Zcat fastq gz

Hi, I have a question about fastq and fastq.gz files. I understand that fastq.gz is the compressed version of fastq file. ... Apart from that, using cat doesn't …I could decompress the files and do "cat" on them, but is there any faster way? can I use gzcat file1.fastq.gz file2.fastq.gz | gzip > merged.fastq.gz ? merge fastq • 110k views ADD COMMENT • link updated 8 months ago by henry-keen 40 • written 9.3 years ago by newDNASeqer 750 0 have a try seqtk mergepe A: Merging two fastq files scott rasmussen paternity court Of course there is. In Linux, you can view contents of a compressed .gz file without uncompressing (uncompress on the fly actually or in temp directory) which makes perfect sense for those who deal with large log files and does forensic stuffs. The way it’s done is by using Z commands. Z commands for example: zcat allows you to view …Select the output according to the strandedness of your data. Note, if you have stranded data and choose one of the columns 3 or 4, the other column (4 or 3) will give you the count of antisense reads.zcat file.gz | wc -c If you wish to create a single archive file with multiple members so that members can later be extracted independently, use an archiver such as tar or zip. GNU tar supports the -z option to invoke gzip transparently. gzip is designed as a complement to tar, not as a replacement. Jellyfish can be instructed to open multiple file at once. For example, to read two short read archive files simultaneously: jellyfish count -F 2 < (fastq-dump -Z file1.sra) < (fastq-dump -Z file2.sra) ... Another way is to use "generators". First, create a file containing, one per line, commands to generate sequence. musc paystub zcat sample1_R1.fastq.gz | echo $((`wc -l`/4)). Are there equal number of sequence reads in both the paired FASTQ files? Also it is useful to convert FASTQ ... heavyweights movie ben stiller The “.gz” at the end of the FASTQ file name indicates that the fastq file was compressed using a program named gzip. This is pretty common because FASTQ files can be huge. …Likely that your fastq file is not successfully download based on unexpected end of file. Try zcat SRR494099.fastq.gz | tail. fastqc by the way does read gzipped files, no need for decompression. @ATpoint yeah I was just trying to see if the problem was with fastqc or with the file itself. But none of the files that I download from ENA are working. coach madison shoulder bagYour solution is zcat ing the files, so they're uncompressed, and then storing them in a file with the extension .gz. Either it should not be .gz, or you should recompress. Note however if your end result is compressed, there's no reason to zcat at all, just use cat and avoid the decompress/compression steps. – phemmer Apr 25, 2018 at 16:58for i in `ls *.fastq.gz`; do echo $(zcat ${i} | wc -l)/4|bc; done of note: ` are around ls .fastq.gz; Explanation: For all gzip compressed fastq files, display the number of reads since 4 lines = 1 reads *Just a good one-liner to see how many reads obtained from something like demultiplexing went ros2 big sur The sequences are in fastq format. The fastq file may contain both "filtered" and "not filtered" reads, depending on the instrument used. Files from the NextSeq500 contain only "not filtered" reads, i.e. reads that pass Illumina's Chastity filter. The pass filter status is indicated by a flag (Y/N) in the sequence header for each read. Tour Start here for a quick overview of the site Help Center Detailed answers to any questions you might have Meta Discuss the workings and policies of this sitezcat is essentially the same as gunzip -c, but keep in mind this command will scan and decompress an entire compressed file or files and sends the result to STDOUT. Therefore, zcat requires the redirect operator ‘<‘ to direct the file to it, which zcat redirects automatically to STDOUT, which you can then control with a pipe.First, 22[71-94]*R1_001.fastq.gz does not expand to what you think it expands to This is effectively 22[1-9]*R1_001.fastq.gz - in this, [71-94] is a character grouping where "7 OR 1 to 9 OR 4" simplifies to "1 to 9".. 22{71..94}*R1_001.fastq.gz is most likely the expansion you were looking for, but your loop will perform zcat once for …gzip圧縮されたfastqファイルを結合するにはどうすればよいですか? 私はこれをread 1とread 2で試しました. zcat file_1.fastq.gz file_2.fastq.gz | gzip > combined.fastq.gz. ただし、読み取り回数が不均等になっています。