Activity for MitoSAlt
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Pauline Ng created ticket #4
Possible bug - dels called as dups?
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Adarsh PP modified a comment on discussion General Discussion
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Hi I have updated the setup file with this new URL and setup.sh file downloaded and compiled this. However I got the following error: Total time for call to driver() for forward index: 00:29:24 ./setup.sh: line 232: bin/last/src/lastdb: No such file or directory Does this mean, it was not compiled properly? Because I cannot find lastdb in the bin/last/src/. Please find the attached image with contents of the src directory It did not throw any error during installation. I am using MitoSAlt_1.1.1
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Hi I have updated the setup file with this new URL and setup.sh file downloaded and compiled this. However I got the following error: Total time for call to driver() for forward index: 00:29:24 ./setup.sh: line 232: bin/last/src/lastdb: No such file or directory Does this mean, it was not compiled properly? Because I cannot find lastdb in the bin/last/src/
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Swaraj Basu posted a comment on discussion General Discussion
Attaching the file for your usage Selina, the link seems to be working right now. You could also download it from here https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz
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selina feng posted a comment on discussion General Discussion
Hi, I would like to ask what is the specific content of hg19_g1k.size, because I did not download successfully. The error message is as follows: [97;41m Mon Mar 18 16:41:46 CST 2024:Download and index human genome: [m --2024-03-18 16:55:16-- https://www.dropbox.com/s/e1xwzye9hieewxz/human_g1k_v37.fasta.gz Resolving www.dropbox.com (www.dropbox.com)... 2a03:2880:f130:83:face:b00c:0:25de, 192.133.77.133 Connecting to www.dropbox.com (www.dropbox.com)|2a03:2880:f130:83:face:b00c:0:25de|:443... failed:...
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Hi Daniel, I missed this comment in the dicussion. Please find a potential solution here https://sourceforge.net/p/mitosalt/discussion/general/thread/71867dc46f/#dc44 -Regards Swaraj
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Hello Halima and Valentin. Unfortunately I am not able to maintain this repo since the past year and a half, hence the delay in my responses. Apologies. MitSalt currently generates a PERL hash oject to process the alignments generated by last. In regular sequencing we would have less mitochondrial origin reads and hence the hash object is not large enough to occupy entire memory. However in enriched sequencing, a due to a large number of reads, the hash object creation step is killed. Here I would...
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Valentin L'Hôte posted a comment on discussion General Discussion
Hi, I am having the exact same issue. Did you solve it? Thanks, Valentin
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Michael Nagy posted a comment on discussion General Discussion
No apologies needed! I totally understand, and you've honestly been extremely generous with your support over the course of my use of your program!
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Hi All! I know that this codebase is no longer maintained but figured I'd still share this in case somewhat can help or has any thoughts. Essentially on one of my bam files, which for all purposes doesn't appear to be any different than the hundreds of others I've run, encountered an error I've never seen before. Wed Aug 2 16:59:16 2023: Generate non-split read BED Wed Aug 2 16:59:23 2023: Process hash to get best deletion/duplication candidates Wed Aug 2 16:59:28 2023: Build split read clusters...
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Halima Alachram posted a comment on discussion General Discussion
Hello, I am running MitoSalt with fastq.gz mtDNA enriched data. However, the run is killed after 'Build split read hash'. Is it a memory issue? The log file is attached. Thank you Halima
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Daniel Martin Ruiz posted a comment on discussion General Discussion
Dear Dr Basu, I have downloaded the files from MitoSalt1.1.1 and followed the instructions in the README file for the installation. When using the command ./setup.sh the installation begins but it reports an ERROR when trying to download the file from https://last.cbrc.jp/last-941.zip. The ERROR says that the certificate doesn't work and to use the following command: --no-check-certificate. However, I've tried to execute again the setup command with and without this --no-check-certificate option...
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Good to know Eliezer that version update of plotrix solved the issue. I am sure your input will help others as well who are using MitoSAlt. Thank you Swaraj
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Hi Michael, Immensely sorry for my late replies. I am not actively maintaining MitoSAlt as of now and due to several other commitments taking up my time there is a delay. If you'd like to use hg38 aligned BAM, then it should not hinder the other steps as the unaligned/MT aligned reads will be re-aligned to the MitoSAlt MT genome fasta file stored in genome/human_mt_rCRS.fasta thus negating any bias due to a difference in genome version. -Regards Swaraj
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Hello Bengsiu, A few others are also facing an issue running MitoSAlt on single end reads, where the plot and tsv files are not generated. Could you please share your experience with the issue and how you could get it to work. Is this a MitoSAlt_SE specific problem? -Regards Swaraj
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Hello Bengsiu, A few others are also facing an issue running MitoSAlt on single end reads, where the plot and tsv files are not generated. Could you please share your experience with the issue and how you could get it to work. Is this a MitoSAlt_SE specific problem?
