Oh god. Luciana, On Fri, Nov 5, 2021 at 5:56 PM Rob Patro ***@***. . Doesn't sound like you're using transcripts, which Salmon is built to do. Well occasionally send you account related emails. over 20,000 samples. ERROR: Could not create the directory ["transcripts_quant"]. You can visit Salmon's GitHub page here, and check out the Salmon source code, feature requests, known issues etc. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. privacy statement. Update Salmon's main output is its quantification file. I thought that it could be a problem with fastqc, so I uninstalled it and then installed it manually (through the fastqc.zip file), but the output remained the same. This the output from the command you suggested. Is the problem tar? privacy statement. @sq SN:NC_003070.9:3995-4276 LN:281 To subscribe to this RSS feed, copy and paste this URL into your RSS reader. ./src/salmon-1.5.2_linux_x86_64/bin/salmon quant was invoked improperly. --validateMappings \ that NC_003070.9:12104890-12105118 I have all the right files in place and can get Salmon (v1.4) to start but it runs for such a long time that I started wondering if there are problems. 3: The executor used (in the above case: local) 4: The first process is executed once (1) and starts with a unique hexadecimal (see TIP below) and ending with the percentage and job completion information. Exception : [Error: This version of salmon does not support indexing using the RapMap index.] Connect and share knowledge within a single location that is structured and easy to search. and inside the transcripts_index folder, ref_indexing.log has several lines of "XXX was longer than 200000 nucleotides. (2005) monocytogenes Scott A Lmap2 1/2a Cured dry sausage Gnanou Besse et al. I wrote an R package to make ChatGPT AI plot stuff for me. Reddit and its partners use cookies and similar technologies to provide you with a better experience. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. I really don't understand the message error. I tried to build an index by salmon below: Then I got "salmon index was invoked improperly." Create an account to follow your favorite communities and start taking part in conversations. This suggests something is awry with the BAM file / header. In this case, it performs quasi-mapping (a lightweight stand in for alignment), and so it is not necessary to provide the BAM file. https://github.com/svn2github/staden-io_lib/blob/master/trunk/io_lib/bam.c#L300. On the fence? 2. It is developed openly on GitHub. ./bin/salmon alignment-quant was invoked improperly. I think you need a cdna.all.fa.gz instead of dna file. The text was updated successfully, but these errors were encountered: This suggests that the machine was not able to allocate enough memory to perform the requested operation. Other samples have a exit code 0. Well occasionally send you account related emails. MathJax reference. [House Hearing, 117 Congress] [From the U.S. Government Publishing Office] THE CLEAN WATER ACT AT FIFTY: HIGHLIGHTS AND LESSONS LEARNED FROM A HALF CEN- TURY OF TRANSFORMATIVE LEGISLATION ===== (117-59) REMOTE HEARING BEFORE THE SUBCOMMITTEE ON WATER RESOURCES AND ENVIRONMENT OF THE COMMITTEE ON TRANSPORTATION AND INFRASTRUCTURE HOUSE OF REPRESENTATIVES ONE HUNDRED SEVENTEENTH CONGRESS SECOND . The argument to the -t flag should be a FASA file that contains the sequence of the reference transcripts, and the names and lengths of those reference transcripts should match the names and lengths encoded in the BAM file. How do I arrange multiple quotations (each with multiple lines) vertically (with a line through the center) so that they're side-by-side? Organization . Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. Have a question about this project? Sign in data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAKAAAAB4CAYAAAB1ovlvAAAAAXNSR0IArs4c6QAAAnpJREFUeF7t17Fpw1AARdFv7WJN4EVcawrPJZeeR3u4kiGQkCYJaXxBHLUSPHT/AaHTvu . After downloading the Salmon source distribution and unpacking it, change into the top-level directory: > cd salmon. Please help. *Luciana Oliveira * 2: The script and version names. Another issue that I just found is the following (the last command that salmon is trying to execute): Then I searched online for the issue and found the following thread: https://github.com/COMBINE-lab/salmon/issues/129. Specifically, this line of code seems to be triggering the error that is printed (https://github.com/svn2github/staden-io_lib/blob/master/trunk/io_lib/bam.c#L300). Have a question about this project? We figured it out by md5sum command output comparison. Is word of religious people? Sign in NC_003070.9:12106952-12107084 How can I use a VPN to access a Russian website that is banned in the EU? Read 0] salmon quant was invoked improperly, Help us identify new