to perform a blastx. but when im unzipping this file terminal is giving an error like, "gzip: uniprot_sprot_human.dat.gz: not in gzip format". please direct me on correct path. thank you
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to convert the merged file into a fastq file using:
`gunzip merged.fastq.gz`
and I got an error:
gzip: merged.fastq.gz: not in gzip format
I have tried gunzip on the individual fastq.gz files and it worked.
Can anyone help
updated 3.0 years ago • Kai_Qi
an .rds.gz file with the command:
```
gunzip filename.rds.gz
```
But keep receiving the error,
```
gzip: filename.rds.gz: not in gzip format
```
Any suggestions
states the following:
> BGZF is block compression implemented on top of the standard gzip file format....a compliant gunzip utility can decompress a BGZF compressed file
I would like be able to read a BAM file using...gzip, as the specification says I should be able to. However, when I open a BAM file using the inbuilt python library gzip I am able...I feel given the explicit declaration…
slow. I recently switched to fasterq-dump, which is great in terms of speed, but its inability to gzip the fastq files on the fly is causing me lots of issues (the uncompressed fastq files are just too big for the system I am...fasterq-dump does not allow any gzipping of its output. Is there, however, any trick I could use to gzip these files before they take so much space? I tried piping a gzip …
updated 2.4 years ago • pomodoro_sinensis
using HISAT2 and when I am doing quantification using the
> featureCounts
I am getting the GZIP ERROR:-2 as follows:
> GZIP ERROR:-2
the data is paired ended so I am using the same command given in the manual of subhead package
and run time as well.
So far I can think of it as -
```
use strict;
use warnings;
use IO::Compress::Gzip qw(gzip $GzipError);
#-------check the input file specified-------------#
$num_args = $#ARGV + 1;
if ($num_args != 1) {
print "\nUsage: name.pl Filelist.txt \n";
exit...print $outputfile $line ;
}
}
close(IN);
my $Final_combied_zip = new IO::Compress::Gzip($combined_fi…
updated 20 months ago • PAn
I align forward and reverse fastq reads to a fasta reference using bwa, then sort the alignment file:
bwa mem -M -t 16 ref_galr2a_AA.fa E01_S49_L001_R1_001.fastq.gz E01_S49_L001_R2_001.fastq.gz | samtools sort > test.bam
Now say I want to convert back this bam to fastq files; I am used to doing:
bedtools bamtofastq -i test.bam -fq forward.fastq -fq2 reverse.fastq
Then put the …
updated 3.1 years ago • francois
so I can work with it in the machine. I have a problem wirh BAM files: they are recognized as gzip but they do not have extension .zip or similar. Anyway, when I try to extract them I have the message: an error occurred while
Exception in thread "main" java.lang.RuntimeException: java.util.zip.ZipException: Not in GZIP format
at fileIO.ReadWrite.getGZipInputStream(ReadWrite.java:1048)
at fileIO.ReadWrite.getInputStream(ReadWrite.java...at jgi.PartitionReads.main(PartitionReads.java:42)
Caused by: java.util.zip.ZipException: Not in GZIP format
at java.base/java.util.zip.GZIPInput…
updated 4.3 years ago • Ric
by using `gunzip -f transmute.Linux.gz` command, but something wrong occurs to me, as shown below:
gzip: transmute.Linux.gz: invalid compressed data--format violated
i}.fastq.gz ;
done
I then did the dumb way, guzip all files, cat them together and then gzip them all, but now the files size is about 15Gb.
gunzip *.gz
for i in $(ls *.fastq | rev | cut -c 19- | rev | uniq);
do cat ${i}_L001_R1_001.fastq...i}_L003_R1_001.fastq ${i}_L004_R1_001.fastq > ./cat_fastq/${i}.fastq ;
done
gzip *.fastq
Can anyone please advice…
updated 3.2 years ago • dazhudou1122
38] Mapping left_kept_reads to genome readsFASTA with Bowtie2
Error: could not open writer pipe gzip -cf - < orftp3_out/tmp/left_kept_reads_seg124.fq.z
Apparently the left_kept_reads_seg124.fq.z file is empty. How...can I get around this? Also when I tried exported gzip to path:
$export PATH=$PATH:/gzip
$echo PATH
> PATH
That is what happens. I don't know what's goi…
for reference genome.so, vi [UCSC][1] website, i provide all items for downloading my GTF format vi gzip file but when I click on "get output" button, I referred to new [URL][2] in browser and I can't download as gzip file.