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Hi Tomasz, Could you please refer to my answer to Joan above and confirm if the R packages are installed and output from the PERL part of the pipeline is generated that is tab/tag.tab which is followed by .breakpoint, .bed, .cluster. Please let me know what are your observations. Thanks Swaraj
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Hello Joan, Could you please make these preliminary checks 1) Are the libraries installed in your system, else the R script would fail to run a) library(plotrix) b) library(RColorBrewer) c) library(Biostrings) 2) If you run the pipeline with rmtmp = no #REMOVE TEMPORARY FILES Then what are the temporary files generated (they will all have a prefix of tmp) 3) Do you get a tab/tag.tab file (where tag is the name given to MitoSAlt) and also .breakpoint, .bed and .cluster file. This would indicate that...
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Hi Bengisu, Could you please re-run the script for the sample which gives an error with the configuration option rmtmp = no #REMOVE TEMPORARY FILES This would retain all temprary files which include two files tmp_tag._bps.bed -tmp_tag._bpE.bed tag here being the name you gave to MitoSAlt for the particular sample. The error you have got comes from the two tmp files not being generated. These tmp files have the start and end position of each deletion/duplication saved, and are generated from the file...
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Bengisu posted a comment on discussion General Discussion
Hi, Thank you for developing this tool and helping me with my previous problem. I´m analyzing multiple pair-read files using MitoSAlt. I don´t know why but the tool gave the error as: "readline ( ) on closed filehandle BPS at MitoSAlt MitoSAlt1.1.1.pl line 874." "readline ( ) on closed filehandle BPE at MitoSAlt MitoSAlt1.1.1.pl line 886." for some of my samples. Do you know how I can fix them? Could you please help me with this issue? Thank you so much!
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Tomasz posted a comment on discussion General Discussion
I have the same problem. The program generates intermediate files, but does not generate the final tsv file and the plot. The program generates the intermediate file "nosplit.bed" but does not generate the files "split.start.bed" and "split.end.bed".* Below is what I show in the terminal program: hisat2 = bin/hisat2/hisat2 lastal = bin/last/src/lastal lastsp = bin/last/src/last-split mfcv = bin/last/src/scripts/maf-convert reformat = bin/bbmap/reformat.sh samtools = bin/samtools/samtools sambamba...
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Joan Josep Cervera Piñana posted a comment on discussion General Discussion
Dear Dr Basu I have some problems to generate the output files .tvs and the plots. When I run the command "perl MitoSAlt_SE1.1.1.pl /home/joan/Downloads/MitoSAlt_1.1.1/config_human.txt /home/joan/Downloads/MitoSAlt_1.1.1/BRAIN_8.assembled.fastq <name>" seems that everything is working and clusters are generated, which makes me think that deletions/duplications are detected. However, when I go to the plot folder nothing appears, the same happens with .tvs files. When I installed MitoSAlt I used Last-1296...
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UPDATE: Output problem regarding plots and tvs files has been solved. However, we are not sure if merging fastq files into one and analysing them with the single read end script. Your recommendation and commend about this issue is important for us. Thank you so much!
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Dear Dr Basu, First of all, I would like to thank you for your previous help. We changed our methodology Ion Torrent to Illumina. However, we merged paired-end reads to one fastq file. In this format, we are trying to analyze our seqs with the MitoSAlt_SE.pl script which is suitable for the single ends. Is this script suitable for analyzing this format? Currently, we have a problem obtaining plots and tvs files although we can see the detected clusters on the terminal.. Could this problem be associated...
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Is it an issue that my bams are in HG38? it seems like most of the reference files for mitosalt are hg19....
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UPDATE: I changed the config file to look for chrM, not MT, as that is how MT reads are described in my HG38 FASTA. That seems to have done the trick. Thanks!
