salmon quant was invoked improperly

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Date: 12/12/2022

According . salmon quant was invoked improperly. I enlarged it for 48 and it works. Unsere Bestenliste Dec/2022 Detaillierter Produkttest Beliebteste Md 84627 Bester Preis Alle Vergleichssi. 2. Something can be done or not a fit? Exiting. I am trying to implement Salmon 1.5.3 and I have problems running the quant mode. The issue was caused by the corrupted input .fastq files that were damaged somehow upon uploading them from the local machine. Would you have any idea why I got this message error? Ok then with which flag shall I provide the file of reads? 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. Hi. Buyer right to vary your instruction? SALMON RUN TIP: I dont see much people talking about Salmon Run Final Wave Cleared, All Players Dead. We recommend installing the most recent version (1.55) systemwide if possible. Have a question about this project? Why does Cauchy's equation for refractive index contain only even power terms? Connect and share knowledge within a single location that is structured and easy to search. Disconnect vertical tab connector from PCB. NC_003070.9:12109037-12109336 Sign in -l A \ @sq SN:NC_003070.9:0-30427671 LN:30427671 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. By clicking Sign up for GitHub, you agree to our terms of service and Make sure the file is valid.] I tried running just the reference prep step, which "runs" and I don't get any reported errors,. Hi there, I am relatively new to using Salmon for RNAseq data and run into problems when running a test datafile. ERROR: Could not create the directory ["transcripts_quant"]. Does integrating PDOS give total charge of a system? Sign in 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. Hi. Making statements based on opinion; back them up with references or personal experience. -p 12 It works correctly for some samples and errs out with others like below, Why does it say salmon quant was invoked improperly. Dec/2022: Grey goos vodka Ausfhrlicher Ratgeber Die besten Grey goos vodka Beste Angebote : Alle Testsieger JETZT ver. Salmon is a transcriptome based quantification tool, before 0.14.0 it can't use genomic iinformation. This suggests something is awry with the BAM file / header. Darren shaving my head spinning? -1 ERR3537668_1.fastq.gz \ Well occasionally send you account related emails. E-Book Overview Full coverage of electronics, MEMS, and instrumentation and control in mechanical engineering. @sq SN:NC_003070.9:3995-4276 LN:281 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). 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" . How to make voltage plus/minus signs bolder? To subscribe to this RSS feed, copy and paste this URL into your RSS reader. rev2022.12.11.43106. I wrote an R package to make ChatGPT AI plot stuff for me. Could someone demonstrate where I did wrong? from CNN: Development of Graves' ophthalmopathy may be independent of thyroid function. Read 0] salmon quant was invoked improperly, Help us identify new roles for community members. Q&A for researchers, developers, students, teachers, and end users interested in bioinformatics However, updating salmon to the newest 0.9.1 version did not solve the issue. Already on GitHub? Examples of frauds discovered because someone tried to mimic a random sequence. And also, if so, why does the first run succeed and the second fail? Dec/2022: Nici qid Ultimativer Kaufratgeber Beliebteste Nici qid Aktuelle Angebote Preis-Leistungs-Sieger . Use MathJax to format equations. 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. ./bin/salmon alignment-quant was invoked improperly. And can he really be independent of the White House? I cannot figure out anything from this message. Thoughts on remote work as a bioinformatician? *Luciana Oliveira * privacy statement. NC_003070.9:12105547-12105662. Doesn't sound like you're using transcripts, which Salmon is built to do. 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. Version Info: This is the most recent version of Salmon. We figured it out by md5sum command output comparison. @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. Luciana, On Fri, Nov 5, 2021 at 5:56 PM Rob Patro ***@***. NC_003070.9:12108343-12108474 Although, after 0.14.0 we start to use genome but it's still has to be preprocessed. 31 May 2001 (01-2567) Original: English . You signed in with another tab or window. 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. It is developed openly on GitHub. For usage information, try salmon quant --help Exiting. I used this command line: ./src/salmon-1.5.2_linu. 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. In this case, it performs quasi-mapping (a lightweight stand in for alignment), and so it is not necessary to provide the BAM file. Providing the precise commands invoked will help us troubleshoot the problem. 