClust1_3_amit_memex.txt SeqGapSizesChromBreak '[10000]' PGDBIdsToMap GTP

This was based on suggestions by your documentations.

While running, I got this message-

Setting up environment variables

LD_LIBRARY_PATH is .:/home/amit8chiba/software/v91/runtime/glnxa64:/home/amit8chiba/software/v91/bin/glnxa64:/home/amit8chiba/software/v91/sys/os/glnxa64:/home/amit8chiba/software/v91/sys/opengl/lib/glnxa64
Parameter 1: -pgdb
Value: /mnt/md0/Gene_cluster_analysis/test/PlantClusterFinder/csubellipsoidea/pgdb/csubellipsoideacyc/1.0/data/
Parameter 2: -rmdf
Value: /mnt/md0/Gene_cluster_analysis/test/PlantClusterFinder/Inputs/ReactionMetabolicDomainClassification.txt
Parameter 3: -md
Value: {'Amines and Polyamines Metabolism'; 'Amino Acids Metabolism'; 'Carbohydrates Metabolism'; 'Cofactors Metabolism'; 'Detoxification Metabolism'; 'Energy Metabolism'; 'Fatty Acids and Lipids Metabolism'; 'Hormones Metabolism'; 'Inorganic Nutrients Metabolism'; 'Nitrogen-Containing Compounds'; 'Nucleotides Metabolism'; 'Phenylpropanoid Derivatives'; 'Polyketides'; 'Primary-Specialized Interface Metabolism'; 'Redox Metabolism'; 'Specialized Metabolism'; 'Sugar Derivatives'; 'Terpenoids'}
Parameter 4: -psf
Value: /mnt/md0/Gene_cluster_analysis/test/PlantClusterFinder/csubellipsoidea/CsubellipsoideaC_169_227_v2.0.protein.pcf13.fa
Parameter 5: -gtpf
Value: /mnt/md0/Gene_cluster_analysis/test/PlantClusterFinder/csubellipsoidea/gtpf_CsubellipsoideaC_169_227_v2.0.annotation_info.txt.txt
Parameter 6: -glof
Value: /mnt/md0/Gene_cluster_analysis/test/PlantClusterFinder/csubellipsoidea/glof_CsubellipsoideaC_169_227_v2.0.gene.gff3.txt
Parameter 7: -dnaf
Value: /mnt/md0/Gene_cluster_analysis/test/PlantClusterFinder/csubellipsoidea/CsubellipsoideaC_169_227_v2.0.hardmasked.fa
Parameter 8: -sitf
Value: /mnt/md0/Gene_cluster_analysis/test/PlantClusterFinder/Inputs/scaffold-tailoring-reactions-05082016.tab
Parameter 9: -gout
Value: /mnt/md0/Gene_cluster_analysis/test/PlantClusterFinder/csubellipsoidea/ARAGene1_3_amit_memex.txt
Parameter 10: -cout
Value: /mnt/md0/Gene_cluster_analysis/test/PlantClusterFinder/csubellipsoidea/ARAClust1_3_amit_memex.txt
Parameter 11: SeqGapSizesChromBreak
Value: [10000]
Parameter 12: PGDBIdsToMap
Value: GTP
Initializing parameters and running PlantClusterFinder
Check files for reading and writing
Warning: Discarding metabolic domain information of Macromolecules Metabolism

In PlantClusterFinder>f_get_metabolic_domains (line 2340)
In PlantClusterFinder (line 859)
Warning: Discarding metabolic domain information of NA

In PlantClusterFinder>f_get_metabolic_domains (line 2340)
In PlantClusterFinder (line 859)
Warning: Discarding metabolic domain information of NOT IN METACYC

In PlantClusterFinder>f_get_metabolic_domains (line 2340)
In PlantClusterFinder (line 859)
Warning: Discarding metabolic domain information of Other

In PlantClusterFinder>f_get_metabolic_domains (line 2340)
In PlantClusterFinder (line 859)
Warning: Discarding metabolic domain information of Unclassified

In PlantClusterFinder>f_get_metabolic_domains (line 2340)
In PlantClusterFinder (line 859)
Error using fgets
Invalid file identifier. Use fopen to generate a valid file identifier.