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hello! Thanks for suggestions, I started a run using the modifications and below was the log output orihe = 407 [23/187] orils = 5730 orile = 5763 score_threshold = 80 evalue_threshold = 0.00001 split_length = 15 paired_distance = 1000 deletion_threshold_min = 30 deletion_threshold_max = 30000 breakthreshold = -2 cluster_threshold = 5 breakspan = 15 sizelimit = 10000 hplimit = 0.01 flank = 15 split_distance_threshold = 5 dna = yes enriched = no nu_mt = yes rmtmp = yes o_mt = yes i_del = yes cn_mt...
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Hi All, I implemented the suggested changes, and encountered the following issues. Wed Nov 30 17:11:40 2022: Map to NU+MT genome Wed Nov 30 17:11:40 2022: Extract reads [E::hts_open_format] Failed to open file tmp_A0719.sam samtools view: failed to open "tmp_A0719.sam" for reading: No such file or directory [main_samview] region "MT" specifies an unknown reference name. Continue anyway. Wed Nov 30 17:11:40 2022: Create FASTQ [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed...
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Thanks a tonne Eliezer for your insights !! This is indeed very helpful for the community of users. Apologies that I could not help you out myself by testing the code. Most likely you would have already edited, we would also need to change the line 386 mt.axis$deg.axis<-90+(358*mt.axis$position/mlength)
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Thanks a tonne Eliezer for your insights !! This is indeed very helpful for the community of users. Apologies that I could not help you out myself by testing the code.
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Hi Varvara, Could you please run MitoSAlt once with the following config option rmtmp = no #REMOVE TEMPORARY FILES Next for your run a BAM folder is created which has a file named bam/$tag.bam where $tag being the study name you had given. Please run this command on the terminal on the bam sambamba depth window -w $msize bam/$tag.bam|cut -f 1,5 and check if you get an output. If sambamba does not give any output, might indicate the BAM file is empty or some other issue. It could be that very few...
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Hi Michael, Please find below the steps which would allow you to use external BAMs (assuming you will use paired end sequencing data). 1) The config file should have the following options ` dna = yes enriched = no #IF THE SEQUENCING IS MITOCHONDRIAL DNA ENRICHED THEN SKIP THE INITIAL NUCLEAR GENOME ALIGNMENT STEP nu_mt = yes #MAPPING TO NUCLEAR AND MITOCHONDRIAL GENOME WITH HISAT2 rmtmp = yes #REMOVE TEMPORARY FILES o_mt = yes #MITOCHONDRIAL READ EXTRACTION AND REMAPPING TO ONLY MITOCHONDRIAL GENOME...
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Hi Michael, Please find below the steps which would allow you to use external BAMs (assuming you will use paired end sequencing data). 1) The config file should have the following options dna = yes enriched = no #IF THE SEQUENCING IS MITOCHONDRIAL DNA ENRICHED THEN SKIP THE INITIAL NUCLEAR GENOME ALIGNMENT STEP nu_mt = yes #MAPPING TO NUCLEAR AND MITOCHONDRIAL GENOME WITH HISAT2 rmtmp = yes #REMOVE TEMPORARY FILES o_mt = yes #MITOCHONDRIAL READ EXTRACTION AND REMAPPING TO ONLY MITOCHONDRIAL GENOME...
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Hello, In our pipeline we generate Bam files through Illumina's Dragen aligner. Would it be possible to modify Mitosalt to intake these files? Henceforth, skipping the alignment steps involved with fastqs. I'm happy to modify the logic of the program myself, if given some direction on how to tackle the problem. Thank you! Michael
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Valentina created ticket #3
Empty cluster file and no .tsv output
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Varvara Koraki Folli posted a comment on discussion General Discussion
Hello, I seem to be encountering an error that has been mentioned by a few people. ***** ERROR: Requested column 8, but database file tmp_random_GH_298.cov only has fields 1 - 0. I have tried the solution you have mentioned before but it does not seem to work. I am working on hg38. The bam file and the random.bed file are not empty so I really do not understand why sambamba depth is producing an empty file, only containing the column names: # chrom chromStart chromEnd F3 F4 F5 readCount meanCoverage...
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Eliezer Lichter posted a comment on discussion General Discussion
Update 2: In lines 341 and 342, switching deg1 to be the "end" and deg2 to be "start and changing degrees to 270-(358...) as follows: dat$deg1<-270-(358dat$end/mlength) dat$deg2<-270-(358dat$Start/mlength) Works. Haven't checked the breakpoints and if they change (reverse or something else) too, but pictorially, the above works.
