# \#fastqsanger **URL:** https://help.galaxyproject.org/tag/fastqsanger/245.md [Latest](https://help.galaxyproject.org/latest.md) · [Categories](https://help.galaxyproject.org/categories.md) · [Tags](https://help.galaxyproject.org/tags.md) --- ## [Error in using FastQC in Galaxy EU](https://help.galaxyproject.org/t/error-in-using-fastqc-in-galaxy-eu/16330)
**Author:** [@Pedro\_Fernandes\_de\_S](https://help.galaxyproject.org/u/Pedro_Fernandes_de_S)\ **Replies:** 2\ **Last updated:** [October 2, 2025, 7:40am UTC](https://help.galaxyproject.org/t/error-in-using-fastqc-in-galaxy-eu/16330 "2025-10-02T07:40:17Z")
I have already used fastqc sometimes inGalaxy, but for a specific dataset it is not working, it says something about it being a not GZip archive but i dont even know what isthis, can someone help? --- ## [error with format .txt](https://help.galaxyproject.org/t/error-with-format-txt/13818)
**Author:** [@nicksam](https://help.galaxyproject.org/u/nicksam)\ **Replies:** 2\ **Last updated:** [November 5, 2024, 12:39pm UTC](https://help.galaxyproject.org/t/error-with-format-txt/13818 "2024-11-05T12:39:00Z")
when I uploaded my data set in to the galaxy I exposé this error: faster-dump.log an error occurred with this dataset. format .txt database how can I handle this. I upload files from GEO2R-SRA RUN selector --- ## [De-Multiplexing with Je-Demultiplex-Illu](https://help.galaxyproject.org/t/de-multiplexing-with-je-demultiplex-illu/13784)
**Author:** [@jkagle](https://help.galaxyproject.org/u/jkagle)\ **Replies:** 1\ **Last updated:** [October 30, 2024, 5:20pm UTC](https://help.galaxyproject.org/t/de-multiplexing-with-je-demultiplex-illu/13784 "2024-10-30T17:20:18Z")
I just tried to use Je-Demultiplex-Illu to demultiplex my Illumina reads. I thought I entered everything correctly, but I got the following error. Any suggestions how to fix this? Picked up \_JAVA\_OPTIONS: -Xmx4G -Xms256… --- ## [FASTQ Groomer, fastq.qz and fastqsanger](https://help.galaxyproject.org/t/fastq-groomer-fastq-qz-and-fastqsanger/13749)
**Author:** [@Tahleel](https://help.galaxyproject.org/u/Tahleel)\ **Replies:** 4\ **Last updated:** [October 23, 2024, 7:45am UTC](https://help.galaxyproject.org/t/fastq-groomer-fastq-qz-and-fastqsanger/13749 "2024-10-23T07:45:19Z")
As the quality scores of the FASTQ files (.fastqsanger.gz) generated by the Illumina 1.9 pipeline scaled to Sanger Phred+33 , I do not need to apply FASTQ Groomer. Do I still need to manually assign the format/datatype … --- ## [How can I gunzip a file?](https://help.galaxyproject.org/t/how-can-i-gunzip-a-file/11900)
**Author:** [@Michael\_Thon](https://help.galaxyproject.org/u/Michael_Thon)\ **Replies:** 2\ **Last updated:** [March 10, 2024, 8:58pm UTC](https://help.galaxyproject.org/t/how-can-i-gunzip-a-file/11900 "2024-03-10T20:58:31Z")
Hi all - This should be really simple but I cannot find a tool to gunzip a fasta file. Could it be that there is no tool for this? Thanks! Mike --- ## [Trim galore not taking fastq dataset](https://help.galaxyproject.org/t/trim-galore-not-taking-fastq-dataset/11544)
**Author:** [@Souptik\_Basu](https://help.galaxyproject.org/u/Souptik_Basu)\ **Replies:** 1\ **Last updated:** [January 22, 2024, 9:46pm UTC](https://help.galaxyproject.org/t/trim-galore-not-taking-fastq-dataset/11544 "2024-01-22T21:46:46Z")
Hi I am new to Galaxy and have been trying to trim off the adapter and overhang, followed by build a collection, flatten and QC. But Trimgalore is not accepting any fastq paired collection. What is the other way to go a… --- ## [From fastq.gz to fastq](https://help.galaxyproject.org/t/from-fastq-gz-to-fastq/11545)