Error in fgetl (line 33)

Error in PlantClusterFinder>f_read_MCL_clustering_File (line 2402)

Error in PlantClusterFinder>f_get_MCL_clustering (line 2534)

Error in PlantClusterFinder (line 941)
MATLAB:FileIO:InvalidFid

I am therefore not able to use this tool. I am not sure if this is some bug or the issue is within my installed Matlab runtime. I think that since no error in establishing LD_LIBRARY_PATH, it may be fine. But I am not sure. Do i must buy Matlab to run this tool?

Please guide me.

[pschlapfer]

This looks like a file IO issue.
Did you change the permissions to the files once you downloaded it?

[Frybank]

你好

我正在尝试使用 PlantClusterFinder。我正在研究植物基因组，想用这个工具来搜索我感兴趣的基因簇。

因此，我下载了最新版本的PlantClusterFinder。我没有 matlab，按照指示，我下载了 matlab 运行时 （2016b），安装了它（我在本地安装了它，然后在 ~/.bashrc 中添加了路径，如下所示-export PATH=“/home/amit8chiba/software/v91/runtime/glnxa64：/home/amit8chiba/software/v91/bin/glnxa64：/home/amit8chiba/software/v91/sys/os/glnxa64：/home/amit8chiba/software/v91/extern/bin/glnxa64：$PATH”）

在此之后，我尝试使用此命令执行测试运行- /mnt/md0/Gene_cluster_analysis/test/PlantClusterFinder/run_PlantClusterFinder.sh /home/amit8chiba/software/v91 -pgdb /mnt/md0/Gene_cluster_analysis/test/PlantClusterFinder/csubellipsoidea/pgdb/csubellipsoideacyc/1.0/data/ -rmdf /mnt/md0/Gene_cluster_analysis/test/PlantClusterFinder/Inputs/ReactionMetabolicDomainClassification.txt -md “{'胺和多胺代谢';氨基酸代谢';“碳水化合物代谢”;“辅因子代谢”;“排毒代谢”;“能量代谢”;“脂肪酸和脂质代谢”;“荷尔蒙代谢”;“无机营养素代谢”;“含氮化合物”;“核苷酸代谢”;“苯丙烷衍生物”;“聚酮”;“初级-特化界面代谢”;“氧化还原代谢”;“专门的新陈代谢”;“糖衍生物”;'Terpenoids'}“ -psf /mnt/md0/Gene_cluster_analysis/test/PlantClusterFinder/csubellipsoidea/CsubellipsoideaC_169_227_v2.0.protein.pcf13.fa -gtpf /mnt/md0/Gene_cluster_analysis/test/PlantClusterFinder/csubellipsoidea/gtpf_CsubellipsoideaC_169_227_v2.0.annotation_info.txt.txt -glof /mnt/md0/Gene_cluster_analysis/test/PlantClusterFinder/csubellipsoidea/glof_CsubellipsoideaC_169_227_v2.0.gene.gff3.txt -dnaf/mnt/md0/Gene_cluster_analysis/test/PlantClusterFinder/csubellipsoidea/CsubellipsoideaC_169_227_v2.0.hardmasked.fa -sitf /mnt/md0/Gene_cluster_analysis/test/PlantClusterFinder/Inputs/scaffold-tailoring-reactions-05082016.tab -gout /mnt/md0/Gene_cluster_analysis/test/PlantClusterFinder/csubellipsoidea/ARAGene1_3_amit_memex.txt -cout /mnt/md0/Gene_cluster_analysis/test/PlantClusterFinder/csubellipsoidea/ARAClust1_3_amit_memex.txt SeqGapSizesChromBreak '[10000]' PGDBIdsToMap GTP