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Update: On line 386, under #BUILD MT AXIS, change: mt.axis$deg.axis<-90+(358mt.axis$position/mlength) to mt.axis$deg.axis<-90-(358mt.axis$position/mlength) This will change the labels, but not the arcs* To change the arcs, lines 341 and 342, under #ADD DEGREES must somehow be changed. dat$deg1<-90+(358dat$start/mlength) dat$deg2<-90+(358dat$end/mlength) I have so far failed to find to which number. I tried 90 -(358*....) as well as many other angles. For small arcs, 90-358 as above works, but once...
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Update: On line 386, under #BUILD MT AXIS, change: mt.axis$deg.axis<-90+(358mt.axis$position/mlength) to mt.axis$deg.axis<-90-(358mt.axis$position/mlength) This will change the labels, but not the arcs* To change the arcs, lines 341 and 342, under #ADD DEGREES must somehow be changed. dat$deg1<-90+(358dat$start/mlength) dat$deg2<-90+(358dat$end/mlength) I have so far failed to find to which number. I tried 90 -(358*....) as well as many other angles. For small arcs, -90 as above works, but once you...
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Update - may be useful for others too. On line 386, under #BUILD MT AXIS, change: mt.axis$deg.axis<-90+(358mt.axis$position/mlength) to mt.axis$deg.axis<-90-(358mt.axis$position/mlength) This will change the labels, but not the arcs* To change the arcs, lines 341 and 342, under #ADD DEGREES must somehow be changed. dat$deg1<-90+(358dat$start/mlength) dat$deg2<-90+(358dat$end/mlength) I have so far failed to find to which number. I tried 90 -(358*....) as well as many other angles. For small arcs,...
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Update - may be useful for others too. Changing the following in the delplot.R script will switch the plots to clockwise: On lines 341 and 342, under #ADD DEGREES, change dat$deg1<-90+(358dat$start/mlength) dat$deg2<-90+(358dat$end/mlength) to dat$deg1<-90-(358dat$start/mlength) dat$deg2<-90-(358dat$end/mlength) Then, on line 386, under #BUILD MT AXIS, change: mt.axis$deg.axis<-90+(358mt.axis$position/mlength) to mt.axis$deg.axis<-90-(358*mt.axis$position/mlength)
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Update. I solved it by copying the version of Plotrix I had on my machine into the MitoSAlt bin and removing the Plotrix version (which was old) from there.
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Hi, I am rerunning MitoSAlt - previously ran with no issues. Now, it is running fine until the end(bed, BW, cluster, etc generated). However, the plots are not created. When looking at the delpot.Rout file, I get the following message: "Error: package or namespace load failed for ‘plotrix’: package ‘plotrix’ was installed before R 4.0.0: please re-install it Execution halted" I tried uninstalling and reinstalling plotrix with the same results. I also tried installing plotrix from source using wget...
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Thanks, I will try to do so on my end too. In the delpot,R file, I think I located the chunk of code that needs to be changed, starting at line 81 - please see attached image. I am just unclear exactly how. Thanks
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Ok Eliezer that's a relevant point. At the moment the delplot.r would need adjustment and testing to recreate the same plot flipped. I will try to add the feature but unfortunately I have moved to the industry in a different field hence may not be able to work on it anytime soon. Shall update you if I have a new script. Sorry for the inconvenience. SwarajBasu84 - Chat @ Spike [1r0bqq] On September 30, 2022 at 13:34 GMT, Eliezer Lichter elichter@users.sourceforge.net wrote: I used illustrator, not...
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I used illustrator, not sure how to remove the numbers. Besides, I have 50+ files, and it would be a lot more efficient to rerun mitosalt with a flipped axis than to manually flip them with a graphic tool.
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Xie Xie posted a comment on discussion General Discussion
Hi Eliezer, I believe that if you open the pdf file in illustrator or in affinity designer, you can flip the image, remove the old number, and add new ones. On Fri, Sep 30, 2022 at 01:48 Eliezer Lichter elichter@users.sourceforge.net wrote: Thanks, I already tried flipping the umages. The issue with that is that fhe numbers(the ticks around the circle) get flipped as well and ends up being hard to read. I saw some stuff in the R script where I think it could be modified, but would rather not tinker...