なぜですか? これを行う他の方法はありますか?kallisto quant -i transcripts.idx -o output -b 100 <(gzcat reads_1.fastq.gz) <(gzcat reads_2.fastq.gz) or with linux, you replace gzcat with zcat or any other program that writes the FASTQ to stdout. This utilizes an additional core to uncompress the FASTQ files, and speeds up the program by 10–15%. Single end readsApr 16, 2019 · At this point, zcat throws an error, because the input file ( file1.fastq.gz) has no content - not even the GZip header - and the pipeline falls apart. You may find that file1.fastq.gz is actually a few bytes in size (not zero), and this will be caused by gzip compressing and writing its null input. spa with sauna near me The “.gz” at the end of the FASTQ file name indicates that the fastq file was compressed using a program named gzip. This is pretty common because FASTQ files can be huge. cat is a program for viewing text files, zcat is a special version of this program that lets you view compressed text files without first decompressing them.zcat will uncompress files that have the correct magic number whether they have a .gz suffix or not. To verify this, we removed the .gz extension from one of the compressed files, and tried running zcat on it. So you can see the tool was still able to learn that it's a compressed file, and was able to display its content on STDOUT. Q4. ford ranger eec relay location The ”.gz” at the end of the FASTQ file name indicates that the fastq file was compressed using a program named gzip. This is pretty common because FASTQ files can be huge. cat is a program for viewing text files, zcat is a special version of this program that lets you view compressed text files without first decompressing them. land for sale jefferson county mo zcat CONN.20111109.0057.gz|head CONN.20111109.0057.gz.Z: A file or directory in the path name does not exist. zcat1可由压缩机1或gzip1提供。在您的系统上,它似乎是compress1-它正在查找扩展名为.Z的文件. 切换到gzip-cd代替zcat,您的命令应该可以正常工作: gzip -cd CONN.20111109.0057.gz | head 解释Hi, The following code uploads a file to a mock S3 bucket using boto, and downloads the same file to the local disk using boto3. I apologize for bringing both of the libraries into this, but the code I am testing in real life still uses both (definitely trying to get rid of all the boto code and fully migrate to boto3 but that isn't going to happen right away).(On some systems, zcat may be installed as gzcat to preserve the original link to compress.) zcat uncompresses either a list of files on the command line or its standard input and writes the uncompressed data on standard output. zcat will uncompress files that have the correct magic number whether they have a .gz suffix or not. optiver graduate interview Settings This page contains information and settings options for DuckStation, settings will need to be adjusted depending on the machine that DuckStation is running on.Please be aware that enabling some settings can have some side effects. Contents 1 General Settings 1.1 Controller Backend 2 BIOS Settings 3 Console Settings. 11h ago.zcat file.fastq.gz | str8rzr -c configFile > allSequences.txt or for Windows users: 7z file.fastq.gz -so | str8rzr -c configFile > allSequences.txt Otherwise str8rzr only operates on (uncompressed) fastq files. grep can be used to parse out particular markers (e.g., grep -w vWR allsequences.txt > vWR.txt todaypercent27s nfl scores 10x Genomics Chromium Single Cell Gene Expression. Cell Ranger7.1 (latest), printed on 01/25/2023. Specifying Input FASTQ Files for 10x Pipelines. The cellranger pipeline requires FASTQ files as input, which typically come from running cellranger mkfastq, a 10x-aware convenience wrapper for bcl2fastq.However, it is possible to use FASTQ files from other sources, such as Illumina's bcl2fastq or ...Hi, I have a question about fastq and fastq.gz files. I understand that fastq.gz is the compressed version of fastq file. ... Apart from that, using cat doesn't …The ”.gz” at the end of the FASTQ file name indicates that the fastq file was compressed using a program named gzip. This is pretty common because FASTQ files can be huge. cat is a program for viewing text files, zcat is a special version of this program that lets you view compressed text files without first decompressing them.for i in `ls *.fastq.gz`; do echo $(zcat ${i} | wc -l)/4|bc; done of note: ` are around ls .fastq.gz; Explanation: For all gzip compressed fastq files, display the number of reads … branson tractor reviews 2020 1 Answer Sorted by: 4 You're running wc -l on the .gz files, which is not what you want. To verify, you can use something like this instead: zcat *R1*.fastq.gz | wc -l zcat Sample_51770BL1_R1.fastq.gz | wc -l Although you might want to use a proper checksum