**Author:** [@Ahmed\_OUNI](https://help.galaxyproject.org/u/Ahmed_OUNI)\ **Replies:** 1\ **Last updated:** [January 22, 2024, 8:07pm UTC](https://help.galaxyproject.org/t/from-fastq-gz-to-fastq/11545 "2024-01-22T20:07:50Z")
I have R1 and R2 (Illumina) in fastq.gz form how to convert in fastq form, tanks for your help in advance. --- ## [Assistance with Filtlong Tool for Quality Filtering of FastQ Data](https://help.galaxyproject.org/t/assistance-with-filtlong-tool-for-quality-filtering-of-fastq-data/11141)
**Author:** [@ge96dah](https://help.galaxyproject.org/u/ge96dah)\ **Replies:** 3\ **Last updated:** [November 14, 2023, 11:04pm UTC](https://help.galaxyproject.org/t/assistance-with-filtlong-tool-for-quality-filtering-of-fastq-data/11141 "2023-11-14T23:04:04Z")
Hello forum members, I’m encountering an issue while attempting to filter my FastQ data based on a mean quality score greater than or equal to 20 using the Filtlong tool. Despite applying the tool, the FastQC report sho… --- ## [Problem with uploading data](https://help.galaxyproject.org/t/problem-with-uploading-data/10909)
**Author:** [@PPM](https://help.galaxyproject.org/u/PPM)\ **Replies:** 2\ **Last updated:** [October 11, 2023, 6:27am UTC](https://help.galaxyproject.org/t/problem-with-uploading-data/10909 "2023-10-11T06:27:38Z")
Hello, I received raw data from 16s sequencing on Illumina and I have list of folders: " name of sample\_run.fastq" and inside of every one of them there are 2 files named: “forward.fastqsanger.gz” and “reversed.fastqsan… --- ## [fastq to fastqsanger stuck in orange](https://help.galaxyproject.org/t/fastq-to-fastqsanger-stuck-in-orange/10748)
**Author:** [@biotemon](https://help.galaxyproject.org/u/biotemon)\ **Replies:** 1\ **Last updated:** [September 11, 2023, 5:28pm UTC](https://help.galaxyproject.org/t/fastq-to-fastqsanger-stuck-in-orange/10748 "2023-09-11T17:28:46Z")
I encountered an issue: I was working on (https://usegalaxy.eu/) and trying to convert some files from fastq to fastqsanger using the pencil tool but this triggered a “Metadata is being auto-detected” operation on each f… --- ## [How to convert fastq.gz to fastqsanger.gz](https://help.galaxyproject.org/t/how-to-convert-fastq-gz-to-fastqsanger-gz/10684)
**Author:** [@Sheng-Chieh\_Hsu](https://help.galaxyproject.org/u/Sheng-Chieh_Hsu)\ **Replies:** 4\ **Last updated:** [August 24, 2023, 5:54pm UTC](https://help.galaxyproject.org/t/how-to-convert-fastq-gz-to-fastqsanger-gz/10684 "2023-08-24T17:54:25Z")
Hi, I’m attempting to analyze my ChIP-seq data in UseGalaxy. The data is in fastq.gz format and was generated by the NextSeq 2000. I’m aware that most tools in UseGalaxy require the fastqsanger format, so I’m trying to … --- ## [Unpacking fq.gz files](https://help.galaxyproject.org/t/unpacking-fq-gz-files/10583)
**Author:** [@AOEynes](https://help.galaxyproject.org/u/AOEynes)\ **Replies:** 6\ **Last updated:** [August 7, 2023, 8:39pm UTC](https://help.galaxyproject.org/t/unpacking-fq-gz-files/10583 "2023-08-07T20:39:08Z")
On my workstation I use winzip to unpack these. I hoped to unpack these with the online tools, but none of the ziptools recognized the fq.gz files. How can I unpack these here on galaxy? Or is it possible to analyze a… --- ## [RAD-seq remove samples from raw data](https://help.galaxyproject.org/t/rad-seq-remove-samples-from-raw-data/10449)