I appreciate
updated 5.9 years ago • modarzi
I currently have 33 gzipped files in beagle format. The sum file size is 55871611132 (55Gb).
I am trying to concatenate these with the following script which should just take the header from a single file and then concatenate all files into a single file with one header.
cat <(zcat Chr1.beagle.gz \
| head -n 1) <(zcat *.beagle.gz \
| grep -v -w marker) | gzip > …
updated 3.6 years ago • selplat21
So in the past I've had reason to gzip large FASTA files, and I'd always noticed that the result seemed roughly 1/4 size, or what I'd expect for the most obvious...So in the past I've had reason to gzip large FASTA files, and I'd always noticed that the result seemed roughly 1/4 size, or what I'd expect for the most obvious space...00, 01, 10, and 11 in its code table. And that's already 2bit enc…
updated 6.2 years ago • Nick Stoler
When I used the command:
samtools view -bS [filename].sam > [filename].bam
I get a GZIP file with the name "[filename].bam
I then try to convert to sorted.bam using command:
samtools sort [filename].bam -o [filename...sorted.bam
And I just get a bunch (~11) gzip files, and then my Ubuntu terminal just starts displaying gibberish.
What could be the issue
running it
the following error occurs:
[E::fai_build3_core] Cannot index files compressed with gzip, please use bgzip
./annotate_vep.sh: line 16: 14589 Segmentation fault
Here you can find my command:
/home/user/ensembl-vep
updated 2.1 years ago • Filago
Good evening,
My mapping process (`hisat2`) stopped with message in stdout:
gzip: stdout: Broken pipe
(ERR): hisat2-align died with signal 9 (KILL)
At the same time, the large `sam` file is partially generated
Reading uncompress file size from a gzip file is easy. The value is stored in the last 4 bytes of the gzip file.
But it doesn't with bgzip file ! Any idea how can I get this
outFileNamePrefix $RDS/projects/sequ/live/mapped/Genecode/EEtest
But I get this error message;
gzip: S*_R1_002.fastq.gz: No such file or directory
gzip: S*_R1_003.fastq.gz: No such file or directory
gzip: S*_R1_004.fastq.gz...No such file or directory
gzip: S*_R1_005.fastq.gz: No such file or directory
gzip: S*_R1_006.fastq.gz: No such file or directory
gzip: S*_R1_007.f…
updated 3.9 years ago • ipalmisa
can not be indexed directly because the file is not `BGZIP` compressed.
The file is gzipped with `x-gzip` aplication. Therefore, I tried to unzip it using `gzip -dc` command in order to perform `BGZIP` compression but it tells me that...the file not in gzip format. From some explanations of diffrence between `gzip` and `x-gzip` formats seems that they are equivalent.
Any suggestions
updated 5 months ago • Katsiaryna
have a transcriptome data of 10.8gb R1.fastq and R2.fastq each. I then compressed these pairs using `gzip R1.fastq` and `gzip R2.fast2`, and now the files are 2.2gb and 2.4gb. Is it possible for two compressed files to have different
SRA RNA-seq data at ones, buy don't know how. Thanks in advance
```
--fastq-dump SRR12491510 --gzip --split-3
--fastq-dump SRR12491509 --gzip --split-3
...
--fastq-dump SRR12491506 --gzip --split-3
```
↓↓↓
want to change like
--fastq-dump SRR12491510...SRR12491509 ... SRR12491506 --gzip --split-3
updated 16 months ago • wyt1995
tar -xvzf sratoolkit.3.0.0-ubuntu64.tar.gz´
I have the following error:
/usr/bin/gzip: 1: ELF : not found
/usr/bin/gzip: 3: : not found
/usr/bin/gzip: 4: Syntax error: "(" unexpected
tar: Child returned status 2
tar: Error is not
updated 18 months ago • Vicente
error:
"[bgzip] Value too large for defined data type: largefile.vcf"
i tried to compress it using gzip, and it compressed it successfuly, anyways, when i tried to index the resulting largefile.vcf.gz from the gzip compression...i got an error because it is a GZIP file, and not a BGZIP file which is the one needed.
anyone knows why bgzip tool finds the value to large, and not the gzip tool
updated 6.4 years ago • ricfoz
I would like to use another compression algorithm on fastq files than gzip for long term storage. Decompressing and re compressing could free about half the disk space I am using, which would save...It boasts very good compression rates (about twice smaller compressed files when compared to gzip), is fast enough, installs easily.