algorithm, e.g. with the sha256sum tool, for that. tdcj polo shirts for i in `ls *.fastq.gz`; do echo $(zcat ${i} | wc -l)/4|bc; done of note: ` are around ls .fastq.gz; Explanation: For all gzip compressed fastq files, display the number of reads since 4 lines = 1 reads *Just a good one-liner to see how many reads obtained from something like demultiplexing wentzcat FILE.tar.gz | head -nNO_READS > FILE.fastq Obtaining Read Lengths from FASTQ In order to plot histograms of reads lengths and other experiments such as filtering short reads, we can do the ...FASTQ format Data repositories Course data Read QC and trimming Read mapping Mapping with STAR Genome Browser Mapping with Salmon MultiQC report Differential expression analysis Functional analysis Final project Resources Mapping using STAR For the STARrunning options, see STAR Manual. cali plug smarties cartridge Jellyfish can be instructed to open multiple file at once. For example, to read two short read archive files simultaneously: jellyfish count -F 2 < (fastq-dump -Z file1.sra) < (fastq-dump -Z file2.sra) ... Another way is to use "generators". First, create a file containing, one per line, commands to generate sequence.zcat CONN.20111109.0057.gz|head CONN.20111109.0057.gz.Z: A file or directory in the path name does not exist. zcat1可由压缩机1或gzip1提供。在您的系统上,它似乎是compress1-它正在查找扩展名为.Z的文件. 切换到gzip-cd代替zcat,您的命令应该可以正常工作: gzip -cd CONN.20111109.0057.gz | head 解释2. 转换为Fastq. samtools fastq [email protected] $ (nproc) -1 D1_1.fq.gz -2 D1_2.fq.gz -s /dev/null -0 /dev/null D1.rn.sort.bam -c 9. 1. -1 代表输出的R1端Fastq.gz文件名. -2 代表输出的R2 … carrier reefer status light not working If you mean to separate an interleaved fastq ( (2n-1)-th read to one file; (2n)-th to another): seqtk seq -1 interleaved.fq.gz > read1.fq seqtk seq -2 interleaved.fq.gz > read2.fq. If tophat2 support streaming, you can do something like the following without creating temporary files (bash only):案例描述:. 需要将Sample_test1_R1.fastq.gz和Sample_test2_R2.fastq.gz合并为test.fastq.gz. 操作方法1:. 先zcat再gzip. zcat Sample_test_1.R1.fastq.gz ...On server.example.com the file will be recompressed using zcat and bzip2 resulting in the corresponding file with .gz replaced with .bz2. If you want the resulting bz2-file to be transferred back to the local computer add --return {.}.bz2 :zcat file.gz | wc -c If you wish to create a single archive file with multiple members so that members can later be extracted independently, use an archiver such as tar or zip. GNU tar supports the -z option to invoke gzip transparently. gzip is designed as a complement to tar, not as a replacement. jbef zcat sample1_R1.fastq.gz | echo $((`wc -l`/4)). Are there equal number of sequence reads in both the paired FASTQ files? Also it is useful to convert FASTQ ...A file storing biological sequences with extension '.fastq' or '.fq' is a file in FASTQ format, if it is also compressed with GZIP the suffix will be '.fastq.gz' or '.fq.gz'. A FASTQ file usually contain millions of sequences and takes up dozens of Gigabytes in a disk. ... > zcat reads.fq.gz | echo $((`wc -l`/4)) 256678360 ...zcat will uncompress files that have the correct magic number whether they have a .gz suffix or not. To verify this, we removed the .gz extension from one of the compressed files, and tried running zcat on it. So you can see the tool was still able to learn that it's a compressed file, and was able to display its content on STDOUT. Q4. xr15 remote manual jellyfish count <(zcat file1.fastq.gz) <(zcat file2.fasta.gz) ... 2.2 How to read multiple les at once? Often, jelly sh can parse an input sequence le faster than gzip or fastq-dump (to parse SRA les) can output the sequence. This leads to many threads in jelly sh going partially unused. Jelly shI could decompress the files and do "cat" on them, but is there any faster way? can I use gzcat file1.fastq.gz file2.fastq.gz | gzip > merged.fastq.gz ? merge fastq • 110k views ADD COMMENT • link updated 8 months ago by henry-keen 40 • written 9.3 years ago by newDNASeqer 750 0 have a try seqtk mergepe A: Merging two fastq files chance of passing nclex @sfchen Yes, but the reads number is different from the reads_number_after_filter in json file. And read1 number is not same as read2 number.It seems like the fa.gz did not complete!Available to input gz compressed fastq files (zcat is needed). #Version 1.2.0.1 July 11, 2018. Correct bug that hlahd outputs incorrect positions to ...2018/08/25 ... If you want lines from the tail-end of a file rather than the head-end, use tail instead of head : $ zcat /var/log/syslog.2.gz | tail -1 Aug ... igniter media This tool takes unprocessed FASTQ files as an input, and it outputs FASTQ files in which any reads associated with bad tiles have been removed. ... To ungzip the file we should use the zcat ...zcat *.fastq.gz # concatenates compressed files to one output stream seqtk seq-A - # seqtk is a toolkit for manipulating sequence data. The -A converts input to fasta output. grep-v "^>" # grep searches for lines beginning (^) with the string > and excludes them (-v) ...for i in `ls *.fastq.gz`; do echo $(zcat ${i} | wc -l)/4|bc; done of note: ` are around ls .fastq.gz; Explanation: For all gzip compressed fastq files, display the number of reads … zf 8hp adapter Tour Start here for a quick overview of the site Help Center Detailed answers to any questions you might have Meta Discuss the workings and policies of this site fairview elementary school fairfax Tour Start here for a quick overview of the site Help Center Detailed answers to any questions you might have Meta Discuss the workings and policies of this siteThis command will work on essentially every *nix and Linux system. zcat < FILENAME_1.gz FILENAME_N.gz | somecommand. zcat is essentially the same as gunzip -c, but keep in mind this command will scan and decompress an entire compressed file or files and sends the result to STDOUT. roblox decal library link This command will work on essentially every *nix and Linux system. zcat < FILENAME_1.gz FILENAME_N.gz | somecommand. zcat is essentially the same as gunzip -c, but keep in mind this command will scan and decompress an entire compressed file or files and sends the result to STDOUT.Single cell tutorial¶. Important update: We now recommend the use of alevin for droplet-based scRNA-Seq (e.g 10X, inDrop etc). alevin extends the directional method used in UMI-tools to correct UMI errors with …Jellyfish can be instructed to open multiple file at once. For example, to read two short read archive files simultaneously: jellyfish count -F 2 < (fastq-dump -Z file1.sra) < (fastq-dump -Z file2.sra) ... Another way is to use "generators". First, create a file containing, one per line, commands to generate sequence. nj road closures todayNote that you can confirm that this works in most cases by doing something like the following: cat file1.gz file2.gz file3.gz > allfiles-cat.gz zcat file1.gz file2.gz file3.gz | gzip …FASTQ File Format | Genome Sequencing Data | FQ Guide | Sequencing.com Learn about the different types of FASTQ files, such as paired FASTQ and concatenated FASTQ, and which types are compatible with DNA analysis apps and reports.The “.gz” at the end of the FASTQ file name indicates that the fastq file was compressed using a program named gzip. This is pretty common because FASTQ files can be huge. cat is a program for viewing text files, zcat is a special version of this program that lets you view compressed text files without first decompressing them. six flags platinum membership benefits 2022 Aug 30, 2016 · Here I’ll summarize some Linux commands that can help us to work with millions of DNA sequences from New Generation Sequencing (NGS). A file storing biological sequences with extension ‘.fastq’ or ‘.fq’ is a file in FASTQ format, if it is also compressed with GZIP the suffix will be ‘.fastq.gz’ or ‘.fq.gz’. bangor daily news obituaries Jellyfish can be instructed to open multiple file at once. For example, to read two short read archive files simultaneously: jellyfish count -F 2 < (fastq-dump -Z file1.sra) < (fastq-dump -Z file2.sra) ... Another way is to use "generators". First, create a file containing, one per line, commands to generate sequence.FastQ files are the starting point for all downstream bioinformatics data analysis. The file name suffix for a FastQ file is: .fastq For example, a typical FastQ file name could be sample.fastq FastQ files are often found in gzip-compressed format with the file name: sample.fastq.gz The Illumina FastQ file format is shown below.jellyfish count < (zcat file1.fastq.gz) < (zcat file2.fasta.gz) ... How to read multiple files at once? Often, jellyfish can parse an input sequence file faster than gzip or fastq-dump (to parse SRA files) can output the sequence. This leads to many threads in jellyfish going partially unused.First, 22[71-94]*R1_001.fastq.gz does not expand to what you think it expands to This is effectively 22[1-9]*R1_001.fastq.gz - in this, [71-94] is a character grouping where "7 OR 1 to 9 OR 4" simplifies to "1 to 9".. 