Closed schmucr1 closed 2 years ago
Hi @schmucr1,
Can you type the below command and let me know if the release is 0.0.9 or different?
$conda list | grep "mirge"
Thank you, Arun
Dear Arun
Thank you for your rapid answer. Here is the result of the command:
conda activate /scratch/site/u/schmucr1/envs/mirge3
(mirge3) $ conda list | grep "mirge"
# packages in environment at /scratch/site/u/schmucr1/envs/mirge3:
mirge3 0.0.9 pyh5e36f6f_0 bioconda
So, it seems to be the same version.
I also looked for a docker image containing mirge3 and found this one here "gcfntnu/mirge3:0.0.9"
But it seems to have the same issue: the version is also 0.0.9
singularity run docker://docker-cache.repository.intranet.roche.com/gcfntnu/mirge3:0.0.9 conda list | grep "mirge"
INFO: Using cached SIF image
# packages in environment at /scratch/site/u/schmucr1/envs/mirge3:
mirge3 0.0.9 pyh5e36f6f_0 bioconda
and the help is the same as in my installation but different to the documentation
singularity run docker://docker-cache.repository.intranet.roche.com/gcfntnu/mirge3:0.0.9 miRge3.0 --help
INFO: Using cached SIF image
usage: miRge3.0 [options]
miRge3.0 (Comprehensive analysis of small RNA sequencing Data)
optional arguments:
-h, --help show this help message and exit
--version show program's version number and exit
Options:
-s, --samples list of one or more samples separated by comma or a file with list of samples separated by new line (accepts *.fastq, *.fastq.gz)
-db, --mir-DB the reference database of miRNA. Options: miRBase and miRGeneDB (Default: miRBase)
-lib, --libraries-path the path to miRge libraries
-on, --organism-name the organism name can be human, mouse, fruitfly, nematode, rat or zebrafish
-ex, --crThreshold the threshold of the proportion of canonical reads for the miRNAs to retain. Range for ex (0 - 0.5), (Default: 0.1)
-phr, --phred64 phred64 format (Default: 33)
-spk, --spikeIn switch to annotate spike-ins if spike-in bowtie index files are located at the path of bowtie's index files (Default: off)
-ie, --isoform-entropy switch to calculate isomir entropy (default: off)
-cpu, --threads the number of processors to use for trimming, qc, and alignment (Default: 1)
-ai, --AtoI switch to calculate A to I editing (Default: off)
-tcf --tcf-out switch to write trimmed and collapsed fasta file (Default: off)
-gff --gff-out switch to output isomiR results in gff format (Default: off)
-bam --bam-out switch to output results in bam format (Default: off)
-trf --tRNA-frag switch to analyze tRNA fragment and halves (Default: off)
-o --outDir the directory of the outputs (Default: current directory)
-dex --diffex perform differential expression with DESeq2 (Default: off)
-mdt --metadata the path to metadata file (Default: off, require '.csv' file format if -dex is opted)
-cms --chunkmbs chunk memory in megabytes per thread to use during bowtie alignment (Default: 256)
-shh --quiet enable quiet/silent mode, only show warnings and errors (Default: off)
Data pre-processing:
-a, --adapter Sequence of a 3' adapter. The adapter and subsequent bases are trimmed
-g, --front Sequence of a 5' adapter. The adapter and any preceding bases are trimmed
-u, --cut Remove bases from each read. If LENGTH is positive, remove bases from the beginning. If LENGTH is negative, remove bases from the end
-nxt, --nextseq-trim NextSeq-specific quality trimming (each read). Trims also dark cycles appearing as high-quality G bases
-q, --quality-cutoff Trim low-quality bases from 5' and/or 3' ends of each read before adapter removal. If one value is given, only the 3' end is trimmed
If two comma-separated cutoffs are given, the 5' end is trimmed with the first cutoff, the 3' end with the second
-l, --length Shorten reads to LENGTH. Positive values remove bases at the end while negative ones remove bases at the beginning. This and the following
modifications are applied after adapter trimming
-NX, --trim-n Trim N's on ends of reads
-m, --minimum-length Discard reads shorter than LEN. (Default: 16)
of time)
-mEC, --miREC Enable miRNA error correction (miREC)
If you need further information, let me know please.
Thank you! R.
@schmucr1,
This is interesting, can you try a few things mentioned below and if the results are the same then probably the installation is not complete. (Also, I was doubtful that conda environment name and package name may be the conflict but it is not)
conda activate mirge3
miRge3.0 -h | tail -30
(tail -30 command gives the last 30 lines of the miRge3.0 help command)
Please run a small file test file as described here, if you get any error please let us know.
If the last 30 lines are not as is in the documentation and the test run is not successful then let's troubleshoot any error you may get and in the worst case, we will reinstall miRge3.0 by the following command:
conda activate mirge3
conda remove mirge3
conda install -c bioconda mirge3
What operating system are you on and can you send the packages installed in this conda environment like below:
conda list > env_packages.txt
Thank you, Arun.
