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Genome not found, Picard's command line syntax is changing, violing plot not generated, expression.tsv not generated #84
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it is libcrypto.so.1.0.0 ImportError: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory |
rule get_top_barcodes: -- why this message don't know because I am using python 3.6 |
libcrypto.so.1.0.0 I see "expression.tsv" file generated initially but replaced by long format file. I wish to keep wide for downstream analysis. Can convert from long to wide using library(tidyr) and other r packages though. So, "final report" is showing path and names of temporary files as well. That is somewhat misleading. Still need help on violon plot. |
Hey @abmmki This is gonna be a tough one. The main purpose of conda is to help deal with those problematic package conflicts and all... The main advice I would give you is to try to create the envs for each step then activate them manually for the specific step. Is that not working for the violin plots? |
When installing from bioconda you'll always have to use
instead of just
Also, what is the reason that you install packages manually? |
OK, finally Seurat installed following ways (thnks @grst): conda install -c conda-forge -c r -c bioconda r-seurat I re-run the last part of command ......... But Now it is giving another error: Error in rule violine_plots: ................. barcodes.tsv |
Sorry for that struggle, it's rather difficult to manage versions with evolving software.
@Hoohm , this might maybe also explain the empty seurat objects you mentioned. dropSeqPipe/envs/plots_ext.yaml Line 15 in 9430013
|
Closing this for now since it seems to be fixed. |
Here I am reporting several Errors/warnings.
I am using Fedora 30. The Guideline (Wiki) asked to install miniconda3. I tried that way, but it could not get all required dependent packages. I installed them manually from bioconda/conda-forge. However, during "meta" step it complained for a missing library.so.1 .... (forgot exact name, not in my record now). So, I deleted miniconda, and then "conda create" a new environment and "conda activate myconda". Then I installed manually all the dependent packages, for example
conda install -c bioconda cutadapt
[0] Violin plot and expression.tsv not generated
However, it gave some errors and finally everything generated except the violin plot and the desired expression matrix file "..../sample/read/expression.tsv
all other expression.long, expression.mtx, barcode.tsv files are there. This happened for both UMI and READ.
Knee plot looks good
When I generated final report, it is showing the file ".../sample/expression.tsv" --- but actually no file there. May be the final report generate without checking existence of actual file? It also says there are files like
samples/....../Aligned.merged.bam
This file is also not there in the location ......... Well, final.bam is there but the report doesn't talk about that.
Note that I used my own downloaded genome with a GFP gene sequence inserted in genome.fa and also annothation there for in annotation.gtf
Base is Ensembl 37 and release 74. However, I used the file Homo_sapiens.GRCh37.74.dna.toplevel.fa.gz -- to cover additional genome locations like immunologic chromosomes etc there
[1] Genome fasta file could not download:
Well, next round I tried not my genome.fa file, but wanted the pipeline to download the genome (this time no additional sequence)
I tried human genome 37, ensembl release 74. So, the pipeline generated to download a file:
Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz
from following FTP:
http://ftp.ensembl.org/pub/release-74/fasta/homo_sapiens/dna/
However, actual file name there is (with ".74)
Homo_sapiens.GRCh37.74.dna.primary_assembly.fa.gz
I fixed it manually (not syntext regular expression)
[2] I am using Drop-seq_tools-2.3.0/ and latest picard tools in it (2.20.2)
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/tmp
INFO 2019-06-27 09:14:35 ReduceGtf
********** NOTE: Picard's command line syntax is changing.
********** For more information, please see:
********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)
********** The command line looks like this in the new syntax:
[3] Violin plot not generated:
conda install -c bioconda r-seurat # could not make it **
conda install -c russh r-seurat
..... etc
I tried several repositories of conda. Also tried latest Seurat-3 and Old Seurat 2
I am using R 3.5.3. But now way it was installed.
Just saying that
PackagesNotFoundError: The following packages are not available from current channels:
Well, those packages I have installed one by one manually, but still could not get Seurat installed. After installing those packages, Seurat installtion still not possible
conda install -c bioconda r-seurat
UnsatisfiableError: The following specifications were found to be in conflict:
Thanks,
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