Many people have high bandwidth connections, but this varies by installation and geography.
rna seq - Download multiple fastq files using fastq-dump ```bash ``` esearch -db sra -query SRX3808505 | esummary Please try our new 2.10.9 release. ``` #### Pulling out fastq files # 2022-01-21T19:58:53 prefetch.2.11.0: 'SRR7695235' is valid
SRA-Toolkit - National Institutes of Health # GSM3331075 2020-07-16T09:29:36 fasterq-dump.2.10.7 fatal: SIGNAL - Segmentation fault The process for downloading is quickest when done in two steps:
Downloading files from NCBI's SRA database 2021-12-26T13:53:00 fasterq-dump.2.11.3 err: error unexpected while resolving query within virtual file system module - failed to resolve accession 'SRR17055838' - The object is not available from your location. For more information, see https://www.ncbi.nlm.nih.gov/sra/?term=SRX4553616 prefetch prioritizes downloads by size and it asks for user input for a go-ahead on very large runs. --- ls *.fastq
2018/03/18 Once there, downloading using wget with the https link https://sra-download.ncbi.nlm.nih.gov/sos/sra-pub-run-1/SRR6294776/SRR6294776.1 takes a long time to respond and is very slow, but it does eventually start. You only have ~21 GB. Thank you. It says clearly in the message above that /f/ProjectSRAFiles/SRR#.sra.tmp.7523.tmp can't be written, meaning that /f/ProjectSRAFiles/ likely does not have enough space. https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR6294776, https://sra-download.ncbi.nlm.nih.gov/sos/sra-pub-run-1/SRR6294776/SRR6294776.1, https://www.ebi.ac.uk/ena/data/view/SRR6294776, https://github.com/notifications/unsubscribe-auth/AC66ETPOKSWEHF66763TU7DQILJAHANCNFSM4IKZU5GQ. Thank you for everyone' help! docker run -t --rm -v $PWD:/output:rw -w /output ncbi/sra-tools:latest fasterq-dump -e 2 -p SRR getting the same error after running: docker run -t --rm -v $PWD:/output:rw -w /output ncbi/sra-tools:latest fasterq-dump -e 2 -p SRR
Prefetch can be used to correct and finish an incomplete Run download. ------ real 0m35.910s fastq-dump --outdir fastq --skip-technical --readids --read-filter pass --dumpbase --split-3 --clip $SRR If you are using fasterq-dump we usually use this command: Already on GitHub? I cannot even tell you what exactly these cache files are that prefetch saves on disk, but they are large and take up space while not necessary for proper download. ``` esearch -db sra -query PRJNA438545 | esummary | head -n 20 ``` # 2022-01-21T19:58:53 prefetch.2.11.0: 'SRR7695235' has 0 unresolved dependencies user 81m19.204s ((py3k)) [obotvinnik@tscc-login2 fastq_dump]$ cd /oasis/tscc/scratch/obotvinnik/external_singlecell/tasic2015/1645630/, ((py3k)) [obotvinnik@tscc-login2 1645630]$ ls, SRR2140205_1.fastq.gz SRR2140205.fastq SRR2140205.sra, ((py3k)) [obotvinnik@tscc-login2 1645630]$ ll, -rw-r--r-- 1 obotvinnik yeo-group 232 Jul 28 08:53 SRR2140205_1.fastq.gz, -rw-r--r-- 1 obotvinnik yeo-group 453M Jun 24 20:41 SRR2140205.fastq, -rw-r--r-- 1 obotvinnik yeo-group 428M Jun 18 12:20 SRR2140205.sra, ((py3k)) [obotvinnik@tscc-login2 1645630]$ fastq-dump --gzip --split-files SRR2140205.sra, 2016-07-28T15:54:04 fastq-dump.2.5.4 err: name not found while resolving tree within virtual file system module - failed SRR2140205.sra, ((py3k)) [obotvinnik@tscc-login2 1645630]$ fastq-dump --gzip --split-files -A SRR2140205.sra, 2016-07-28T15:54:13 fastq-dump.2.5.4 err: name not found while resolving tree within virtual file system module - failed SRR2140205.sra, ((py3k)) [obotvinnik@tscc-login2 1645630]$ fastq-dump --gzip --split-files -A ./SRR2140205.sra, 2016-07-28T15:55:27 fastq-dump.2.5.4 err: name not found while resolving tree within virtual file system module - failed ./SRR2140205.sra, ((py3k)) [obotvinnik@tscc-login2 