Dear @arunhpatil
Thank you for your suggestions. I did the following,
conda activate /scratch/site/u/schmucr1/envs/mirge3
miRge3.0 -h | tail -30
-m, --minimum-length Discard reads shorter than LEN. (Default: 16)
and got only one line. That is weird. I am using a bash shell in a browser window. Then, I tried the same in a fresh Putty terminal, and got the correct output, all 30 lines:
miRge3.0 -h | tail -30
-m, --minimum-length Discard reads shorter than LEN. (Default: 16)
-umi, --uniq-mol-ids Trim nucleotides of specific length at 5’ and 3’ ends of the read, after adapter trimming. eg: 4,4 or 0,4. (Use -udd to remove PCR duplicates)
-udd, --umiDedup Specifies argument to removes PCR duplicates (Default: False); if TRUE it will remove UMI and remove PCR duplicates otherwise it only remove UMI and keep the raw counts (Require -umi option)
-qumi, --qiagenumi Removes PCR duplicates of reads obtained from Qiagen platform (Default: Illumina; "-umi x,y " Required)
miRNA Error Correction:
microRNA correction method for single base substitutions due to sequencing errors (Note: Refines reads at the expense of time)
-mEC, --miREC Enable miRNA error correction (miREC)
-kh, --threshold the value for frequency threshold τ (Default kh = 5)
-ks, --kmer-start kmer range start value (k_1, default 15)
-ke, --kmer-end kmer range end value (k_end, default 20)
Predicting novel miRNAs:
The predictive model for novel miRNA detection is trained on human and mouse!
-nmir, --novel-miRNA include prediction of novel miRNAs
-minl, --minLength the minimum length of the retained reads for novel miRNA detection (default: 16)
-maxl, --maxLength the maximum length of the retained reads for novel miRNA detection (default: 25)
-c, --minReadCounts the minimum read counts supporting novel miRNA detection (default: 2)
-mloc, --maxMappingLoci the maximum number of mapping loci for the retained reads for novel miRNA detection (default: 3)
-sl, --seedLength the seed length when invoking Bowtie for novel miRNA detection (default: 25)
-olc, --overlapLenCutoff the length of overlapped seqence when joining reads into longer sequences based on the coordinate
on the genome for novel miRNA detection (default: 14)
-clc, --clusterLength the maximum length of the clustered sequences for novel miRNA detection (default: 30)
Optional PATH arguments:
-pbwt, --bowtie-path the path to system's directory containing bowtie binary
-psam, --samtools-path the path to system's directory containing samtools binary
-prf, --RNAfold-path the path to system's directory containing RNAfold binary
Thus, I think the installation is good. I need to figure out with my local IT support the reason for the weird behaviour in the browser terminal.
Many thanks for your kind help and best wishes, R.
PS: Maybe there is some specical characters in the help, because when I do display only the last 19 lines it seems to work properly,
-ks, --kmer-start kmer range start value (k_1, default 15)
-ke, --kmer-end kmer range end value (k_end, default 20)
Predicting novel miRNAs:
The predictive model for novel miRNA detection is trained on human and mouse!
-nmir, --novel-miRNA include prediction of novel miRNAs
-minl, --minLength the minimum length of the retained reads for novel miRNA detection (default: 16)
-maxl, --maxLength the maximum length of the retained reads for novel miRNA detection (default: 25)
-c, --minReadCounts the minimum read counts supporting novel miRNA detection (default: 2)
-mloc, --maxMappingLoci the maximum number of mapping loci for the retained reads for novel miRNA detection (default: 3)
-sl, --seedLength the seed length when invoking Bowtie for novel miRNA detection (default: 25)
-olc, --overlapLenCutoff the length of overlapped seqence when joining reads into longer sequences based on the coordinate
on the genome for novel miRNA detection (default: 14)
-clc, --clusterLength the maximum length of the clustered sequences for novel miRNA detection (default: 30)
Optional PATH arguments:
-pbwt, --bowtie-path the path to system's directory containing bowtie binary
-psam, --samtools-path the path to system's directory containing samtools binary
-prf, --RNAfold-path the path to system's directory containing RNAfold binary
but not with 20 lines
miRge3.0 -h | tail -20
<empty output in my browser shell>
@schmucr1,
That is great. I guess you are right about the special character (threshold τ
) [especially on a browser window]. You may replace that with (threshold T
) in the following line in any text editor:
Line 104:
/scratch/site/u/schmucr1/envs/mirge3/lib/python3.8/site-packages/mirge/libs/parse.py
you could replace the following line as shown below:
-kh, --threshold the value for frequency threshold τ (Default kh = 5)
to
-kh, --threshold the value for frequency threshold T (Default kh = 5)
Let us know if this prints out the whole help message?
Thank you, Arun.
Dear @arunhpatil
Yes, that workaround helped and as a result mirge3.0 help is properly shown, also in the browser shell. I tried to find a way to configure my browser shell so that it can also display special characters such as tau (Unicode Character “τ” (U+03C4) but have not found a solution. If you know something that would be very much appreciated.
In anycase you may close this issue as solved.
Many thanks for your rapid support and best wishes, R.
Hello
I installed the latest version of miRge3.0
into a conda environment. However, when I look at the help/documentation I see different output than on the documentation website. Here is what I see
Do you have any ideas?
Thanks a lot and best wishes, Roland