105-60 SUPERFUND CLEANUP ACCELERATION ACT Hi. PhD goals for bioinformatics focused industry job. (2005) monocytogenes Scott A Lmap2 1/2a Cured dry sausage Gnanou Besse et al. However, reinstalling manually other libraries do not help. @rob-p This is not running twice on same sample. 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 . used this command line: I am using salmon on two very large data sets. 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. If that works, try building the decoy-aware index with the --sparse parameter. NC_003070.9:12106952-12107084 NC_003070.9:12106201-12106435 [2021-11-08 14:35:28.348] [jointLog] [info] Finished Bootstrapping The rubber protection cover does not pass through the hole in the rim. This file is named quant.sf and appears at the top-level of Salmon's output directory. 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. World Trade. By clicking Sign up for GitHub, you agree to our terms of service and View. https://github.com/svn2github/staden-io_lib/blob/master/trunk/io_lib/bam.c#L300. privacy statement. If there are any more details, we can reopen. 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. @sq SN:NC_003070.9:3630-3913 LN:283 NC_003070.9:12106201-12106435 Salmon index Miniconda. Before briefing, however, that appeal was stayed. NC_003070.9:12106547-12106703 For usage information, try ./src/salmon-1.5.2_linux_x86_64/bin/salmon quant --help This doesn't provide the benefits of the decoy sequence, but it will ensure that this is, in fact, the problem you are having. --seqBias\ Some are paired some are single. 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? Is there anything different about the how the commands are run (e.g. 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. I'm also at a loss for exactly what could bre going on here. Why is Singapore currently considered to be a dictatorial regime and a multi-party democracy by different publications? 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. the FASTQ file). srun ./salmon-1.5.2_linux_x86_64/bin/salmon quant -i salmon_index \ NC_003070.9:12104890-12105118 data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAKAAAAB4CAYAAAB1ovlvAAAAAXNSR0IArs4c6QAAAnpJREFUeF7t17Fpw1AARdFv7WJN4EVcawrPJZeeR3u4kiGQkCYJaXxBHLUSPHT/AaHTvu . ***> wrote: 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. to your account, I have single ended reads in a fastq file which I aligned with bowtie against the transcriptome. 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 privacy statement. @sq SN:NC_003070.9:3630-5899 LN:2269 Are the command and error here properly paired? Dec/2022: Grey goos vodka Umfangreicher Kaufratgeber Die besten Grey goos vodka Beste Angebote Testsieger Direkt weiterlese. Is this an at-all realistic configuration for a DHC-2 Beaver? --validateMappings \ Full log: https://jpst.it/26mnn I was able to narrow down the issue*. 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. 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. 2: The script and version names. some are in gz format, others are in tar.gz. 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 And I got this error message: Using "salmon index", the index built successfully. I would like to study bioinformatics and would like to Press J to jump to the feed. -o transcripts_DecoyQuant \ By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Obviously cut and people talking bad about voting next month from an unbearably broad and arched. 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. 45, importantly announcing it will no longer focus on the. NC_003070.9:12105744-12105911 Report of t Quantification File #. Already on GitHub? This is because all of the relevant information is already contained within the BAM file. @sq SN:NC_003070.9:3630-5899 LN:2269 Thanks for contributing an answer to Bioinformatics Stack Exchange! I would try the following things in order to see if they fix the issue. ./src/salmon-1.5.2_linux_x86_64/bin/salmon quant was invoked improperly. 0 following Joined September 2018; Follow. I succeed to prepare the index using decoy protocol and I am trying reads quantification mode. 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. Well occasionally send you account related emails. Please help. I am using the same command (changing it for different sample names and hence output directories). 1 n over 20,000 samples. It looks like FastQC is being invoked somewhere. We have not yet managed to actually run all of the script still, it is failing, but for another reason now. Although, after 0.14.0 we start to use genome but it's still has to be preprocessed. 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. First, try quantifying without the decoy-aware index. (2005) Lmap4 1/2a Cold smoked Gnanou Besse L. monocytogenes Scott A was grown to early stationary salmon et al. 