**Now these are important data, so I need to be sure that in 2 or …
updated 20 months ago • Eric Normandeau
GEO, unpack the .tar file, and read it into scanpy.
!tar -xzf GSE159115_RAW.tar
Traceback:
gzip: stdin: not in gzip format
tar: Child returned status 1
tar: Error is not recoverable: exiting now
[1]: https://www.ncbi.nlm.nih.gov
a single .fastq.gz file from many .fastq.gz files with the following command
zcat 15_S15*.fastq.gz | gzip -c > combined_file.fastq.gz
* I like to keep my original fastq.gz files and create a combined fastq.gz file, that's why...using gzip -c
Now, I want to do it with gnu parallel command.
Anyone help me
BGZF block
Then, I tried to unzip the gz file as follows to check whether I can unzip it:
gzip -d ALL.2of4intersection.20100804.genotypes.vcf.gz
Again, there is an error as follows:
gzip: ALL.2of4intersection.20100804.genotypes.vcf.gz...invalid compressed data--crc error
gzip: ALL.2of4intersection.20100804.genotypes.vcf.gz: invalid compressed data--length error
It would be very helpf…
Greetings,
I'm working on a single cell datasets, sequenced using 10× chromium single-cell platform, which was deposited [here][1].
I have downloaded the barcodes, features and the count matrix and saved when in the same folder.
However, then trying to load them into an R object there is an error:
lung_rawc = Read10X(data.dir = "/home/rribeiro/scRNAseq_GSE136831/data")
Error …
updated 2.3 years ago • Rogerio Ribeiro
identifiers:
zcat 001_T1_1.fastq.gz | paste - - - - | sort -k1,1 -t " " | tr "\t" "\n" | gzip -c > 001_T1_1_sorted.fastq.gz
zcat 001_T1_2.fastq.gz | paste - - - - | sort -k1,1 -t " " | tr "\t" "\n" | gzip -c > 001_T1_2_sorted.fastq.gz
It
updated 2.2 years ago • dzisis1986
star.edu.sg/docs/software/clustalw-mpi-0.13.tar.gz" , i cnanot unzipped the file and the error said
gzip: stdin: not in gzip format
tar: Child returned status 1
tar: Error is not recoverable: exiting now
Thank you in advanced
updated 3.2 years ago • Maryam Sophea
Slicer
Slice a text file to smaller files by lines, with gzip compression for input/output supported. This tool can be used to slice big `FASTQ` files to smaller ones for parallel processing...files
slicer -i <input_file_name> -l <how_many_lines_per_slice> -o <output_dir>
# force gzip
slicer -i <input_file_name> -l <how_many_lines_per_slice> -o <o…
Dear all,
I have a Dockerfile image with gzip utilite:
FROM alpine
RUN apk update && apk add gzip
ENTRYPOINT ["unzip"]
Consider I have two fastq.gz files and I want...to unzip it using my image.
cwlVersion: v1.0
class: CommandLineTool
label: "gzip wrapper"
baseCommand: [unzip, -p]
requirements:
- class: InlineJavascript…
Hello,
I'm trying to run Hisat2 on 2 fastq files which are currently fastq.gz as downloaded from the servers of the people that did the sequencing for us.
When I try to run it though, even though my code specifies fastq.gz, I keep getting the error that the files are not gziped.
This is the code im using :
hisat2 -p 7 -x -known-splicesite-infile /usr/local/src/gtf.gtf mm10idx -1 WTCHG_284…
response. I get this error when trying to do `gunzip /vcf.gz` of the output of HaplotypeCaller:
```
gzip: /file: invalid compressed data--crc error
gzip: /file: invalid compressed data--length error
```
Anyone know what might be wrong
updated 4.5 years ago • vctrm67
CEL-Seq-pipeline-stable$ bc_demultiplex --out-dir test_out index sample_sheet_example.txt --not-gzip SRR9609653_1.fastq SRR9609653_2.fastq
usage: bc_demultiplex [-h] [--bc-index FILENAME] [--bc-seq-column N]
[--bc-index-used string...min-bc-quality N]
[--out-dir DIRNAME] [--is-gzip] [--not-gzip]
[--stats-file …
updated 4.1 years ago • yueli7
by different compressed block, but how to read it with biopython ?