roles for community members. Although, after 0.14.0 we start to use genome but it's still has to be preprocessed. However, updating salmon to the newest 0.9.1 version did not solve the issue. privacy statement. climate change and the u.s. agriculture and forestry sectors 117th congress (2021-2022) 31 May 2001 (01-2567) Original: English . The issue was caused by the corrupted input .fastq files that were damaged somehow upon uploading them from the local machine. @rob-p These are running parallel on different EC2 instances, I am checking to see if this happens on the same samples - I am rerunning it, The way this is setup - each sample gets qc_trimmed etc (our thread on bbmap and bbduk) and then it goes to salmon quant, Strangely enough - with the above error message of mine, when I go to the logs directory and look up salmon_quant.log, it has correct info (last line below), And the output directory has a quant.sf file and it has all the records I want -- however, salmon is exiting with the above error message. Thoughts on remote work as a bioinformatician? Even this runs fine, but what triggers that error message - I am not sure, I also reran my whole pipeline (qc_trimming etc and finally salmon) - this time with 5 samples only (and included the above sample) - the pipeline runs successfully. --seqBias\ do I need to extract the tar file first? The text was updated successfully, but these errors were encountered: Does it always error out on the same samples? How to input data for DESeq2 from individual HTSeq count? This is because all of the relevant information is already contained within the BAM file. Salmon isoform Salmon 2 reads ( fastq ) sam/bam () StringTie + DESeq2 RNA-seq featureCounts reads RNA-seq Salmon StringTie featureCounts, DESeq2 Salmon NC_003070.9:12108343-12108474 @rob-p This is not running twice on same sample. Version Info: This is the most recent version of Salmon. NC_003070.9:12105547-12105662 SALMON RUN TIP: I dont see much people talking about Salmon Run Final Wave Cleared, All Players Dead. I am using Java8: I am running the script on a cluster with SLURM. -- By clicking Sign up for GitHub, you agree to our terms of service and Site design / logo 2022 Stack Exchange Inc; user contributions licensed under CC BY-SA. It looks like the log points to a sample that completed successfully at 19:45:18.487 before the sample at the top of the post started 19:51:56.392. On my server there is a hard limit on the virtual memory, I believe it's 16GB and apparently salmon quant needs more than that. For usage information, try ./src/salmon-1.5.2_linux_x86_64/bin/salmon quant --help On the other hand, in quasi-mapping mode, you index the set of reference transcripts (using salmon index) and then provide salmon with the location of the index and the raw reads (i.e. To learn more, see our tips on writing great answers. If Boost is not . Are you certain the relative path to the file is correct from the current working directory? When you are using the alignment-based mode (i.e. I cannot figure out anything from this message. Combining read counts from three separate GEO studies, How to input data and metadata from NCBI for RNA-Seq analysis in R, Calling isoforms from long read data generated from partially degraded RNA. NC_003070.9:12109037-12109336 It works correctly for some samples and errs out with others like below, Why does it say salmon quant was invoked improperly. NC_003070.9:12104783-12109336 NC_003070.9:12105744-12105911 E-Book Overview Full coverage of electronics, MEMS, and instrumentation and control in mechanical engineering. ./src/salmon-1.5.2_linux_x86_64/bin/salmon quant -i salmon_index -l ISF -1 rawDataPE/ERR3537668_1.fastq.gz -2 rawDataPE/ERR3537668_2.fastq.gz --validateMappings -o transcripts_quant_test. salmon quant was invoked improperly. Is there anything different about the how the commands are run (e.g. Is energy "equal" to the curvature of spacetime? The text was updated successfully, but these errors were encountered: It looks like you are providing the -t flag with the reads rather than the target transcriptome (i.e. Check the values of fq1 and fq2 and make sure they are coming through properly. NC_003070.9:12105744-12105911 And also, if so, why does the first run succeed and the second fail? Already on GitHub? When salmon cannot read the index, it propagates an exception, which is what you are seeing here. The command I am running is the following one: The command is run by Pypiper: https://github.com/epigen/pypiper Then, create and out-of-source build directory and change into it: > mkdir build > cd build. The article examines the nature of Chan/Zen Buddhism in its interaction with other schools of thought in pre-modern China. (2005) Lmap4 1/2a Cold smoked Gnanou Besse L. monocytogenes Scott A was