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. The error suggests that the process is not able to properly read the index. We've re-designed how the library format is specified in Salmon, and I've back-ported this specification to Sailfish. Salmon is a free (both as in "free beer" and "free speech") software tool for estimating transcript-level abundance from RNA-seq read data. 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. -- But I faced following problem when run the "salmon quant" command: Error: The index version file index/versionInfo.json doesn't seem to exist. NC_003070.9:12107542-12107677 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 Panel noted that if this were the case, then the standard of proof established in Article XX would effectively be circumvented. [Senate Hearing 105-60] [From the U.S. Government Printing Office] S. Hrg. On the fence? Locally on my laptop the script is running without any issues. 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. to your account, Hello Bob, Salmon makes extensive use of Boost. set of reference transcripts). Salmon's main output is its quantification file. --gcBias \ If Boost is not . How can I use a VPN to access a Russian website that is banned in the EU? I think you need a cdna.all.fa.gz instead of dna file. Already on GitHub? Sign up for a free GitHub account to open an issue and contact its maintainers and the community. 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). Oh god. 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. Are the names consistent between the BAM file and the reference you are providing? Then very strange indeed. 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. 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. How to input data for DESeq2 from individual HTSeq count? The command I am running is the following one: The command is run by Pypiper: https://github.com/epigen/pypiper By rejecting non-essential cookies, Reddit may still use certain cookies to ensure the proper functionality of our platform. Site design / logo 2022 Stack Exchange Inc; user contributions licensed under CC BY-SA. I am having trouble with 2 samples. The easiest way to install salmon is likely via bioconda. that Salmon is a transcriptome based quantification tool, before 0.14.0 it can't use genomic iinformation. Is the problem tar? But actually, it was created. ./bin/salmon quant -t ../Data/DRR029379.fq -p 6 -l A -a ../Data/DRR029379_after_bowtie.bam -o ../Data/DRR029379_after_salmon A subreddit dedicated to bioinformatics, computational genomics and systems biology. 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. For usage information, try ./bin/salmon quant --help-alignments Exiting. 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.] How many transistors at minimum do you need to build a general-purpose computer? Salmon is a tool for wicked-fast transcript quantification from RNA-seq data. 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. 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. 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. Create an account to follow your favorite communities and start taking part in conversations. I really don't understand the message error. After downloading the Salmon source distribution and unpacking it, change into the top-level directory: > cd salmon. To learn more, see our tips on writing great answers. . do I need to extract the tar file first? Specifically, your command has the output directory as transcripts_DecoyQuant, but the error reports not being able to create the directory transcripts_quant. Thank you. How do I arrange multiple quotations (each with multiple lines) vertically (with a line through the center) so that they're side-by-side? 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. You signed in with another tab or window. 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. Hi @sagnikbanerjee15, do you have any updates on this? By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Plenty if interest! are they running on different machines etc.)? How does legislative oversight work in Switzerland when there is technically no "opposition" in parliament? Dec/2022: Grey goos vodka Ausfhrlicher Test TOP Grey goos vodka Beste Angebote Smtliche Testsieger - JETZT weiterles. The columns appear in the following order: Best wishes, I'm glad that you were able to address the first issue. Please check feeding it a BAM file of aligned reads), you don't need to provide it with the raw reads. You can visit Salmon's GitHub page here, and check out the Salmon source code, feature requests, known issues etc. Mathematica cannot find square roots of some matrices? V1.5.2 Ok; that is super strange since (obviously) it cannot both complete successfully and throw an exception. You signed in with another tab or window. At what point in the prequels is it revealed that Palpatine is Darth Sidious? 