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