1645630]$ fastq-dump --gzip --split-files ./SRR2140205.sra, 2016-07-28T15:55:31 fastq-dump.2.5.4 err: name not found while resolving tree within virtual file system module - failed ./SRR2140205.sra. I think now I have to search if I can add any temporary space. ## Conda env sys 0m5.916s real 10m23.171s oh alright, thanks so much for the update. Trying with pigz: This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. gzip SRR7695235_2.fastq > p2.fastq.gz title: Examples downloading fastq data from NCBI's SRA fasterq-dump: "disk-limit exeeded!" Issue #750 ncbi/sra-tools ``` So much faster doing prefetch first, then splitting that. database incorrect while opening manager within database module. That example above was just downloading the fastq data for a single SRR. # SRR7695236 SRP158306 SRX4553616 GSM3331118_r10 GSM3331118 Thanks! spots read : 4,388,472 $ fasterq-dump -p -3 SRR316212.sra -O fastq time prefetch --max-size 100G --progress -O ./ SRR7695235 SRR7695236 ```bash Instantly share code, notes, and snippets. super sorry to bother. Really wish they would prioritize maintaining sratoolkit considering how important it has become for many data mining pipelines. cat ${sample_ID}-tmp/*_2.fastq.gz > ${sample_ID}_R2_raw.fastq.gz You could try to set -t to a location that is not on /aci/mnt. Yes, we received your report and will get back to you as soon as we can. user 5m23.072s I, unfortunately, don't have the exact SRR# or those other error messages handy at the moment. user 0m0.012s 1 comment wisdomadewumi commented on May 25, 2022 edited -A SRR14432671 This is an option for fastq-dump ( and even there it is optional and obsolete ) not fasterq-dump. As a result the tools ( prefetch as well as fastq-dump/fasterq-dump ) cannot find the reference. You can to run vdb-config to set locations for temp space. printf "\n\n Concatenating\n\n" # GSM3331071 But if I get a spare moment I can do some digging. Traffic: 1125 users visited in the last hour, User Agreement and Privacy Which was super slow. PS: why a screenshot when you can just copy-n-paste the text ? SRX3808543 SRR6853342 Illumina HiSeq 4000 ## From GSE user 0m10.612s In this case, multiple "runs" (first column IDs) belong to a single sample these are delineated by the "experiment_accession" column, and the "experiment_alias" column matches up to the sample names in the [GSE118502](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE118502) page linked above. Code Revisions 1 Embed Download ZIP Errors with fastq-dump Raw fastq-dump_errors.txt ( (py3k)) [obotvinnik@tscc-login2 fastq_dump]$ fastq-dump --gzip --split-files /oasis/tscc/scratch/obotvinnik/external_singlecell/tasic2015/1645630/SRR2140205.sra --outdir /oasis/tscc/scratch/obotvinnik/external_singlecell/tasic2015/1645630/ ```bash ``` And from there we can pull out all the run accessions associated with this BioProject we are searching for (along with the same additional information we pulled above), and write it to a file: rm -rf SRR7695235-tmp/ prefetch --max-size 500G --progress -O ${sample_ID}-tmp/ ${curr_run_accs} 2022-01-20T01:56:00 prefetch.2.11.0: HTTPS download succeed time cat GSM3331071-tmp/*_1.fastq.gz > GSM3331071_R1_raw-pigz.fastq.gz fasterq-dump --split-files SRR11848434 [fails], 2020-07-16T09:29:36 fasterq-dump.2.10.7 err: cmn_iter.c cmn_read_uint8_array( #4308993 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted) done So in this case maximal 3 identifier would be handled at the same time. If the file is on your disk, try to run vdb-validate on it. # Note on `prefetch` By clicking Sign up for GitHub, you agree to our terms of service and The text was updated successfully, but these errors were encountered: Sorry for the delay in responding.