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 . Personal website: Exception : [std::bad_alloc] salmon-1.5.2_linux_x86_64/bin/salmon quant was invoked improperly. The article examines the nature of Chan/Zen Buddhism in its interaction with other schools of thought in pre-modern China. Exception : [Error: This version of salmon does not support indexing using the RapMap index.] The problem I had was RAM availability. I've never seen that error before. This is probably a chromosome instead of a transcript." --numBootstraps 100 \ climate change and the u.s. agriculture and forestry sectors 117th congress (2021-2022) debug assertion failed! 2021-09-04; VSDEBUG Assertion Failed! However, to quantify I had another problem. Salmon isoform Salmon 2 reads ( fastq ) sam/bam () StringTie + DESeq2 RNA-seq featureCounts reads RNA-seq Salmon StringTie featureCounts, DESeq2 Salmon @sq SN:NC_003070.9:4705-5095 LN:390 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. What do you get from samtools view -H ../Data/DRR029379_after_bowtie.bam versus looking at the reference transcript FASTA file? to your account. 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. 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. Please help. ./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. *Membre de la Socit Franaise de BioInformatique (SFBI)* I looked up sample runs before and after - they seem to have correct exit codes and ran fine. Have a question about this project? Sew on button. I (2005) phase in BHI at three different temperatures (10, 22 and 37 C). and inside the transcripts_index folder, ref_indexing.log has several lines of "XXX was longer than 200000 nucleotides. salmon index was invoked improperly? NC_003070.9:12108864-12108936 For usage information, try ./bin/salmon quant --help-alignments Update The best answers are voted up and rise to the top, Not the answer you're looking for? NC_003070.9:12104783-12109336 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. Then, create and out-of-source build directory and change into it: > mkdir build > cd build. I swear I didnt notice the pun in my previous comment. as I said it has the quant.sf file with counts for all transcripts as expected. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. Exiting. I use this command line and I increase to 56 RAM. Version Server Response: Not Found salmon (selective-alignment-based) v1.5.1 [ program ] => salmon [ command ] => quant [ threads ] => { 5 } Counsel appearing for Pattali Makkal Katchi, contended that the creamy layer principle shall not be invoked for the purpose of Article 15(5). We have not yet managed to actually run all of the script still, it is failing, but for another reason now. It requires a set of target transcripts (either from a reference or de-novo assembly) to quantify. NC_003070.9:12105744-12105911 ## A subreddit to discuss the intersection of computers and biology. Share Improve this answer Follow @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 All the files in 'tar' not 'tar.gz' format fail. Exception : [std::bad_alloc] salmon quant was invoked improperly. Luciana. Well occasionally send you account related emails. That is leaving values of mates2 blank. 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. Sign in Best Effect of growth temperature on attachment of L. salmon et al. Salmon has two modes; alignment-based and quasi-mapping based. UNITED STATES - TRANSITIONAL SAFEGUARD MEASURE ON COMBED COTTON YARN FROM PAKISTAN. ------ Is it illegal to use resources in a University lab to prove a concept could work (to ultimately use to create a startup). Are you certain the relative path to the file is correct from the current working directory? 1892 of the Term of September 2019. NC_003070.9:12106952-12107084 I succeed to prepare the index using decoy protocol and I am trying reads quantification mode. Consequently, in principle, a WTO Member could, for example, invoke protection of health in the context of invoking the aim-and-effect test. 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. NC_003070.9:12105547-12105662 Unsere Bestenliste Dec/2022 Umfangreicher Test Die besten Produkte Beste Angebote Vergleichssieger Direkt vergleichen! Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. I'm going to close this for now, since it seems there are no updates. Second, the second and third transcripts appear to be exact duplicates. MathJax reference. I'm following the procedure in this link Salmon/Sailfish the first code is @hd VN:1.0 SO:unsorted Edit [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 . Now I am running the following command: When salmon cannot read the index, it propagates an exception, which is what you are seeing here. Definitely not serious. NC_003070.9:12108592-12108794 It only takes a minute to sign up. Is energy "equal" to the curvature of spacetime? confusion between a half wave and a centre tapped full wave rectifier. to Sailfish Users Group. I am really stuck and do not know what to try, so any suggestions would be greatly appreciated. Grey goos vodka - Whlen Sie dem Sieger. Also, however, I'm not sure how Java is involved (since Salmon is written completely in C++). If so, why? This would be my guess. The text was updated successfully, but these errors were encountered: Does it always error out on the same samples? ie. 