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Thanks, I already tried flipping the umages. The issue with that is that fhe numbers(the ticks around the circle) get flipped as well and ends up being hard to read. I saw some stuff in the R script where I think it could be modified, but would rather not tinker unless I know I am changing the correct fields. Thanks
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Hi Elizier, It is possible but might need changes in all the angles in the R script to generate in reverse. Another quick fix option could be to convert the plot into a JPEG from PDF and flip it horizontally in the pic editor. -Regards On Fri, 30 Sep, 2022, 00:54 Eliezer Lichter, elichter@users.sourceforge.net wrote: Hi, Is there a way to change the plots to show the genome clockwise rather than counterclockwise? I looked in the delplot.R file, but I am unclear if that is the correct place to do...
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Hi, Is there a way to change the plots to show the genome clockwise rather than counterclockwise? I looked in the delplot.R file, but I am unclear if that is the correct place to do so, if at all possible. Thanks, Eli
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Hu Shaomin, The last repository has moved to github where you could check all the versions here https://gitlab.com/mcfrith/last/-/tags and select a version for download and installation https://gitlab.com/mcfrith/last/-/archive/1296/last-1296.zip Ideally if you replace the values in the setup.sh script LAST_URL=https://gitlab.com/mcfrith/last/-/archive/1296/last-1296.zip LAST_V=last-1296 It should work but I have not tested it yet. -Regards Swaraj
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shaomin wu posted a comment on discussion General Discussion
Hi MitoSalt team, I tried to install the MitoSalt by following the README file. However, the link of the LAST software was unavailable (http://last.cbrc.jp/last-941.zip). How do I obtain the LAST software? Could you possible send me a copy of the LAST software? Thank you.
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Hello Danielle, Apologies for the delay in my response. I have made a shift from academia to industry and a few current commitments and travel lead to my inability to give a prompt response. However please be assured, I shall give or try to give a quick response, to help in your work. Thank you for your kind words on MitoSAlt! From your configuration I can notice that your FASTQ reads are enriched in Mt sequences and you've opted for direct alignment to the Mt genome. In this case the first step...
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Danielle Reid posted a comment on discussion General Discussion
Hello! Thank you for making this awesome bioinformatic tool and allowing publlic access! I have been working with MitoSAlt for a little bit of time and was given an error today and I was hoping I could get some guidance. The error stated that it cannot open my tmp.fq file for a particular sample. After checking the directory, I noticed the file was never created. I was able to generate the bed, bam, and other tmp files. I used the same config file as previous samples that did not receive the error....
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Hi Swaraj, Thanks for your response, you are correct, the .bg file is empty, the .cov however is not, it has all the columns. In fact, I tried the solution you mention is the linked post for that prior to creating the ticket, but when I try this step: groupBy -g 5 -c 8 -o mean -i random.cov I get the same * ERROR: Requested column 8, but database file random.cov only has fields 1 - 0 In general, I don't understand why the bg file is empty to begin with, is it something on my system or with the sample...
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Hi Eliezer, could you check the thread below. The large memory error might be because the bed to bigwig converted is getting an empty file. https://sourceforge.net/p/mitosalt/discussion/general/thread/0cd3fa85ad/?limit=25#b99c If you run the pipeline with the delete temporary files option as "no", then one can check what each intermediate file generates. The order of the files would be: 1) tmp_$tag.bam: The alignment against Nuclear + Mitochondrial genome 3) tmp1_$tag.bam and tmp2_$tag.bam: Unmapped...
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Hi Eliezer, could you check the thread below. The large memory error might be because the bed to bigwig converted is getting an empty file. https://sourceforge.net/p/mitosalt/discussion/general/thread/0cd3fa85ad/?limit=25#b99c If you run the pipeline with the delete temporary files option as "no", then one can check what each intermediate file generates. The order of the files would be: 1) tmp_$tag.bam: The alignment against Nuclear + Mitochondrial genome 2) tmp1_$tag.bam and tmp2_$tag.bam: Unmapped...
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Problem aligning to nuclear genome
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Yes Michael. That would be conclusion for the parameters chosen. You might want to relax the parameters in case the coverage of sequencing on the Mt genome is low. On Fri, 14 Jan, 2022, 00:32 Michael Nagy, fidibidi@users.sourceforge.net wrote: So to clarify: If I'm getting no .tsv file, does that mean that no deletions are being detected? Troubleshooting Advice Sent from sourceforge.net because you indicated interest in < https://sourceforge.net/p/mitosalt/discussion/general/> To unsubscribe from...
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So to clarify: If I'm getting no .tsv file, does that mean that no deletions are being detected?
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This helps a ton, Thank you!