grown to early stationary salmon et al. /Users/jcm161/anaconda3/envs/salmon/bin/salmon quant was invoked improperly. The columns appear in the following order: 0 comments poconnel3 commented on Aug 20, 2021 edited Which version of salmon was used? For usage information, try /Users/jcm161/anaconda3/envs/salmon/bin/salmon quant --help Exiting. rev2022.12.11.43106. For usage information, try ./bin/salmon quant --help-alignments We figured it out by md5sum command output comparison. You signed in with another tab or window. Dec/2022: Grey goos vodka Ausfhrlicher Test TOP Grey goos vodka Beste Angebote Smtliche Testsieger - JETZT weiterles. Best Hello Bob, I am trying to implement Salmon 1.5.3 and I have problems running the quant mode. 2021-09-08; A failure occurred while executing org.jetbrains.kotlin.gradle.internal.KaptExecution 2021-10-19; C++ Debug Assertion Failed 2021-07-18; Biztalk Web ServiceInternal SOAP Processing Failure 2022-03-02 rapidjson 2021-09-24; Internal SOAP Processing Failure - Testing web services . According . I would like to study bioinformatics and would like to Press J to jump to the feed. -o transcripts_DecoyQuant \ set of reference transcripts). This would be my guess. By accepting all cookies, you agree to our use of cookies to deliver and maintain our services and site, improve the quality of Reddit, personalize Reddit content and advertising, and measure the effectiveness of advertising. The rubber protection cover does not pass through the hole in the rim. Counsel appearing for Pattali Makkal Katchi, contended that the creamy layer principle shall not be invoked for the purpose of Article 15(5). Unsere Bestenliste Dec/2022 Detaillierter Produkttest Beliebteste Md 84627 Bester Preis Alle Vergleichssi. Hi @sagnikbanerjee15, do you have any updates on this? and this the error I am getting. For usage information, try salmon quant --help Exiting. NC_003070.9:12106952-12107084 Also, however, I'm not sure how Java is involved (since Salmon is written completely in C++). If so, why? I succeed to prepare the index using decoy protocol and I am trying reads quantification mode. I am using salmon on two very large data sets. Further, the output you printed around the exception happens at the start of program execution, so I don't understand the timeline of events here for a single run / execution. Why is Singapore currently considered to be a dictatorial regime and a multi-party democracy by different publications? But actually, it was created. How does legislative oversight work in Switzerland when there is technically no "opposition" in parliament? Thanks for contributing an answer to Bioinformatics Stack Exchange! Something can be done or not a fit? If there are any more details, we can reopen. Luciana. The thing that's strange about the second is that somehow the output path you are providing in the command doesn't match the directory name in the error message. Now I am running the following command: Salmon is a transcriptome based quantification tool, before 0.14.0 it can't use genomic iinformation. It requires a set of target transcripts (either from a reference or de-novo assembly) to quantify. Providing the precise commands invoked will help us troubleshoot the problem. @sq SN:NC_003070.9:4485-4605 LN:120 ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_32/gencode.v32.transcripts.fa.gz, https://bioconductor.org/packages/release/bioc/html/tximport.html. How to make voltage plus/minus signs bolder? However, reinstalling manually other libraries do not help. Already on GitHub? One question is "is it running twice for the same sample?" @sq SN:NC_003070.9:5438-5899 LN:461. and the headers in the fasta file are something like this: NC_003070.9:12107542-12107677 Specifically, your command has the output directory as transcripts_DecoyQuant, but the error reports not being able to create the directory transcripts_quant. NC_003070.9:12107542-12107677 I have a dataset with about 30 samples or so, in some cases salmon quant (1.2.0) runs fine, with some samples I get the error below. Could you please help me to solve this problem? ------ -p 12 Darren shaving my head spinning? Concomitantly, Chan is invited as pivot for a "dialogue" between early Daoist/Confucian classics (from the Yi Jing to the Dao De Jing) and modern Western philosophy--a dialogue pointing to an underlying communality of problems. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. Unsere Bestenliste Dec/2022 Ultimativer Produktratgeber TOP Nici qid Aktuelle Schnppchen Preis-Leistungs. Already on GitHub? I'm glad that you were able to address the first issue. Full log: https://jpst.it/26mnn I was able to narrow down the issue*. Hi there, I am relatively new to using Salmon for RNAseq data and run into problems when running a test datafile. Would you have any idea why I got this message error? ## A subreddit to discuss the intersection of computers and biology. -2 ERR3537668_2.fastq.gz \ The question is why this would happen for some samples and not others, so I'd look to find differences between the invocations, or the machines where samples are running / not running properly. This doesn't provide the benefits of the decoy sequence, but it will ensure that this is, in fact, the problem you are having. You signed in with another tab or window. Unsere besten Testsieger - Suchen Sie hier die Nici qid Ihren Wnschen entsprechend Unsere Bestenliste Dec/2022 Ausfhrlicher Kaufratgeber Beliebteste Nici qid Bester Preis : Vergleichssieger Direkt weiterlesen. salmon quant was invoked improperly. [Senate Hearing 105-60] [From the U.S. Government Printing Office] S. Hrg. Dec/2022: Grey goos vodka Umfangreicher Kaufratgeber Die besten Grey goos vodka Beste Angebote Testsieger Direkt weiterlese. NC_003070.9:12108864-12108936 By rejecting non-essential cookies, Reddit may still use certain cookies to ensure the proper functionality of our platform. NC_003070.9:12108592-12108794 For usage information, try ./bin/salmon quant --help-alignments Exiting. @sq SN:NC_003070.9:5173-5326 LN:153 from CNN: Development of Graves' ophthalmopathy may be independent of thyroid function. 2.1 Salmon conda create --name rnaseq conda activate rnaseq conda install -y salmon 2.2 index salmon index -t Homo_sapiens.GRCh38.cdna.all.fa.gz -i homo38_index [Error reading from the FASTA/Q stream. Ok then with which flag shall I provide the file of reads? I enlarged it for 48 and it works. 45, importantly announcing it will no longer focus on the. ie. I succeed to prepare the index using decoy protocol and I am trying reads quantification mode. I looked up sample runs before and after - they seem to have correct exit codes and ran fine. ./bin/salmon quant -t ../Data/DRR029379.fq -p 6 -l A -a ../Data/DRR029379_after_bowtie.bam -o ../Data/DRR029379_after_salmon Asking for help, clarification, or responding to other answers. -l A \ Please refer to quasi-mapping based mode and alignment-based mode in the documentation for more details. Salmon is a tool for wicked-fast transcript quantification from RNA-seq data. And I got this error message: Actually, the format specification is a bit more important in Salmon than in Sailfish, as Salmon (both the alignment-free and alignment-based modes) makes better use of paired-end information. Second, the second and third transcripts appear to be exact duplicates. Announcing Cengage Learning's Global Environmental Ethics Watch Help your students t d t thi think k outside t id th the classroom l and see the impact of environmental ethics issues Updated several times a day, Cengage Learning's Global Environmental Ethics Watch is an ideal one-stop site for classroom discussion and research projects. --gcBias \ It produced the "N2" folder" but it dose not contain thje .sf files (the quant files). @sq SN:NC_003070.9:3630-5899 LN:2269 failed to read 8 bytes salmon quant invoked improperly I also reran my whole pipeline (qc_trimming etc and finally salmon) - this time with 5 samples only (and included the above sample) - the pipeline runs successfully (2005) phase in BHI at three different temperatures (10, 22 and 37 C). @sq SN:NC_003070.9:3630-5899 LN:2269 Please check Salmon---readstranscriptomes (SMEM-based) lightweight-alignment quasi-mapping SMEM-based mappingSalmon quasi-mapping quant quasi-mapping a combination of data structuresa hash table, suffix array (SA) and efficient rank data structure to Sailfish Users Group. You signed in with another tab or window. Thanks On Nov. 10, the FTC released a new policy statement interpreting its enforcement authority under Section 5 of the FTC Act, 15 U.S.C. Grey goos vodka - Whlen Sie dem Sieger. I also checked the names that you are referring to and I found that the first part of the names match but for the entries in the bam file the lines end with "LN:xxx" . I am having trouble with 2 samples. @sq SN:NC_003070.9:3630-3913 LN:283 Exiting. . [2021-11-08 14:35:28.348] [jointLog] [info] Finished Bootstrapping salmon quant was invoked improperly. NC_003070.9:12106547-12106703 Locally on my laptop the script is running without any issues. What are the major differences between transcriptome alignment and genome alignment? It looks like FastQC is being invoked somewhere. to your account, I have single ended reads in a fastq file which I aligned with bowtie against the transcriptome. However, to quantify I had another problem. srun ./salmon-1.5.2_linux_x86_64/bin/salmon quant -i salmon_index \ Use MathJax to format equations. This file is named quant.sf and appears at the top-level of Salmon's output directory. and I got this message error: I checked, the