**Author:** [@melissajbetters](https://help.galaxyproject.org/u/melissajbetters)\ **Replies:** 3\ **Last updated:** [July 12, 2023, 8:10pm UTC](https://help.galaxyproject.org/t/rad-seq-remove-samples-from-raw-data/10449 "2023-07-12T20:10:48Z")
Hi All! So, I need some help getting off the ground :sweat\_smile: I sent in a plate of 96 samples for RAD-seq: Half were my samples, half were a colleague’s. However, the company returned a single file of all sequences … --- ## [HISAT2 error failed to read header from "-"](https://help.galaxyproject.org/t/hisat2-error-failed-to-read-header-from/10381)
**Author:** [@Nicolas\_Romero\_Villa](https://help.galaxyproject.org/u/Nicolas_Romero_Villa)\ **Replies:** 4\ **Last updated:** [July 4, 2023, 11:36pm UTC](https://help.galaxyproject.org/t/hisat2-error-failed-to-read-header-from/10381 "2023-07-04T23:36:28Z")
Hello today i was using HiSAT2 to fo a mapping of my fastq paired-end secuences to the reference genome of my organism (Hydractinia symbiolongicarpus) and the software returned this error: Total time for call to driver(… --- ## [Error in paired-end analysis](https://help.galaxyproject.org/t/error-in-paired-end-analysis/10052)
**Author:** [@mallamuneer123](https://help.galaxyproject.org/u/mallamuneer123)\ **Replies:** 17\ **Last updated:** [May 19, 2023, 6:58pm UTC](https://help.galaxyproject.org/t/error-in-paired-end-analysis/10052 "2023-05-19T18:58:59Z")
Dear All I am getting an unexpected during pear end read merger fastq error showing: An error occurred with this dataset: format fastqsanger database. However two samples are merged successfully. Kindly suggest what… --- ## [Minimap2 fails immediately on mapping fasta to hg38](https://help.galaxyproject.org/t/minimap2-fails-immediately-on-mapping-fasta-to-hg38/10041)
**Author:** [@nblewett](https://help.galaxyproject.org/u/nblewett)\ **Replies:** 2\ **Last updated:** [May 15, 2023, 8:49pm UTC](https://help.galaxyproject.org/t/minimap2-fails-immediately-on-mapping-fasta-to-hg38/10041 "2023-05-15T20:49:50Z")
Minimap2 should be able to map from fastq or fasta files. Galaxy Minimap2 cannot see fastq files. When galaxy minimap2 is run on fasta files it fails where it previously ran effectively. This same data was processed t… --- ## [Dataset collection not recognized as possible input](https://help.galaxyproject.org/t/dataset-collection-not-recognized-as-possible-input/9905)
**Author:** [@waynelim](https://help.galaxyproject.org/u/waynelim)\ **Replies:** 3\ **Last updated:** [April 18, 2023, 11:03am UTC](https://help.galaxyproject.org/t/dataset-collection-not-recognized-as-possible-input/9905 "2023-04-18T11:03:01Z")
Hi, I am trying to run Trim Galore! on my set of dataset pairs and I have previously created a dataset collection of forward and reverse reads. They are also in the fastqsanger data format. However, Trim galore does not… --- ## [Unicycler hybrid assembly fail (personal and tutorial data)](https://help.galaxyproject.org/t/unicycler-hybrid-assembly-fail-personal-and-tutorial-data/9763)
**Author:** [@Joanna\_Colovas](https://help.galaxyproject.org/u/Joanna_Colovas)\ **Replies:** 3\ **Last updated:** [March 31, 2023, 5:41pm UTC](https://help.galaxyproject.org/t/unicycler-hybrid-assembly-fail-personal-and-tutorial-data/9763 "2023-03-31T17:41:07Z")
Hi all, I have been trying to work through the training tutorial for hybrid assembly using unicycler, and the tool continues to fail using both the tutorial data and personal data: Unicycler Assembly The error(s) displ… --- ## [Fastqsanger.gz not recognized in trim galore/ D interlacer](https://help.galaxyproject.org/t/fastqsanger-gz-not-recognized-in-trim-galore-d-interlacer/9530)