from Bio import SeqIO
import gzip
from Bio import bgzf
import struct
import gzip
handle = bgzf.BgzfReader("Example.bam", "r")
print handle.read(100)
Thanks
in all three samples
$ vcf-isec -n +3 4751_97PASS.vcf.gz 4751_42PASS.vcf.gz 4751PASS.vcf.gz | gzip -c > 4751shared.vcf.gz &
2)Error
$ Leading or trailing space in attr_key-attr_value pairs is discouraged:
[Description...1]+ Done vcf-isec -n +3 4751_97PASS.vcf.gz 4751_42PASS.vcf.gz 4751PASS.vcf.gz | gzip -c > 4751shared.vcf.gz
updated 7.7 years ago • zengtony743
the .rfq file can be much smaller than .fq.gz, and the compressing time is usually less than 1/5 of gzip compression.
The biggest advantage is that the .rfq file can be further compressed with xz, which is based on LZMA algorithm
SLIDINGWINDOW:10:20 MINLEN:60, and I ran tophat and got this error:
prep_reads v2.1.1 (13b3420)
---------------------------
gzip: /lustre/beagle2/xyang/NB/Target/RNAseq/FastQ_trim/SRR1559168_1.fastq.gz: unexpected end of file
Error: qual length...13) differs from seq length (101) for fastq record SRR1559168.54082770!
gzip: stdout: Broken pipe
Is there a tool to fix…
updated 7.3 years ago • zz105
the grch38 assembly downloads it as a gz file, and it seems to take forever to expand, and using gzip on it at the command line also says "gzip: standard input is a terminal -- ignoring".
Does anyone have a recommendation on how
updated 3.5 years ago • ian_chiquier
bioinf sra/2.9.6
>
> cd /g100_work/IscrC_PanSV/NA20847
>
> fastq-dump --gzip SRR13606073
> fastq-dump --gzip SRR13606074
>
> cd /g100_work/IscrC_PanSV/NA20509
>
> fastq-dump --gzip SRR13606071...gt; fastq-dump --gzip SRR13606072
Sorry about the format but each fastq-dump is on a separate, new …
updated 2.1 years ago • Matteo Ungaro
bgzip files are backward compatible with gzip, but I have issues when using bgzip compressed vcf files with snpeff (java) or perl scripts that uses IO::Uncompress::Gunzip...after a few hundred lines aprox. I could be totally wrong but I was wondering if zlib (or whatever gzip compatible library they are using) is getting confused with the bgzip bloks and only processing one or a few of them leavi…
updated 3.1 years ago • Pablo Marin-Garcia
100%
/bin/tar: This does not look like a tar archive
gzip: stdin: not in gzip format
/bin/tar: Child returned status 1
/bin/tar: Error is not recoverable: exiting now
Download completed
updated 13 months ago • mbk0asis
clone https://github.com/lh3/bwa.git
cd bwa; make
./bwa index ref.fa
./bwa mem ref.fa read-se.fq.gz | gzip -3 > aln-se.sam.gz
./bwa mem ref.fa read1.fq read2.fq | gzip -3 > aln-pe.sam.gz
```
I face with yhis error:
[E::bwa_idx_load_from_disk
VCF/00-All.vcf.gz
When I try to gunzip the file:
gunzip -k 00-All.vcf.gz
I get the error:
gzip: 00-All.vcf.gz: invalid compressed data--crc error
gzip: 00-All.vcf.gz: invalid compressed data--length error
I tried to
zcat PAW*.fastq.gz > fld.fastq.gz, I encountered an error indicating that the files are not in gzip format. However, the files were basecalled by the ONT machine and have the .gz extension.
How can I resolve this issue and...ensure that the files are in the correct gzip format?
I tried to unzip them using gunzip but again error says the same
the following error when uncompressed.
```
[Tia@biopower2 Downloads]$ tar xvf carrot_genome.tgz
gzip: stdin has more than one entry--rest ignored
tar: Child returned status 2
tar: Error is not recoverable: exiting now
```
Error...with gunzip
```
[Tia@biopower2 Downloads]$ gunzip -c carrot_genome.tgz
gzip: carrot_genome.tgz has more than one entry--rest ignored
```
Any insights are appreciated
updated 22 months ago • tmart091
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