file is in fact present in that path. All you need to run Salmon is a FASTA file containing your reference transcripts and a (set of) FASTA/FASTQ file (s) containing your reads. By clicking Sign up for GitHub, you agree to our terms of service and This will build the sparse index instead of the dense index, which is a bit smaller and may therefore fit in RAM on the machine where you are doing quantification. I just provided the list of transcripts in fasta format with the -t flag but its still giving me the same error. I'm also at a loss for exactly what could bre going on here. Are the names consistent between the BAM file and the reference you are providing? Any ELN talks would be independent of Edit The appellant noted an appeal, which was docketed as Case No. @sq SN:NC_003070.9:0-30427671 LN:30427671 Effect of growth temperature on attachment of L. salmon et al. They are in 'tar.gz' format. Salmon has two modes; alignment-based and quasi-mapping based. Quantification File #. *PhD in Bioinformatics* I would try the following things in order to see if they fix the issue. Could someone demonstrate where I did wrong? Anton Kulaga @antonkulaga I think I am blocked in terms of decoy indexes for mammals as I have only 64GB of RAM and most of them require larger ammount. Personal website: Exception : [std::bad_alloc] salmon-1.5.2_linux_x86_64/bin/salmon quant was invoked improperly. Well occasionally send you account related emails. We've re-designed how the library format is specified in Salmon, and I've back-ported this specification to Sailfish. I am trying to run salmon and it keeps giving me 2 java exceptions: I installed salmon using Anacondas' conda install -c bioconda salmon and all other necessary packages in the same way. Exiting. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. If that works, try building the decoy-aware index with the --sparse parameter. Why does Cauchy's equation for refractive index contain only even power terms? Using "salmon index", the index built successfully. What could convince you to take an academic What's an effective way to build a bioinformatics PhD student, feeling motivated but a little confused. That is leaving values of mates2 blank. I am trying to implement Salmon 1.5.3 and I have problems running the quant mode. Make sure the file is valid.] The easiest way to install salmon is likely via bioconda. We recommend installing the most recent version (1.55) systemwide if possible. NC_003070.9:12107766-12108159 Where the standard output shows (line by line): 1: The Nextflow version executed. An attempt was made at running salmon quant on the next sample but failed with: Exception : [Error: This version of salmon does not support indexing using the RapMap index.] Is this an at-all realistic configuration for a DHC-2 Beaver? 0 following Joined September 2018; Follow. Examples of frauds discovered because someone tried to mimic a random sequence. For usage information, try salmon quant --help Exiting. Browse other questions tagged, Start here for a quick overview of the site, Detailed answers to any questions you might have, Discuss the workings and policies of this site, Learn more about Stack Overflow the company. Making statements based on opinion; back them up with references or personal experience. If you want to do genome based alignment, try using STAR instead, Based on your last post it seems like you want gene level expression. The text was updated successfully, but these errors were encountered: Copy link rob-p . Exception : [Failed to read 8 bytes from input stream! The error suggests that the process is not able to properly read the index. Hermione raised an eyebrow and drop the hint already. And can he really be independent of the White House? This is probably a chromosome instead of a transcript." Share Improve this answer Follow Some are paired some are single. For usage information, try salmon quant --help Exiting. The Panel noted that if this were the case, then the standard of proof established in Article XX would effectively be circumvented. So, unless the clock is messed up, it seems the successful completion (which, obviously required loading the complete index for alignment) happens before the exception. as I said it has the quant.sf file with counts for all transcripts as expected. UNITED STATES - TRANSITIONAL SAFEGUARD MEASURE ON COMBED COTTON YARN FROM PAKISTAN. I Are the command and error here properly paired? salmon index was invoked improperly? Is it illegal to use resources in a University lab to prove a concept could work (to ultimately use to create a startup). A subreddit dedicated to bioinformatics, computational genomics and systems biology. NC_003070.9:12106547-12106703 I've never seen that error before. The only situations under which one might expect this