**Author:** [@Preet\_Kaur](https://help.galaxyproject.org/u/Preet_Kaur)\ **Replies:** 2\ **Last updated:** [March 1, 2023, 9:42pm UTC](https://help.galaxyproject.org/t/fastqsanger-gz-not-recognized-in-trim-galore-d-interlacer/9530 "2023-03-01T21:42:28Z")
Fastqsanger.gz is not working in the trim galore or trimmomatic flexible trimming tool as a paired end collected. Ive tried to use a D interlacer to get it to work but the drop down list doesnt allow me to select my SRA… --- ## [How to convert fastq files to gz](https://help.galaxyproject.org/t/how-to-convert-fastq-files-to-gz/9467)
**Author:** [@bbarrios](https://help.galaxyproject.org/u/bbarrios)\ **Replies:** 2\ **Last updated:** [February 16, 2023, 6:12pm UTC](https://help.galaxyproject.org/t/how-to-convert-fastq-files-to-gz/9467 "2023-02-16T18:12:56Z")
Hi! I downloaded my 16S files in fastq format and I’m interested in convert this files to fastq.gz files. How do I do that? I’m leaning how to analyze 16S data. Thanks lot --- ## [Problem with Uniclycler](https://help.galaxyproject.org/t/problem-with-uniclycler/8858)
**Author:** [@mlopezm](https://help.galaxyproject.org/u/mlopezm)\ **Replies:** 7\ **Last updated:** [February 10, 2023, 8:09pm UTC](https://help.galaxyproject.org/t/problem-with-uniclycler/8858 "2023-02-10T20:09:38Z")
I have tried to assemble paired reads (Illumina) with nanopore reads but I always obtain the same error: An error occurred with this dataset: format fasta database \[?\] cannot find ‘lr’ Could anyone help me with this? … --- ## [run Unicycler always got " unicycler: command not found" -- RESOLVED at UseGalaxy.org 20230210](https://help.galaxyproject.org/t/run-unicycler-always-got-unicycler-command-not-found-resolved-at-usegalaxy-org-20230210/9297)
**Author:** [@Meadowlawn](https://help.galaxyproject.org/u/Meadowlawn)\ **Replies:** 8\ **Last updated:** [February 10, 2023, 8:05pm UTC](https://help.galaxyproject.org/t/run-unicycler-always-got-unicycler-command-not-found-resolved-at-usegalaxy-org-20230210/9297 "2023-02-10T20:05:59Z")
run Unicycler always got “/jetstream2/scratch/main/jobs/47842391/command.sh: line 110: unicycler: command not found” I am wondering if there are something wrong with my input data or there is something wrong with the Un… --- ## [Unicycler doesn't combine two datasets](https://help.galaxyproject.org/t/unicycler-doesnt-combine-two-datasets/9266)
**Author:** [@Manuel](https://help.galaxyproject.org/u/Manuel)\ **Replies:** 2\ **Last updated:** [January 12, 2023, 9:52am UTC](https://help.galaxyproject.org/t/unicycler-doesnt-combine-two-datasets/9266 "2023-01-12T09:52:17Z")
Hello everyone, I have two sets of sequence data for the same genome (Illumina and PacBio) and I want to combine them via Unicycler (has worked for 5 genomes so far) but somehow it does not work for my current dataset. … --- ## [Using symlinks as user\_library\_import\_dir with network drives not working](https://help.galaxyproject.org/t/using-symlinks-as-user-library-import-dir-with-network-drives-not-working/9182)
**Author:** [@galaxy\_user](https://help.galaxyproject.org/u/galaxy_user)\ **Replies:** 3\ **Last updated:** [December 15, 2022, 2:53pm UTC](https://help.galaxyproject.org/t/using-symlinks-as-user-library-import-dir-with-network-drives-not-working/9182 "2022-12-15T14:53:42Z")
Hi all, we are running our own local galaxy service in a multi-user environment at version 21.09 currently. We want to use the following setup to allow user import of data: a mounted network drive at: /galaxy-clients… --- ## [Je-demultiplex error - Exit code 1](https://help.galaxyproject.org/t/je-demultiplex-error-exit-code-1/9133)