spots read : 4,427,070 do Privacy Policy. Be also sure to deactivate the caching option in vdb-config. ```bash=
MetagenomeILLUMINAIIF4SWPAMPLICONMETAGENOMICRANDOM PRJNA438545SAMN05581708 fasterq-dump SRR17055838 2021-12-26T13:53:00 fasterq-dump.2.11.3 err: error unexpected while resolving query within virtual file system module - failed to resolve accession 'SRR17055838' - The object is not available from your location. prefetch ${accession} They are completely different tools. ## Example getting data for GLDS-427 # SRR7695238 SRP158306 SRX4553616 GSM3331118_r12 GSM3331118 Had the same issue as OP but this answer worked for me! Learn more about bidirectional Unicode characters, ((py3k)) [obotvinnik@tscc-login2 fastq_dump]$ fastq-dump --gzip --split-files /oasis/tscc/scratch/obotvinnik/external_singlecell/tasic2015/1645630/SRR2140205.sra --outdir /oasis/tscc/scratch/obotvinnik/external_singlecell/tasic2015/1645630/, 2016-07-28T15:53:29 fastq-dump.2.5.4 err: name not found while resolving tree within virtual file system module - failed /oasis/tscc/scratch/obotvinnik/external_singlecell/tasic2015/1645630/SRR2140205.sra, =============================================================. 2022-01-20T01:56:41 prefetch.2.11.0: 'SRR7695236' has 0 unresolved dependencies - we can use the helpful program [`pysradb`](https://github.com/saketkc/pysradb) to search for run accessions based on whatever identifiers we have One should not do them too bad, after all thousands of users use it successfully each day, and the SRA manages petabyte of data, but if it does not work at a given time one easily gets frustrated. ## takes one positional argument, the GSM unique sample ID in this case You should know we have been able to duplicate the problem and are analyzing it. cat ${sample_ID}-tmp/*_1.fastq.gz > ${sample_ID}_R1_raw.fastq.gz time fasterq-dump --split-files --progress --threads 8 SRR7695235.sra SRR7695236.sra
sorry to bother again. That grabs them independently. 2022-01-20T01:56:02 prefetch.2.11.0: 2) Downloading 'SRR7695236' ```bash By rejecting non-essential cookies, Reddit may still use certain cookies to ensure the proper functionality of our platform. # splitting into forward and reverse reads The only thing is that pre-release is just waiting on more testing before we release it generally. To: "ncbi/sra-tools" > time prefetch --max-size 500G --progress -O GSM3331071-tmp/ ${curr_run_accs} Fasterq-dump is written to detect such accessions and inform the user to use fastq-dump instead. ```bash time bash test-pigz.sh cat test.sh I develop deep learning methods for the design of proteins. pysradb gse-to-srp GSE118502 fasterq-dump has an option to set the location of these files. and gives this error # 2022-01-21T19:58:49 prefetch.2.11.0: HTTPS download succeed real 4m53.752s curr_obj_paths=$(echo $curr_run_accs | sed 's/ /.sra /g' | sed 's/$/.sra/' | sed "s/SRR/${sample_ID}-tmp\/SRR/g") Recently we have received many complaints from users about site-wide blocking of their own and blocking of their own activities please go to the settings off state, please visit sys 0m20.948s Does it also quit immediately? ``` spots read : 127,942,138 reads read : 127,942,138 reads written : 127,942,138 . Again, we appreciate such reporting as our own monitoring systems are not as sensitive to such issues. 2022-01-20T01:47:26 prefetch.2.11.0: 1) Downloading 'SRR7695235' fasterqDump function - RDocumentation The ID it gets is placed as a positional argumnt at the end of the command we provided # -rw-rw-r-- 1 mlee mlee 3689460183 Jan 19 19:39 GSM3331071_R2_raw.fastq.gz Could you try it again after updating the image? So for this dataset, that one sample with 12 separate runs took like 90 minutes with cat | gzip way, 20 minutes with pigz -> cat way. You switched accounts on another tab or window. Or run: Already have an account? I tried rm and rmdir to clear up space. real 5m28.951s # study_alias study_accession Trying with gzip instead of pigz just to be sure it's due to pigz and not the other changes: And we have two files in our working directory that are each about 1.7GB: # splitting into forward and reverse reads About midway through the page, it says "Samples (48)", and if we count the number of unique entries in the "experiment_alias" column, we get 48: # downloading all of their sra objects with prefetch |-------------------------------------------------- 100% ```bash We are trying to track down these issues as we head into the weekend. printf "\n\n Downloading run sra objects\n\n" 2018/03/18 Well occasionally send you account related emails. fasterq-dump quit with error code 3 Issue #644 ncbi/sra-tools real 5m31.933s ``` fastq-dump quit with error code 3 Issue #548 ncbi/sra-tools These 2 tools do not take the same options! 