22{71..94}*R1_001.fastq.gz is most likely the expansion you were looking for, but your loop will perform zcat once for …zcat file.gz | wc -c If you wish to create a single archive file with multiple members so that members can later be extracted independently, use an archiver such as tar or zip. GNU tar supports the -z option to invoke gzip transparently. gzip is designed as a complement to tar, not as a replacement. shelly bgc reddit zcat is essentially the same as gunzip -c, but keep in mind this command will scan and decompress an entire compressed file or files and sends the result to STDOUT. Therefore, zcat requires the redirect operator '<' to direct the file to it, which zcat redirects automatically to STDOUT, which you can then control with a pipe.I have some fastq data downloaded from Illumina sequence hub. In these data, the sequences from one samples were split into four .gz files (i dont know why illumina does that). All the files together is about 18G. I first try to zcat every four files into one, but the file size inflated significantly from 18G to 78G:The analysis of genome-wide epigenomic alterations including DNA methylation has become a subject of intensive research for many complex diseases. Whole-genome bisulfite sequencing (WGBS) using next-generation sequencing technologies can … 1998 nissan altima Jun 26, 2018 · This will show that zcat exits with code 141, which indicates it stopped because of a SIGPIPE (13 + 128). You can add more post-processing, e.g. with AWK, to only extract the date: zcat logfile.gz | awk ' { print $1; exit }' (On macOS you might need to use gzcat rather than zcat to handle gzipped files.) Share Improve this answer Follow The “.gz” at the end of the FASTQ file name indicates that the fastq file was compressed using a program named gzip. This is pretty common because FASTQ files can be huge. cat is a program for viewing text files, zcat is a special version of this program that lets you view compressed text files without first decompressing them.Note that you can confirm that this works in most cases by doing something like the following: cat file1.gz file2.gz file3.gz > allfiles-cat.gz zcat file1.gz file2.gz file3.gz | gzip … honda tr200 for sale craigslist FastQ files are the starting point for all downstream bioinformatics data analysis. The file name suffix for a FastQ file is: .fastq For example, a typical FastQ file name could be sample.fastq FastQ files are often found in gzip-compressed format with the file name: sample.fastq.gz The Illumina FastQ file format is shown below.Human-specific NOTCH2NL expands cortical progenitors and neuronal output and thus may have contributed to the expansion of the human cortex. kohler 7000 engine surging gzip reads_5.fastq There are many different ways to create this shell script. Here you will use the "yes" and "paste" commands to create this script "myscript.sh". yes "gzip" |head -n 5 > t1 ls -1 reads*fastq > t2 paste -d " " t1 t2 > myscript.sh · yes "gzip" |head -n 5 > t1 : Create a text file with 5 lines of "gzip"Split large .gz files with prefixes. Each of my fastq files is about 20 millions reads (or 20 millions lines). Now I need to split the big fastq files into chunks, each with only 1 million reads (or 1 million lines), for the ease of further analysis. fastq file is just like .txt. My thought is, just count the line, and print out the lines after ... home depot cieling fans Jan 24, 2017 · Hi, The following code uploads a file to a mock S3 bucket using boto, and downloads the same file to the local disk using boto3. I apologize for bringing both of the libraries into this, but the code I am testing in real life still uses ... Faster gzip reading in Python. In this essay I'll describe how I improved chemfp 's gzip read performance by about 15% by replacing Python's built-in gzip … unity webgl player truck games 4 Advanced usage. Multiple compressed files can be concatenated. In this case, gunzip will extract all members at once. If one member is damaged, other members might still be recovered after removal of the damaged member. Better compression can be usually obtained if all members are decompressed and then recompressed in a single step.Inspect the contents of a compressed gff3 file (human.gff3.gz), using these Linux functions: zcat, head, tail, cut, less; Inspect the first and last 100 lines of the file, using "head" and "tail" functions to retrieve first and last lines of the file;If you mean to separate an interleaved fastq ( (2n-1)-th read to one file; (2n)-th to another): seqtk seq -1 interleaved.fq.gz > read1.fq seqtk seq -2 interleaved.fq.gz > read2.fq. If tophat2 support streaming, you can do something like the following without creating temporary files (bash only):What is a fastq GZ file? It is fq. gz’. A FASTQ file can take up a lot of disk space. ZIP format is less efficient than GZIP when it comes to reducing the size of files. …2019/08/27 ... zcat ○○.fastq.gz | awk '{if(NR%4==2){print}}'.zcat *.fastq.gz | jellyfish count /dev/fd/0 ... or by using the '<() ' redirection provided by the shell (e.g. bash, zsh): jellyfish count <(zcat file1.fastq.gz) <(zcat file2.fasta.gz) ... 