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Hi Michael, Regarding the cluster file, the order of file generation by MitoSAlt is - tab file with raw alignments - bed and breakpoint file with individual split reads - cluster and tab with the final clustered output By default MitoSAlt should cluster all reads within breakpoint file which fall in the same position (breakthreshold = -2) and only report those clusters which have support from at least 5 reads (cluster_threshold = 5). This presence of breakpoint file with results but absence of .cluster...
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It seems like the .cluster file is empty in multiple projects where mitoSalt failed. I have all the files (including tmp ones) from a failed run, Any suggestions for troubleshooting? Thanks!
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Hello! Just a quick question: I've been having an interesting issue, where some samples for some reason aren't working, while others from same run are working without issue. I end up with: .log .count.txt .cnmt.txt .cluster .breakpoint .bed .bw .tab.gz .bam.bai .bam but now .tsv, or plot. My question: Is there a good way to have the program start assuming its already completed the alignment step? NU+MT, because that step takes quite a long time, and I'd like to just work on solving the underlying...
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Ok Eliezer, thank you for the update and glad that you have been able to troubleshoot the issue. Unfortunately I have not put a safeguard for broken downloads to continue, sorry about that. At the moment not sure why the issue might persist even after increase in the internet speed. For plotrix and RShiny will check the setup script if the installation works in my system. On Sun, 2 Jan, 2022, 10:31 Eliezer Lichter, elichter@users.sourceforge.net wrote: Hi Swaraj, I just wanted to update you. I was...
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Hi Swaraj, I just wanted to update you. I was able to get the program to run! It looks to me that the reason it initially failed to download and subsequently failed the proceeding steps may be due to size of the genome downloaded and perhaps my internet speed. The reason I think this is the case is because the server connection to NCBI kept resetting, and the genome file ended up being corrupted causing the program to halt at the mito extraction point. What is odd however is when I increased my download...
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Ok Eliezer. Thanks for your feedback. I'll test the setup script in both basic and advanced mode once and get back you. On Thu, 30 Dec, 2021, 23:07 Eliezer Lichter, elichter@users.sourceforge.net wrote: Also, regardless of how I run the setup, the index files are not generated. I have to do so manually. [tickets:#1] Mouse genome is not downloaded Status: open Milestone: 1.0 Created: Mon Dec 27, 2021 10:00 PM UTC by Eliezer Lichter Last Updated: Thu Dec 30, 2021 05:35 PM UTC Owner: nobody Sent from...
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Also, regardless of how I run the setup, the index files are not generated. I have to do so manually.
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Actually now thinking back the url did not work when I ran the setup script in basic mode. However, I was able to get it when I changed the url or if I ran it in advanced mode on a fresh download. My gcc version is 11.1.0, so something else must cause this. The question is what?
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Thanks Eliezer. Could you confirm please if this is the URL in the setup.sh script you are using: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/635/GCF_000001635.26_GRCm38.p6/GCF_000001635.26_GRCm38.p6_genomic.fna.gz I am running the setup.sh commands in my system and am able to download the genome (screenshot attached). Hence would like to change the URL in case its causing download issues. If the genome/mouse_mt.prj is generated and yet lastal is unable to read it, might be a compilation issue...
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Thanks Eliezer. Could you confirm please if this is the URL in the setup.sh script you are using: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/635/GCF_000001635.26_GRCm38.p6/GCF_000001635.26_GRCm38.p6_genomic.fna.gz I am running the setup.sh commands in my system and am able to download the genome (screenshot attached). Hence would like to change the URL in case its causing download issues. If the genome/mouse_mt.prj is generated and yet lastal is unable to read it, might be a compilation issue...
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Thanks Swaraj, I encountered this issue after running the setup. I then went into the setup script and it turns out the url did not work. So I found the correct url. However, the index files did not get made. So I used Samtools afterwards to create the index files. Now I am getting the following lastal problem bin/last/src/lastal: can't open file: genome/mouse_mt.prj. From looking at various forums it seems like it's either a compiler issue or hyperthreading is not enabled. I checked on my machine...
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Hello Eliezer, Could you please try running the setup.sh script which should be able to download the mouse genome and create index. We have not packed the genome and index with the pipeline zip as the size becomes quite large Please let us know if the script is not creating the required files. -Regards Swaraj
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Downloaded the latest version. The mouse config file is there, but the genome is not.