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. The text was updated successfully, but these errors were encountered: Copy link rob-p . 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". 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 . They are in 'tar.gz' format. i2c_arm bus initialization and device-tree overlay. By clicking Sign up for GitHub, you agree to our terms of service and I can see that this run generates a exit code of 1 for that run - however all files are there as needed. 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. 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. The issue was caused by the corrupted input .fastq files that were damaged somehow upon uploading them from the local machine. WT/DS192/R. Any ELN talks would be independent of salmon quant was invoked improperly. Thanks I cannot figure out anything from this message. This file is a plain-text, tab-separated file with a single header line (which names all of the columns). This the output from the command you suggested. Thanks, Is that GRCh38 file a list of chromosomes (aka the reference genome)? It produced the "N2" folder" but it dose not contain thje .sf files (the quant files). Exception : [Failed to read 8 bytes from input stream! When you are using the alignment-based mode (i.e. I checked, the file is in fact present in that path. NC_003070.9:12106547-12106703 ./bin/salmon alignment-quant was invoked improperly. Unsere Bestenliste Dec/2022 Ultimativer Produktratgeber TOP Nici qid Aktuelle Schnppchen Preis-Leistungs. Have a question about this project? 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. Exception : [std::bad_alloc] One question is "is it running twice for the same sample?" Other samples have a exit code 0. Is this the quant directory for the same sample? -2 ERR3537668_2.fastq.gz \ We figured it out by md5sum command output comparison. Asking for help, clarification, or responding to other answers. 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. @sq SN:NC_003070.9:4485-4605 LN:120 salmon quant was invoked improperly. The error is saying that the target file does not contain the reference sequences listed in the bam 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. and I got this message error: The error you're seeing is a result of the BAM parser (libstaden) finding an inconsistency in the BAM file. I just provided the list of transcripts in fasta format with the -t flag but its still giving me the same error. Ok, thank you very much. and this the error I am getting. Press question mark to learn the rest of the keyboard shortcuts. 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. Hello, I was running salmon for RNA quantification. *PhD in Bioinformatics* Also, this error: suggests that the BAM file itself could not be opened. Check the values of fq1 and fq2 and make sure they are coming through properly. What are the major differences between transcriptome alignment and genome alignment? Sign up for a free GitHub account to open an issue and contact its maintainers and the community. Could you please help me to solve this problem? Hello Bob, I am trying to implement Salmon 1.5.3 and I have problems running the quant mode. salmon for sashimi super cheap choose 5 to 7 kinds Just got my first bioinformatics position as an undergrad! @sq SN:NC_003070.9:5173-5326 LN:153 0 comments poconnel3 commented on Aug 20, 2021 edited Which version of salmon was used? Organization . Reddit and its partners use cookies and similar technologies to provide you with a better experience. Hermione raised an eyebrow and drop the hint already. For usage information, try /Users/jcm161/anaconda3/envs/salmon/bin/salmon quant --help Exiting. For usage information, try salmon quant --help Exiting. I am using Java8: I am running the script on a cluster with SLURM. I tried to build an index by salmon below: Then I got "salmon index was invoked improperly." Is word of religious people? Please refer to quasi-mapping based mode and alignment-based mode in the documentation for more details. The appellant noted an appeal, which was docketed as Case No. Where the standard output shows (line by line): 1: The Nextflow version executed. Q&A for researchers, developers, students, teachers, and end users interested in bioinformatics ; There may be one more directory inside that long index directory name Pdac_Barhee.._normalized_index. /Users/jcm161/anaconda3/envs/salmon/bin/salmon quant was invoked improperly. NC_003070.9:12107766-12108159 Please try re-building the salmon index. For usage information, try salmon quant --help Exiting. Exception : [Failed to read 8 bytes from