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Dee-chen / Tree2gd

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Thank you very much for your help #11

Open yingchun323 opened 1 year ago

yingchun323 commented 1 year ago 
    Thank you very much for your help

I run Tree2GD_draw.R and it tells me that I don't have biocmanager installed， I ran it again and he gave me an error like this

testing if installed package can be loaded from temporary location testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path

The downloaded source packages are in ‘/tmp/RtmpdNydhT/downloaded_packages’ Updating HTML index of packages in '.Library' Making 'packages.html' ... done ggtree v3.4.4 For help: https://yulab-smu.top/treedata-book/

If you use the ggtree package suite in published research, please cite the appropriate paper(s):

Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution. 2017, 8(1):28-36. doi:10.1111/2041-210X.12628

LG Wang, TTY Lam, S Xu, Z Dai, L Zhou, T Feng, P Guo, CW Dunn, BR Jones, T Bradley, H Zhu, Y Guan, Y Jiang, G Yu. treeio: an R package for phylogenetic tree input and output with richly annotated and associated data. Molecular Biology and Evolution. 2020, 37(2):599-603. doi: 10.1093/molbev/msz240

Guangchuang Yu. Using ggtree to visualize data on tree-like structures. Current Protocols in Bioinformatics. 2020, 69:e96. doi:10.1002/cpbi.96

Error in $<-.data.frame(*tmp*, describe, value = " %") : replacement has 1 row, data has 0 Calls: $<- -> $<-.data.frame Execution halted

After I check the output directory, I find the error is in step4, Tree2gd_test_out/ step4.wgd /iqtree_out directory is empty, after I run step4.sh, it appears the following error

MUSCLE v3.8.31 by Robert C. Edgar

http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97.

ERROR Cannot open '/data/wanglab/liufangpu/test/Tree2gd_test_out/step4.WGD/all_fa/*.fa' errno=2

Invalid "-B" option. --species=: 2 --bp=: 50 --sub_bp=: 0 --split_tree=: false --quick_file=: --parser_file=: --paml=: false --omega=: --genome=: --isoform=: --save_tree=: true --deepvar=: 1 --root=: MAX_MIX load tree list: /data/wanglab/liufangpu/test/Tree2gd_test_out/step4.WGD/tree.list size=0 load idmap: /data/wanglab/liufangpu/test/Tree2gd_test_out/step1.blastp/all_sample2fa.list 827 genes loaded for 7 species

phyto_5 (index=12, phy=0) Cpapaya (index=0, phy=0) phyto_4 (index=11, phy=0) phyto_1 (index=5, phy=0) | phyto_0 (index=3, phy=0) | | Athaliana (index=1, phy=0) | | Alyrata (index=2, phy=0) | Crubella (index=4, phy=0) phyto_3 (index=10, phy=0) Esalsugineum (index=6, phy=0) phyto_2 (index=9, phy=0) Brapa (index=7, phy=0) Tparvula (index=8, phy=0) outgroup: Cpapaya loading 0 trees set index for 0 trees identifying gene duplications validate and output files -> /data/wanglab/liufangpu/test/Tree2gd_test_out/step4.WGD/Tree2GD_out//summary.txt -> /data/wanglab/liufangpu/test/Tree2gd_test_out/step4.WGD/Tree2GD_out//low_copy_orthologs.info /data/wanglab/liufangpu/test/Tree2gd_test_out/step4.WGD/Tree2GD_out//low_copy_orthologs.quick -> /data/wanglab/liufangpu/test/Tree2gd_test_out/step4.WGD/Tree2GD_out//gd.gene_pairs.txt -> /data/wanglab/liufangpu/test/Tree2gd_test_out/step4.WGD/Tree2GD_out//ortholog.gene_pairs.txt -> /data/wanglab/liufangpu/test/Tree2gd_test_out/step4.WGD/Tree2GD_out//gd.single_gd_pattern.txt -> /data/wanglab/liufangpu/test/Tree2gd_test_out/step4.WGD/Tree2GD_out//gd.single_gd_lineage.txt -> /data/wanglab/liufangpu/test/Tree2gd_test_out/step4.WGD/Tree2GD_out//gd.ancestral_gd_retention.txt -> /data/wanglab/liufangpu/test/Tree2gd_test_out/step4.WGD/Tree2GD_out//gd.recent_gd_retention.txt -> /data/wanglab/liufangpu/test/Tree2gd_test_out/step4.WGD/Tree2GD_out//gd.median_ks.txt -> /data/wanglab/liufangpu/test/Tree2gd_test_out/step4.WGD/Tree2GD_out//GDtype_stat.txt -> /data/wanglab/liufangpu/test/Tree2gd_test_out/step4.WGD/Tree2GD_out//summarytable.txt -> /data/wanglab/liufangpu/test/Tree2gd_test_out/step4.WGD/Tree2GD_out//Phtree.nwk -> rooted trees -> /data/wanglab/liufangpu/test/Tree2gd_test_out/step4.WGD/Tree2GD_out//clusters.ancestors.txt -> isoform_candidates -> /data/wanglab/liufangpu/test/Tree2gd_test_out/step4.WGD/Tree2GD_out//sister_clades.txt

Thank you again for your help

Originally posted by @lfp-a in https://github.com/Dee-chen/Tree2gd/issues/5#issuecomment-1292926745

Dee-chen commented 1 year ago

This step requires a lot of tree building work, so Tree2gd uses multi-threaded operation internally, and step4.sh has been discarded. There should be no sequence problem with the test data set. Tree2gd also installs and checks all dependent software by default, so I guess there is a problem with your server environment. Do you use pip to install or GitHub to download? It is recommended to use pip to install so that your Python environment will be automatically checked and updated. After confirming the installation problem, you can go back to check whether the correct result is output from step 3 to determine the problem. If you still cannot locate the problem, you can contact me through WeChat to solve it in detail (cdy371761145)