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

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