这是基于您的文档的建议。

跑步时，我收到了这条消息——

设置环境变量

LD_LIBRARY_PATH是 .：/home/amit8chiba/software/v91/runtime/glnxa64：/home/amit8chiba/software/v91/bin/glnxa64：/home/amit8chiba/software/v91/sys/os/glnxa64：/home/amit8chiba/software/v91/sys/opengl/lib/glnxa64 参数 1： -pgdb 值： /mnt/md0/Gene_cluster_analysis/test/PlantClusterFinder/csubellipsoidea/pgdb/csubellipsoideacyc/1.0/data/ 参数 2： -rmdf值：/mnt/md0/Gene_cluster_analysis/test/PlantClusterFinder/Inputs/ReactionMetabolicDomainClassification.txt 参数 3：-md 值：{'胺和多胺代谢';“氨基酸代谢”;“碳水化合物代谢”;“辅因子代谢”;“排毒代谢”;“能量代谢”;“脂肪酸和脂质代谢”;“荷尔蒙代谢”;“无机营养素代谢”;“含氮化合物”;“核苷酸代谢”;“苯丙烷衍生物”;“聚酮”;“初级-特化界面代谢”;“氧化还原代谢”;“专门的新陈代谢”;“糖衍生物”;'萜类化合物'} 参数 4： -psf 值： /mnt/md0/Gene_cluster_analysis/test/PlantClusterFinder/csubellipsoidea/CsubellipsoideaC_169_227_v2.0.protein.pcf13.fa 参数 5： -gtpf 值： /mnt/md0/Gene_cluster_analysis/test/PlantClusterFinder/csubellipsoidea/gtpf_CsubellipsoideaC_169_227_v2.0.annotation_info.txt.txt 参数 6： -glof值：/mnt/md0/Gene_cluster_analysis/test/PlantClusterFinder/csubellipsoidea/glof_CsubellipsoideaC_169_227_v2.0.gene.gff3.txt 参数 7：-dnaf 值：/mnt/md0/Gene_cluster_analysis/test/PlantClusterFinder/csubellipsoidea/CsubellipsoideaC_169_227_v2.0.hardmasked.fa 参数 8：-sitf 值：/mnt/md0/Gene_cluster_analysis/test/PlantClusterFinder/Inputs/scaffold-tailoring-reactions-05082016.tab参数 9： -gout 值： /mnt/md0/Gene_cluster_analysis/test/PlantClusterFinder/csubellipsoidea/ARAGene1_3_amit_memex.txt 参数 10： -cout 值： /mnt/md0/Gene_cluster_analysis/test/PlantClusterFinder/csubellipsoidea/ARAClust1_3_amit_memex.txt 参数 11： SeqGapSizesChromBreak 值： [10000] 参数 12： PGDBIdsToMap 值： GTP初始化参数并运行 PlantClusterFinder 检查文件以进行读写 警告：丢弃大分子代谢的代谢域信息

在 PlantClusterFinder 中>f_get_metabolic_domains（第 2340 行） 在 PlantClusterFinder 中（第 859 行） 警告：丢弃 NA 的代谢域信息

在 PlantClusterFinder 中>f_get_metabolic_domains（第 2340 行） 在 PlantClusterFinder 中（第 859 行） 警告：丢弃 NOT IN METACYC 的代谢域信息

在 PlantClusterFinder 中>f_get_metabolic_domains（第 2340 行） 在 PlantClusterFinder 中（第 859 行） 警告：丢弃其他的代谢域信息

在 PlantClusterFinder 中>f_get_metabolic_domains（第 2340 行） 在 PlantClusterFinder 中（第 859 行） 警告：丢弃未分类的代谢域信息

在 PlantClusterFinder 中>f_get_metabolic_domains（第 2340 行） 在 PlantClusterFinder 中（第 859 行） 使用 fgets 时出错 文件标识符无效。使用 fopen 生成有效的文件标识符。

fgetl 中的错误（第 33 行）

PlantClusterFinder 中的错误>f_read_MCL_clustering_File（第 2402 行）

PlantClusterFinder 中的错误>f_get_MCL_clustering（第 2534 行）

PlantClusterFinder 中的错误（第 941 行）MATLAB：FileIO：InvalidFid

因此，我无法使用此工具。我不确定这是某个错误还是问题出在我安装的 Matlab 运行时中。我认为，既然在建立LD_LIBRARY_PATH时没有错误，那可能没问题。但我不确定。我必须购买 Matlab 才能运行此工具吗？

请指导我。

Hello, I would like to ask you whether you have successfully run Plantclusterfinder and hope to get your guidance

[Frybank]

This looks like a file IO issue. Did you change the permissions to the files once you downloaded it?
Hello developer, I would like to know how to get the gtpf file? It doesn't seem to be stated in the operation