**Author:** [@JonasDS01](https://help.galaxyproject.org/u/JonasDS01)\ **Replies:** 2\ **Last updated:** [December 6, 2022, 7:48am UTC](https://help.galaxyproject.org/t/je-demultiplex-error-exit-code-1/9133 "2022-12-06T07:48:58Z")
Hi all, I have used Je-demultiplex successfully on several occasions for demultiplexing my NGS reads, but this time I run into the following error: Fatal error: Exit code 1 (Tool exception) Picked up \_JAVA\_OPTIONS: -… --- ## [Problem in dowloading file in Galaxy Europe](https://help.galaxyproject.org/t/problem-in-dowloading-file-in-galaxy-europe/9073)
**Author:** [@federica](https://help.galaxyproject.org/u/federica)\ **Replies:** 1\ **Last updated:** [November 23, 2022, 10:43am UTC](https://help.galaxyproject.org/t/problem-in-dowloading-file-in-galaxy-europe/9073 "2022-11-23T10:43:40Z")
Hello, I need to dowload my files (they are FASTQ in fastqsanger.gz format) from Galaxy. I concatenated them in August by Concatenate datasets tail-to-head (Galaxy Version 1.0.0). Today, my merged file, are not the same … --- ## [Trimmomatic error: Fatal error](https://help.galaxyproject.org/t/trimmomatic-error-fatal-error/9038)
**Author:** [@Egle](https://help.galaxyproject.org/u/Egle)\ **Replies:** 8\ **Last updated:** [November 20, 2022, 7:38pm UTC](https://help.galaxyproject.org/t/trimmomatic-error-fatal-error/9038 "2022-11-20T19:38:42Z")
Hi, I have tried running some RNAseq datasets on Trimmomatic but they keep failing. The error I get when clicking on the bug icon is the following: Fatal error: When checking the information section, I get “empty” for … --- ## [fasta file begins with carat (\>) and not @](https://help.galaxyproject.org/t/fasta-file-begins-with-carat-and-not/8946)
**Author:** [@abhay03](https://help.galaxyproject.org/u/abhay03)\ **Replies:** 3\ **Last updated:** [November 4, 2022, 5:24pm UTC](https://help.galaxyproject.org/t/fasta-file-begins-with-carat-and-not/8946 "2022-11-04T17:24:50Z")
I have FASTA file which begins with carat(\>) and not @. Hence, FastQC gives following error: Picked up \_JAVA\_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/046/646/46646055/\_job\_tmp -Xmx28g -Xms256m Failed to process AK1… --- ## [Fastq unavailable -- Tool does not recognize inputs? How to check why](https://help.galaxyproject.org/t/fastq-unavailable-tool-does-not-recognize-inputs-how-to-check-why/8925)
**Author:** [@TTP](https://help.galaxyproject.org/u/TTP)\ **Replies:** 9\ **Last updated:** [November 2, 2022, 2:09am UTC](https://help.galaxyproject.org/t/fastq-unavailable-tool-does-not-recognize-inputs-how-to-check-why/8925 "2022-11-02T02:09:38Z")
Trying to use BBMap on an uploaded FASTQ dataset but it shows as unavailable. Also does this if I upload FASTQ.GZ and unzip in Galaxy. Wondering how to get around this. Data is originally pacbio. Thanks. --- ## [Minipolish alternatives](https://help.galaxyproject.org/t/minipolish-alternatives/8860)
**Author:** [@iker](https://help.galaxyproject.org/u/iker)\ **Replies:** 6\ **Last updated:** [October 24, 2022, 6:02am UTC](https://help.galaxyproject.org/t/minipolish-alternatives/8860 "2022-10-24T06:02:55Z")
I am trying to assemble a bacterial genome sequenced with long reads (miNION), with Minimap2/Miniasm. The assembly works fine (it produces 1 contig; the same as with Flye and Raven+Racon) but then I need to polish the as… [Next page](https://help.galaxyproject.org/tag/fastqsanger/245.md?match_all_tags=true&page=1&tags%5B%5D=fastqsanger)