issue to occur is if either (1) your user doesn't have sufficient permission to create the location where the output is to be written or (2) the disk on which the output is to be written has insufficient space. Specifically, this bit confused me: It looks like the log points to a sample that completed successfully at 19:45:18.487 before the sample at the top of the post started 19:51:56.392. Dec/2022: Nici qid Ultimativer Kaufratgeber Beliebteste Nici qid Aktuelle Angebote Preis-Leistungs-Sieger . *Membre de la Socit Franaise de BioInformatique (SFBI)* Plenty if interest! Thank you. Does integrating PDOS give total charge of a system? Sew on button. confusion between a half wave and a centre tapped full wave rectifier. Please help. 1 n Have a question about this project? The problem I had was RAM availability. Anyway, that's when salmon index was run a second time. I generated quant.sf files with salmon tool and now I want to import them into R and later perform a differential expression analysis. I am really stuck and do not know what to try, so any suggestions would be greatly appreciated. Also, this error: suggests that the BAM file itself could not be opened. Report of t 1892 of the Term of September 2019. Hi. I tried running just the reference prep step, which "runs" and I don't get any reported errors,. Problem appears to be the fact that mates2 value is being concatenated at the end of mates1.It is not immediately apparent as to why that is happening. Stack Exchange network consists of 181 Q&A communities including Stack Overflow, the largest, most trusted online community for developers to learn, share their knowledge, and build their careers. Exception : [std::bad_alloc] salmon quant was invoked improperly. i2c_arm bus initialization and device-tree overlay. This second volume of Mechanical Engineers' Handbook covers electronics, MEMS, and instrumentation and control, giving you accessible and in-depth access to the topics you'll encounter in the discipline: computer-aided design, product design for manufacturing and assembly, design . Salmon is a transcriptome based quantification tool, before 0.14.0 it can't use genomic iinformation. salmon for sashimi super cheap choose 5 to 7 kinds Just got my first bioinformatics position as an undergrad! The best answers are voted up and rise to the top, Not the answer you're looking for? WT/DS192/R. Are there any details about how the reference was obtained (or the BAM file created) that might shed light on why the BAM parser finds such an inconsistency? debug assertion failed! 2021-09-04; VSDEBUG Assertion Failed! All the files in 'tar' not 'tar.gz' format fail. 105-60 SUPERFUND CLEANUP ACCELERATION ACT I used this command line: ./src/salmon-1.5.2_linu. V1.5.2 I cannot figure out anything from this message. NC_003070.9:12106201-12106435 I'm following the procedure in this link Salmon/Sailfish the first code is The issue was caused by the corrupted input .fastq files that were damaged somehow upon uploading them from the local machine. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. Hello, I was running salmon for RNA quantification. Please try re-building the salmon index. Thanks, Is that GRCh38 file a list of chromosomes (aka the reference genome)? ; There may be one more directory inside that long index directory name Pdac_Barhee.._normalized_index. Hi. Version Server Response: Not Found salmon (selective-alignment-based) v1.5.1 [ program ] => salmon [ command ] => quant [ threads ] => { 5 } I can see that this run generates a exit code of 1 for that run - however all files are there as needed. are they running on different machines etc.)? @sq SN:NC_003070.9:4705-5095 LN:390 This file is a plain-text, tab-separated file with a single header line (which names all of the columns). Best wishes, Definitely not serious. to your account, Hello Bob, Before briefing, however, that appeal was stayed. used this command line: Salmon 2quasi-mapping reads sam/bam mapping 1 quasi-mapping-based mode reads 2 alignment-based mode FASTA SAM/BAM 1quasi-mapping-based mode salmon index -t transcripts.fa -i transcripts_index -k 31 Ok, thank you very much. What do you get from samtools view -H ../Data/DRR029379_after_bowtie.bam versus looking at the reference transcript FASTA file? NC_003070.9:12105547-12105662. Dec/2022: Grey goos vodka Ausfhrlicher Ratgeber Die besten Grey goos vodka Beste Angebote : Alle Testsieger JETZT ver. Specifically, the first transcript NC_003070.9:0-30427671, appears to be > 30 million nucleotides long --- this is a very suspicious length for a transcript. Consequently, in principle, a WTO Member could, for example, invoke protection of health in the context of invoking the aim-and-effect test. Salmon index Miniconda. Unsere Bestenliste Dec/2022 Umfangreicher Test Die besten