2021-12-26T13:48:20 prefetch.2.11.2: Current preference is set to retrieve SRA Normalized Format files with full base quality scores. By clicking Sign up for GitHub, you agree to our terms of service and fastq-dump - Error says There is not enough space on the disk. By clicking Sign up for GitHub, you agree to our terms of service and fasterq-dump quit with error code 3. A report was generated into the file '/root/ncbi_error_report.xml'. No bother at all - sorry we haven't updated this here. We'll be off over the weekend, of course, but will pick back up on Monday. 2021-12-26T13:53:01 faste. First we want a list of all unique sample IDs as they are in our info table: ```bash This function works best with sratoolkit functions of version 2.9.6 or greater. Should try pigz on directory of files, then cat the gzipped ones together, microbialomics.org/research
Fasterq comes from the latest version of sratools. here is my error information. reads written : 8,776,944 NCBI fastq-dump error : r/bioinformatics - Reddit prefetch --max-size 500G --progress -O ${sample_ID}-tmp/ ${curr_run_accs} sra toolkit - Biostar: S Prefetch is a part of the SRA toolkit. Data Processing github repository. SRX4553616 is not a run accession. Compressed file sizes at the end were roughly in the 3-4 GB range. ```bash 2022-01-20T01:56:41 prefetch.2.11.0: 2) 'SRR7695236' was downloaded successfully join :|-------------------------------------------------- 100% You could try fastq-dump; it's slower but doesn't use as much . A short google search lead me to learn about the general caching mechanisms of the SRA toolkit (I should have read the docs just earlier) and how to quickly manipulate them. Thank you for your help! cat GLDS-427-dl-and-combine-runs-for-a-sample.sh Query SRR17055838: Error 406 The object is not available from your location. just wanted to see if the update has been pushed. As said, the tutorial is for Unix so you would probably need a VM. join :|-------------------------------------------------- 100% time fasterq-dump --split-files --progress --threads 8 SRX4553616 Fasterq-dump is the successor to the older fastq-dump tool, but . ``` Reddit, Inc. 2023. split them into reads -t TEMP. database incorrect while opening manager within database - GitHub Policy. I suggest you do the download chunkwise, so get a sra file, convert to fastq, remove sra, maybe save fastq somewhere else to free disk space. time fasterq-dump --split-files --progress --threads 8 --gz SRR7695235.sra (112), but I have it downloading on a 1Tb hard drive. ( 406 ) Sorry to give a similar answer, but we'd like to ask you to try once again with 2.10.8. Hello, ### Getting info based on the SRA project ID curr_obj_paths=$(echo $curr_run_accs | sed 's/ /.sra /g' | sed 's/$/.sra/' | sed 's/SRR/GSM3331071-tmp\/SRR/g') The `fasterq-dump` tool uses temporary files and multi-threading to speed up the extraction of FASTQ from SRA-accessions. Just noting it here as something to consider in case interested. ``` concat :|-------------------------------------------------- 100% # spots read : 4,388,472 You signed out in another tab or window. Dear SRA people, We are "fasterq-dumping" some SRA files with the following command: fasterq-dump --ngc *****.ngc --split-files -e 15 SRR*****.sra --outdir fastq . Reformatted the hard drive, and the files downloaded. #### Script for doing each individual sample (multiple runs) for GLDS-427 # moving them all up a level to be easier to work with (if they were put in nested directories by prefetch) # prefetch SRAtoolkit functions can (ideally) be in your $PATH, or you can supply a path to them using the sratoolkitPath argument. We still need to get to the run accessions, here we'll start with searching for the bioproject. Sign in
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