2.2 How to read multiple les at once? Often, jelly sh can parse an input sequence le faster than gzip or fastq-dump (to parse SRA les) can output the sequence. 2019 z06 for sale The columns represent: sample_name Sample name for labeling the sample in the pipeline and output files. This can be any arbitrary string. technology: This controls the barcode correction and processing methods to use for the fastq files.Currently only the biorad option involves different processing steps. Otherwise, the value in this field (e.g. standard, …The sequences are in fastq format. The fastq file may contain both "filtered" and "not filtered" reads, depending on the instrument used. Files from the NextSeq500 contain only "not filtered" reads, i.e. reads that pass Illumina's Chastity filter. The pass filter status is indicated by a flag (Y/N) in the sequence header for each read.A magnifying glass. It indicates, "Click to perform a search". nu. nkJun 26, 2018 · This will show that zcat exits with code 141, which indicates it stopped because of a SIGPIPE (13 + 128). You can add more post-processing, e.g. with AWK, to only extract the date: zcat logfile.gz | awk ' { print $1; exit }' (On macOS you might need to use gzcat rather than zcat to handle gzipped files.) Share Improve this answer Follow mad city windows For example, a typical FastQ file name could be sample.fastq. FastQ files are often found in gzip-compressed format with the file name: sample.fastq.gz. The Illumina FastQ file format is shown below. Each record in a FastQ file consists of four lines: Sequence identifier Nucleotide sequence. 1.1 Download and install Ubuntu.parallel zcat {} ">"{.} ::: *.gz Quoting of > is necessary to postpone the redirection. Another solution is to quote the whole command: parallel "zcat {} > {.}" ::: *.gz Other special shell characters (such as * ; $ > < | >> <<) also need to be put in quotes, as they may otherwise be interpreted by the shell and not given to GNU parallel.软件概述. 将基因组等序列文件,按长度为k的字符串进行切割、归类以及频数统计。 软件安装. 软件版本:2.3.0 how to cheat at chess online In this example, show the contents of a text file called resume.txt.gz that has been compressed using gzip and friends. Open the Terminal and then type the following commands. Advertisement Syntax Display resume.txt.gz on screen using cat command like syntax: zcat resume.txt.gz Display access_log_1.gz on screen at a time: zmore access_log_1.gz2020/08/28 ... 今回はこれらのコマンドについて学んでいきます。 gzipコマンドで圧縮する; gzipコマンドで確認する; zcatコマンドで確認する; 参考書籍 ... dnd 5e homebrew monsters pdf To start, let’s compress a FASTQ file in GZIP format: > gzip reads.fq. The resulting file will be named ‘reads.fq.gz’ by default. If we want to check the contents of …If you mean to separate an interleaved fastq ( (2n-1)-th read to one file; (2n)-th to another): seqtk seq -1 interleaved.fq.gz > read1.fq seqtk seq -2 interleaved.fq.gz > read2.fq. If tophat2 support streaming, you can do something like the following without creating temporary files (bash only):module load BBMap/36.86 reformat.sh in=interleaved_reads.fastq out1=reads_R1.fastq out2=reads_R2.fastq Fastq to Fasta. Convert fastq file to fasta … delasalle high school basketball parallel zcat {} ">"{.} ::: *.gz Quoting of > is necessary to postpone the redirection. Another solution is to quote the whole command: parallel "zcat {} > {.}" ::: *.gz Other special shell characters (such as * ; $ > < | >> <<) also need to be put in quotes, as they may otherwise be interpreted by the shell and not given to GNU parallel.thanks Peter, from your command, I made a zzcat alternative to zcat alias zzcat='unpigz -p 8 -c' even on a single core pigz is already faster, more than 4 cores do …A file storing biological sequences with extension ‘.fastq’ or ‘.fq’ is a file in FASTQ format, if it is also compressed with GZIP the suffix will be ‘.fastq.gz’ or ‘.fq.gz’. A FASTQ file usually contain millions of sequences and takes up dozens of Gigabytes in a disk. ... > zcat reads.fq.gz | echo $((`wc -l`/4)) 256678360 ... beretta 1301 factory stock