Produkte Beste Angebote Vergleichssieger Direkt vergleichen! Q&A for researchers, developers, students, teachers, and end users interested in bioinformatics Anton Kulaga @antonkulaga I think I am blocked in terms of decoy indexes for mammals as I have only 64GB of RAM and most of them require larger ammount. View. Ok; that is super strange since (obviously) it cannot both complete successfully and throw an exception. Salmon is a free (both as in "free beer" and "free speech") software tool for estimating transcript-level abundance from RNA-seq read data. But I faced following problem when run the "salmon quant" command: Error: The index version file index/versionInfo.json doesn't seem to exist. Although, after 0.14.0 we start to use genome but it's still has to be preprocessed. Mathematica cannot find square roots of some matrices? How many transistors at minimum do you need to build a general-purpose computer? ./bin/salmon alignment-quant was invoked improperly. I swear I didnt notice the pun in my previous comment. I use this command line and I increase to 56 RAM. -1 ERR3537668_1.fastq.gz \ While I can't see anything immediately problematic from the snippet of the header you posted above, I do see some curious things even in this short region of the header. @hd VN:1.0 SO:unsorted I tried to build an index by salmon below: salmon index -t Homo_sapiens.GRCh38.dna.alt.fa.gz -i transcripts_index --decoys decoys.txt -k 31 Then I got "salmon index was invoked improperly." and inside the transcripts_index folder, ref_indexing.log has several lines of "XXX was longer than 200000 nucleotides. Exception : [Failed to read 8 bytes from input stream! I'm going to close this for now, since it seems there are no updates. NC_003070.9:12105328-12105409 On November 7, 2019, Judge Peters sentenced the appellant to life imprisonment for the first-degree child abuse and to a consecutive term of forty-five years for the second-degree murder. Sign in feeding it a BAM file of aligned reads), you don't need to provide it with the raw reads. some are in gz format, others are in tar.gz. There ought to be a quantitative correlation between the benefits conferred and the extent of the "problem" sought to be remedied, the correlation being "reasonable" and not "proportionate". The error you're seeing is a result of the BAM parser (libstaden) finding an inconsistency in the BAM file. We have not yet managed to actually run all of the script still, it is failing, but for another reason now. Obviously cut and people talking bad about voting next month from an unbearably broad and arched. Inside of salmon_rna_seq.py I am also running commands to treat the data, the salmon part looks the following way: Commands that the Pypiper runs are the following ones (_commands.sh Pypiper file): After running manually gzip -t on a file: So, I guess the file is corrupted and the issue is with some library that is generating the file. to your account. Exception : [std::bad_alloc] At what point in the prequels is it revealed that Palpatine is Darth Sidious? Hi. It only takes a minute to sign up. the FASTQ file). ***> wrote: We have not yet managed to actually run all of the script still, it is failing, but for another reason now. You can use Salmon with the reference transcriptome (ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_32/gencode.v32.transcripts.fa.gz) and then use another tool to sum up the counts, like tximport (an R package) (https://bioconductor.org/packages/release/bioc/html/tximport.html). Buyer right to vary your instruction? First, try quantifying without the decoy-aware index. Is this the quant directory for the same sample? https://github.com/notifications/unsubscribe-auth/ADRT5CUYGXBSY3UOX24RTYDUKQLETANCNFSM5HOIMSQQ, https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675, https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub, https://www.linkedin.com/in/luciana-oliveira-75104056. NC_003070.9:12106201-12106435 World Trade. Then very strange indeed. Q&A for researchers, developers, students, teachers, and end users interested in bioinformatics Salmon makes extensive use of Boost. The error is saying that the target file does not contain the reference sequences listed in the bam file. Press question mark to learn the rest of the keyboard shortcuts. By clicking Sign up for GitHub, you agree to our terms of service and --numBootstraps 100 \ Though that is not an inconsistency itself, there is no benefit to having a transcript present multiple times and it can adversely affect quantification estimates. Disconnect vertical tab connector from PCB. PhD goals for bioinformatics focused industry job. I am using the same command (changing it for different sample names and hence output directories). 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