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Mouse genome is not downloaded
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Swaraj, Thanks for all the help, because of time concerns, we are pursuing a course of unarchiving. But I really appreciated your help! Best Michael
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Hi Michael, Sorry for your inconvenience. Will try to figure out your issue to the best of ability. Could you try once with the following: dna = yes enriched = yes nu_mt = no rmtmp = no o_mt = yes i_del = yes cn_mt = no This translates to direct alignment on the Mt genome, while skipping nuclear genome alignment and no copy number estimation. Also the temporary files generated are retained. Please share the number of lines in each of temporary files generated (they should all start with tmp) -Regards...
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Hi Swaraj, Thank you for the prompt response! I tried this method but it doesn't appear to be working. I generated the fastq files using the following commands: samtools sort -@ 8 -o VAL-F3029.sorted.Test5.bam VAL-F3029.bam samtools view -u -@ 8 -f 12 VAL-F3029.sorted.Test5.bam > VAL-F3029.sorted.Test5.tmp1.bam samtools view -u -@ 8 VAL-F3029.sorted.Test5.bam chrM > VAL-F3029.sorted.Test5.tmp2.bam samtools merge -@ 8 VAL-F3029.sorted.Test5.final.bam VAL-F3029.sorted.Test5.tmp1.bam VAL-F3029.sorted.Test5.tmp2.bam...
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Hi Michael, We are glad to know that MitoSAlt is aiding your research. If you have unmapped + mt reads in Fastq format you can give it as an input to MitoSAlt, and change the following in the config file nu_mt = no cn_mt = no This would lead to the pipeline directly aligning the input reads on the Mt genome using lastal, and skipping the hisat alignment step against the nuclear genome. Hopefully this answers your question. -Regards Swaraj On Fri, 10 Dec, 2021, 00:14 Michael Nagy, fidibidi@users.sourceforge.net...
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LOG FILE: hisat2 = bin/hisat2/hisat2 lastal = bin/last/src/lastal lastsp = bin/last/src/last-split mfcv = bin/last/scripts/maf-convert reformat = bin/bbmap/reformat.sh samtools = bin/samtools/samtools sambamba = bin/sambamba b2fq = bin/bedtools2/bin/bamToFastq gcov = bin/bedtools2/bin/genomeCoverageBed intersectBed = bin/bedtools2/bin/intersectBed sortBed = bin/bedtools2/bin/sortBed clusterBed = bin/bedtools2/bin/clusterBed randomBed = bin/bedtools2/bin/randomBed groupBy = bin/bedtools2/bin/groupBy...
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To clarify what I'm trying to do: samtools sort -@ 8 -o VAL-F3029.sorted.Test5.bam VAL-F3029.bam samtools view -u -@ 8 -f 12 VAL-F3029.sorted.Test5.bam > VAL-F3029.sorted.Test5.tmp1.bam samtools view -u -@ 8 VAL-F3029.sorted.Test5.bam chrM > VAL-F3029.sorted.Test5.tmp2.bam samtools merge -@ 8 VAL-F3029.sorted.Test5.final.bam VAL-F3029.sorted.Test5.tmp1.bam VAL-F3029.sorted.Test5.tmp2.bam samtools fastq -@ 8 VAL-F3029.sorted.Test5.final.bam -1 VAL-F3029.Test5.R1 fastq.gz -2 VAL-F3029.Test5.R2.fastq.gz...
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Hi everyone! Thank you for creating this software! Its been a great success so far. One issue my team is having is that we have alot of the raw data archived, however we have access to BAM files, that have been aligned to HG38. Is it feasible to pursue using these files? I've been thinking that I can just extract the MT + unmapped reads, and pass into the program? Is the alignment going to be an issues? I figured, the fastq conversion removes that bit... Thanks again!
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Hi Bengsiu, Sorry due to a major relocation I was unable to check the MitoSAlt forum for a while. In case you haven't been able to find a workaround, could you please try this below (assuming you only have fastq files which are neither zipped or gzipped): #get paths configFile=/home/bengisu/Documents/MitoSAlt_1.1.1/config_human.txt mitoSAlt=/home/bengisu/Documents/MitoSAlt_1.1.1/MitoSAlt_SE1.1.1.pl fastqDir=/home/bengisu/Documents/MitoSAlt_1.1.1/ASD/fastq #loop through each file (fastq) in directory...
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Hi Adily, One issue with exome data could be that it has very reads which map to the Mt genome. Could you turn of the tmp file deletion parameter, and then check if the tmp_23742.bam file has any reads mapped or not. If not, then check if the corresponding Sam file tmp423742.sam has mapped reads. If the Sam file is also devoid of reads, that might indicate a Hisar alingment issue. If the sam and the bam filea have reads, then probably the sample did not have much mitochondrial reads, thus the extraction...
