Instrain github
Nettet25. aug. 2024 · I installed inStrain v.1.6.2 using bioconda and was trying to run profile with the test data (and with my own) but am getting an error that makes me think the numpy dependency isn't working properly. I tried simply re-installing numpy into the conda environment, but conda recognized that it was already installed. Nettet23. okt. 2024 · When trying to run the .get_raw_coverage_table attribute from the documentation, I get the following error: Type "help", "copyright", "credits" or "license" for more information. >>> import inStrain >>> import inStrain.SNVprofile >>> IS=...
Instrain github
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Nettet16. jun. 2024 · MrOlm / inStrain Public Notifications Fork 26 Star 86 Code Issues 14 Pull requests 1 Actions Projects Security Insights New issue Tutorial 1 comparison error #107 iwilkie opened this issue on Jun 16, 2024 · 14 comments iwilkie … Nettet5. jun. 2024 · Hi Morgan, Thanks for the detailed bug report. I looked into this and think I identified the issue, and have a couple of possible solutions. The problem is that the text of the tutorial is poorly written- it says that you can provide a list of the .fasta files that went in, but inStrain actually wants them as command line arguments.
NettetProcessing inStrain results. See Jupyter Notebooks linked above for details on how inStrain results were processed to make figures. Citations and acknowledgements. This work completely depends on the scientists that originally sequenced these genomes and made their data publicly available. For the intra-patient analysis, this includes: NettetIntern is a complete test system for JavaScript designed to help you write and run consistent, high-quality test cases for your JavaScript libraries and applications. It can …
Nettet3. feb. 2024 · Error plotting plotting · Issue #6 · MrOlm/inStrain · GitHub Hello, I am getting the following errors when running instrain plot. For plotting plot 6: /home/shengwei/anaconda3/envs/InStrain/lib/python3.8/site-packages/inStrain/plottingUtilities.py:743: RuntimeWarning: invalid value encountered … Nettet9. okt. 2024 · inStrain.controller.Controller().main(args) File "/home/user/miniconda3/lib/python3.9/site-packages/inStrain/controller.py", line 44, in …
Nettet8. nov. 2024 · master. 1 branch 1 tag. Code. josharian Merge pull request #2 from datawire/lukeshu/license. 42b52b6 on Nov 8, 2024. 6 commits. LICENSE.md. Rename …
NettetinStrain.logUtils.log_checkpoint("GenomeLevel", "coverage_info", "start") EG_db = genomeLevel_coverage_info(covT, bin2scaffolds, relevant_genomes, s2l, … thinkscript counterNettetInStrain is designed to handle large .bam files as well. Running a huge .bam file (30 Gbp) with 32 cores, for example, will take ~2 hours and use about 128Gb of RAM. The more … thinkscript count number of barsNettet22. sep. 2024 · Hi Matt! I'm working on building some new pipelines and have found inStrain (and your readthedocs) very helpful and informative, especially for someone very new to metagenomics. I found a minor issue with the order of arguments when running inStrain profile. I'm running v1.6.3 installed with conda. thinkscript compoundvalueNettetHi, I have a set of already called genes (not from prodigal) that I would like to use as input to inStrain. Is there any easy way to do this? Based on a previous issue (#56 specifically), it appear... thinkscript createcolorNettet27. mar. 2024 · seems solid, but I'm stuck on a version, bundled with the IDE, that only seems to support "classic" github PATs, not the new "fine-grained" PATs. Now, the … thinkscript concatNettet15. okt. 2024 · Hi, I was running instrain profile (v1.3.9) with 20 samples. Ten of them ran perfectly, however the other 10 got the following error: TypeError: ufunc 'isnan' not … thinkscript custom colorNettetBioinformatics program inStrain. Contribute to MrOlm/inStrain development by creating an account on GitHub. thinkscript custom scan filter