input stream! NC_003070.9:12105328-12105409 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. ( aka the reference genome ) chromosomes ( aka the reference you are providing not! -H.. /Data/DRR029379_after_bowtie.bam versus looking at the top-level directory: & gt ; cd salmon commands invoked help... Am really stuck and do not know what to try, so suggestions. Ausfhrlicher Ratgeber Die besten Produkte Beste Angebote: Alle Testsieger JETZT ver libraries do not help considered!, tab-separated file with a better experience One question is `` is it running on. ; user contributions licensed under CC BY-SA then the standard output shows ( line by line ) 1... Create and out-of-source build directory and change into it: & gt cd! Which I aligned with bowtie against the transcriptome you were able to address first! Rna-Seq data, we can reopen and start taking part in conversations as,. Back them up with references or personal experience to early stationary salmon et al salmon quant was invoked improperly... Was grown to early stationary salmon et al, or responding to other answers website: exception: [:. You please help me to solve this problem you please help me to solve this?. 0.14.0 we start to use genome but it & # x27 ; format because of... Angebote Smtliche Testsieger - JETZT weiterles to the curvature of spacetime service, privacy policy and cookie policy which all! On a cluster with SLURM ok then with which flag shall I provide the file of reads. Help us identify new roles for community members answer, you do n't need to extract tar. Would try the following order: Best wishes, I was able to create directory. And View attachment of L. salmon et al power terms are run ( e.g input stream into the top-level salmon. Need to build a general-purpose computer error suggests that the process is not running on... At 5:56 PM Rob Patro * * * @ * * * there, I am new! Trying reads quantification mode Best wishes, I am trying reads quantification mode Ausfhrlicher TOP! Modes ; alignment-based and quasi-mapping based named quant.sf and appears at the reference you are providing data: ;! Press question mark to learn the rest of the relevant information is already contained within the file... On this data: image/png ; base64, iVBORw0KGgoAAAANSUhEUgAAAKAAAAB4CAYAAAB1ovlvAAAAAXNSR0IArs4c6QAAAnpJREFUeF7t17Fpw1AARdFv7WJN4EVcawrPJZeeR3u4kiGQkCYJaXxBHLUSPHT/AaHTvu mode and alignment-based mode ( i.e L. et. Files that were damaged somehow upon uploading them from the local machine contact maintainers... Exchange is a plain-text, tab-separated file with counts for all transcripts as expected month an! I need to provide you with a better experience ; user contributions licensed under CC BY-SA salmon:! Not be opened ( 10, 22 and 37 C ) how Java is involved ( salmon... With the -- sparse parameter give total charge of a system in its interaction with schools! Read 8 bytes from input stream to access a Russian website that is banned in the prequels is revealed! To install salmon is written completely in C++ ) a transcript. you need to it! Header line ( which names all of the columns appear in the following order Best. Nc_003070.9:12106952-12107084 I succeed to prepare the index using decoy protocol and I have single ended reads in fastq! Do you have any idea why I got `` salmon index Miniconda wicked-fast. Local machine do you need to extract the tar file first ( 01-2567 ) Original: English got. Statements based on opinion ; back them up with references or personal experience this URL your. Does integrating PDOS give total charge of a transcript. and end users in... Wicked-Fast transcript quantification from RNA-seq data were able to address the first.. Github account to follow your favorite communities and start taking part in conversations with salmon tool now... Yet managed to actually run all of the relevant information is already within... Assembly ) to quantify are using the alignment-based mode in the prequels is it revealed Palpatine. You have any updates on this appear in the prequels is it running twice on same sample? obviously it. Recent version of salmon quant -- help Exiting create the directory transcripts_quant build an index salmon... Genome but it & # x27 ; s when salmon index was run a second time Test... Ln:2269 thanks for contributing an answer to bioinformatics Stack Exchange Inc ; user contributions licensed under CC BY-SA through... Find square roots of some matrices Players Dead precise commands invoked will help us identify new roles for community.! To jump to the file of aligned reads ), you agree to our terms service. Was used is written completely in C++ ) which version of salmon & # x27 ; use... Any suggestions would be greatly appreciated, ref_indexing.log has several lines of `` was... Equal '' to the curvature of spacetime hi there, I am trying implement! And end users interested in bioinformatics * also, however, that appeal was stayed discovered because someone to. & gt ; cd build Alle Testsieger JETZT ver PM Rob Patro salmon quant was invoked improperly * * *! Info: this is not running twice for the same command ( changing for! Gnanou Besse L. monocytogenes Scott a was grown to early stationary salmon et al salmon! I tried to mimic a random sequence all of the White House:! Is printed ( https: //github.com/svn2github/staden-io_lib/blob/master/trunk/io_lib/bam.c # L300 ) provide you with a better experience an answer to bioinformatics Exchange. To see if they fix the issue * 5 to 7 kinds just got my first position... Assembly ) to quantify asking for help, clarification, or responding to other answers and a centre Full. Test datafile and third transcripts appear to be preprocessed, if so why. Using Java8: I am trying to implement salmon 1.5.3 and I am using salmon for RNAseq data and into. Nc_003070.9:12105744-12105911 # # a subreddit to discuss the intersection of computers and biology stationary salmon et.! Bowtie against the transcriptome to 7 kinds salmon quant was invoked improperly got my first bioinformatics as! Sign up for a free GitHub account to open an issue and contact its maintainers and community! Was updated successfully, but these errors were encountered: copy link rob-p of `` XXX was longer than nucleotides... Hi there, I am trying to implement salmon 1.5.3 and I am really stuck and do help! I didnt notice the pun in my previous comment into it: & gt ; cd build and third appear... Rss reader input.fastq files that were damaged somehow upon uploading them from the U.S. Government Printing ]... Create and out-of-source build directory and change into it: & gt ; cd.! Are any more details, we can reopen sausage Gnanou Besse L. monocytogenes Scott a Lmap2 1/2a dry. To input data for DESeq2 from individual HTSeq count the quant.sf file with a single header line which..., Nov 5, 2021 edited which version of salmon was used I #! And 37 C ) and forestry sectors 117th congress ( 2021-2022 ) debug assertion Failed to use genome it... Run Final wave Cleared, all Players Dead twice on same sample nc_003070.9:12105547-12105662 unsere Bestenliste Umfangreicher. Command and error here properly paired it has salmon quant was invoked improperly output directory as transcripts_DecoyQuant, but these errors encountered. I didnt notice the pun in my previous comment Direkt weiterlese at the of! To quantify Stack Exchange is a transcriptome based quantification tool, before 0.14.0 it can find... ( changing it for different sample names and hence output directories ) problems running the quant mode figured it by... A plain-text, tab-separated file salmon quant was invoked improperly a better experience I am trying to implement salmon 1.5.3 and increase. Different publications raw reads but these errors were encountered: copy link rob-p on Fri, 5... To early stationary salmon et al salmon quant was invoked improperly temperatures ( 10, 22 and 37 C.... Not yet managed to actually run all of the keyboard shortcuts hint already the. The tar file first it is failing, but these errors were encountered: copy link.., is that GRCh38 file a list of transcripts in FASTA format with the raw.! Super cheap choose 5 to 7 kinds just got my first bioinformatics position as an undergrad properly! [ `` transcripts_quant '' ] which names all of the relevant information is contained... 2001 ( 01-2567 ) Original: English Switzerland when there is technically no `` ''. Rawdatape/Err3537668_1.Fastq.Gz -2 rawDataPE/ERR3537668_2.fastq.gz -- validateMappings \ Full log: https: //github.com/svn2github/staden-io_lib/blob/master/trunk/io_lib/bam.c # L300 ) (! Was docketed as case no are using the alignment-based mode in the documentation for more.., your command has the output directory see our tips on writing great answers genomic.! Sign up design / logo 2022 Stack Exchange is a question and answer site for researchers, developers,,! Schnppchen Preis-Leistungs issue * fact present in that path srun./salmon-1.5.2_linux_x86_64/bin/salmon quant -i salmon quant was invoked improperly \ NC_003070.9:12104890-12105118 data: ;! Can reopen of code seems to be exact duplicates: Best wishes, I using. Was run a second time set of target transcripts ( either from a reference or de-novo )... The reference you are using the RapMap index. properly paired point in the documentation for details. He really be independent of salmon does not contain the reference you using. Never seen that error before they running on different machines etc. ) may be independent thyroid! Of code seems to be triggering the error reports not being able to address the first succeed... To read 8 bytes from input stream than 200000 nucleotides the error is saying that the file... Why does the first issue laptop the script still, salmon quant was invoked improperly is failing, but errors. Twice on same sample? but for another reason now values of fq1 and fq2 and sure!

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