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adily basal modified a comment on discussion General Discussion
Hello, I run MitoSalt on paired end fastq.gz files of exome but got Killed after Extract reads: Thu Sep 30 10:44:03 2021: Map to NU+MT genome Thu Sep 30 10:53:49 2021: Extract reads Killed [E::hts_open_format] Failed to open file tmp_23742.bam Is that posible to run MitoSalt on exome raw data? Should I change some parameters on the script commands? The log file is attached. Thank you in advance, Adily
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Hello, I run MitoSalt on paired end fastq.gz files of exome but got Killed after Extract reads: Thu Sep 30 10:44:03 2021: Map to NU+MT genome Thu Sep 30 10:53:49 2021: Extract reads Killed [E::hts_open_format] Failed to open file tmp_23742.bam Is that posible to run MitoSalt on exome raw data? Should I change some parameters on the script commands? Thank you in advance, Adily
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Hi, Thanks for making this script but unfortunately I couldn´t run it. My files are not in fastq.zip format. All of my files in .fastq format. They are in fastq form independently. I collected them in the same folder, but I couldn´t compressed them in fastq.zip format. I tried to modify the script you made, by writing only .fastq to needed places. But I did it wrongly I guess - Could you please take a look following script for me? Thank you so much #get paths configFile=/home/bengisu/Documents/MitoSAlt_1.1.1/config_human.txt...
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Thanks for your huge help. You can find one of my samples' tsv file. The sample should have only one 5kb deletion. Default parameters gave me 17 more alterations with the deletion sizes vary between 5756 (expected) and 16548 (with a final 21 bp size - duplication event). To remove these alterations I increased the score threshold, split length (the most effective parameter among other filters based on my previous analysis) , breakthreshold and followed these parameters: score_threshold = 90 evalue_threshold...
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Hi Bengsiu, Could you please share with us the final output of MitoSAlt, the TSV file, and add a column, where you mark the deletions and duplications you want to keep and remove. This will help us to figure out how to remove the false positives. Regards Swaraj On Fri, May 28, 2021, 11:06 PM Bengisu bkbulduk@users.sourceforge.net wrote: Hi again, Thanks for your suggestion. I have mtDNA enriched single-end sequences, I think Mity s not useful for me. MitoSAlt tool´s feature and scoring system also...
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Hi again, Thanks for your suggestion. I have mtDNA enriched single-end sequences, I think Mity s not useful for me. MitoSAlt tool´s feature and scoring system also targets the pair-end seqs, and I have been trying to modify these to single-end reads for weeks. I obtained non-specific multiple alterations for my samples and these alterations could only be removed when the split length became 27-28 etc. For instance, although I set sizelimit as 16560 in config file, I still obtain duplication events...
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Hi Bengsiu, Guessing that your fastq files fastq.zip format. This shell script should work, you have to convert it into executable chmod +x runMitoSAlt_SE.sh Also change the paths to the config, fastq directory and MitoSAlt scripts. Let us know if this works. -Regards Swaraj
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Hi, I have just fastq files not a fastq.gz folder. I tried a zip file as an input as following; configFile=config_human.txt for fastqFile in ls|fgrep .zip; do studyName=echo $fastqFile|sed 's/.zip//' perl MitoSAlt_SE1.1.pl $configFile $fastqFile Seq done But I didnt obtain any alteration and received empty bed, breakpoint, cluster files with these output: Use of uninitialized value $elements[6] in pattern match (m//) at MitoSAlt_SE1.1.pl line 217, <config> line 75.</config> Is there any option for...
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Hi, Please let me to share three tvs files belong to one sample to clary myself. Normally, for this sample I should have one 3047 bp sized deletion with 5´ brk at m.13581 and 3´ brk at m.60. Frequency is 4.94. This result based on the eKLIPse tool. However when I apply default parameters I obtained lots of clusters. When I increase the breakthreshold to 50 it didn´t change. But when I increase split length to 27, they could be removed, and I obtained my specific alteration. However I am not confident...
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Hi, Thank you so much. Now I don´t receive any BED format error for the same files. Many thanks.
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Hi Bengsiu, Could you please download the v1.1.1 (updated today) and check with your data. Let us know if you face any issues. -Regards Swaraj
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MitoSAlt released /README
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