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lgmgeo / AnnotSV

Annotation and Ranking of Structural Variation
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make: *** [install-human-annotation] Error 2 #136

Closed CLAIRE-cuhk closed 2 years ago

CLAIRE-cuhk commented 2 years ago

Hi,

I am trying to install AnnotSV. The make PREFIX=. install-mouse-annotation worked fine, but then I got a gzip error with make PREFIX=. install-human-annotation.

$make PREFIX=. install-human-annotation

Download Exomiser supporting data files:

curl -C - -LO https://www.lbgi.fr/~geoffroy/Annotations/2109_hg19.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 111M 100 111M 0 0 3408k 0 0:00:33 0:00:33 --:--:-- 7292k curl -C - -LO https://data.monarchinitiative.org/exomiser/data/2109_phenotype.zip % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 2674M 100 2674M 0 0 139M 0 0:00:19 0:00:19 --:--:-- 150M

Installation of Exomiser data:

install -d -p ./share/AnnotSV/Annotations_Exomiser/2109 tar -xf 2109_hg19.tar.gz -C ./share/AnnotSV/Annotations_Exomiser/2109/ unzip 2109_phenotype.zip -d ./share/AnnotSV/Annotations_Exomiser/2109/ Archive: 2109_phenotype.zip creating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/ inflating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/2109_phenotype.h2.db
inflating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/hp.obo
inflating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/rw_string_10.mv
creating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/phenix/ creating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/phenix/out/ inflating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/phenix/out/4.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/phenix/out/10.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/phenix/out/20.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/phenix/out/17_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/phenix/out/3_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/phenix/out/15.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/phenix/out/11.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/phenix/out/4_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/phenix/out/16.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/phenix/out/5_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/phenix/out/12.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/phenix/out/12_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/phenix/out/17.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/phenix/out/13.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/phenix/out/11_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/phenix/out/15_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/phenix/out/14_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/phenix/out/16_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/phenix/out/18.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/phenix/out/7_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/phenix/out/14.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/phenix/out/10_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/phenix/out/3.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/phenix/out/19.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/phenix/out/18_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/phenix/out/2.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/phenix/out/9_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/phenix/out/9.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/phenix/out/1.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/phenix/out/20_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/phenix/out/8.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/phenix/out/7.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/phenix/out/2_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/phenix/out/6_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/phenix/out/13_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/phenix/out/6.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/phenix/out/8_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/phenix/out/1_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/phenix/out/19_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/phenix/out/5.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/phenix/hp.obo
inflating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype/phenix/ALL_SOURCES_ALL_FREQUENCIES_genes_to_phenotype.txt inflating: ./share/AnnotSV/Annotations_Exomiser/2109/2109_phenotype.sha256
/bin/rm -rf 2109_phenotype.zip /bin/rm -rf 2109_hg19.tar.gz

--> Exomiser data installed

Installation of human annotation:

tar -xf Annotations_Human_3.1.2.tar.gz -C ./share/AnnotSV/

gzip: stdin: unexpected end of file tar: Unexpected EOF in archive tar: Unexpected EOF in archive tar: Error is not recoverable: exiting now make: *** [install-human-annotation] Error 2

Can you please check this and help me out？

Thanks in advance.

lgmgeo commented 2 years ago

Hi Claire,

I just tried a new install on my server, everything seems OK on my side: image ... image

Can you show me the result of the following commands:

ls -l Annotations_Human_3.1.2.tar.gz
ls -l ./share/AnnotSV/

Next, can you show me the result of the following command:

curl -C - -LO https://www.lbgi.fr/~geoffroy/Annotations/Annotations_Human_3.1.2.tar.gz

Best, Véronique

CLAIRE-cuhk commented 2 years ago

Hi Véronique,

Thank you so much for your reply. Here are the results: [@login12 ~/Scratch/bioinfo_tools/AnnotSV/AnnotSV]$ls -l Annotations_Human_3.1.2.tar.gz -rw-r--r-- 1 ucnvlw0 ucnvpc 2173675441 Aug 15 23:24 Annotations_Human_3.1.2.tar.gz [@login12 ~/Scratch/bioinfo_tools/AnnotSV/AnnotSV]$ls -l ./share/AnnotSV/ total 16 drwxr-xr-x 3 ucnvpc 4096 Aug 15 17:52 Annotations_Exomiser drwxr-xr-x 3 ucnvpc 4096 Jul 10 21:54 Annotations_Human drwxr-xr-x 9 ucnvpc 4096 Jul 10 21:56 Annotations_Mouse drwxr-xr-x 2 ucnvpc 4096 Aug 15 17:06 jar [@login12 ~/Scratch/bioinfo_tools/AnnotSV/AnnotSV]$curl -C - -LO https://www.lbgi.fr/~geoffroy/Annotations/Annotations_Human_3.1.2.tar.gz ** Resuming transfer from byte position 2173675441 % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 curl: (33) HTTP server doesn't seem to support byte ranges. Cannot resume.

Many thanks. Claire

Geoffroy Véronique @.***> 于2022年8月16日周二 03:14写道：

Hi Claire,

I just tried a new install on my server, everything seems OK on my side: [image: image] https://user-images.githubusercontent.com/49909073/184700691-ec1b5224-0190-4fc3-a6d4-0ed7752e9378.png ... [image: image] https://user-images.githubusercontent.com/49909073/184700773-485dc5b6-fe32-484f-84b4-b8b2c50a4be8.png

Can you show me the result of the following commands:

ls -l Annotations_Human_3.1.2.tar.gz

ls -l ./share/AnnotSV/

Next, can you show me the result of the following command:

curl -C - -LO https://www.lbgi.fr/~geoffroy/Annotations/Annotations_Human_3.1.2.tar.gz

Best, Véronique

— Reply to this email directly, view it on GitHub https://github.com/lgmgeo/AnnotSV/issues/136#issuecomment-1215629375, or unsubscribe https://github.com/notifications/unsubscribe-auth/APORZ4B4PXCW3RCA2TU3ZATVZKJJ7ANCNFSM56TAJJCA . You are receiving this because you authored the thread.Message ID: @.***>

lgmgeo commented 2 years ago

Hi Claire,

The size of your file Annotations_Human_3.1.2.tar.gz is correct (2173675441). So I'm quite surprised by your error message ("gzip: stdin: unexpected end of file"). Can you run the following command:

tar -xf Annotations_Human_3.1.2.tar.gz -C ./share/AnnotSV/

Do you still have the same message? If yes, can you redo the following steps:

rm Annotations_Human_3.1.2.tar.gz
curl -C - -LO https://www.lbgi.fr/~geoffroy/Annotations/Annotations_Human_3.1.2.tar.gz
tar -xf Annotations_Human_3.1.2.tar.gz -C ./share/AnnotSV/

In my opinion, the bug is in curl. But I don't really understand... On my side, I use an old curl version: image

Véronique

lgmgeo commented 2 years ago

cf "Curl : (33) HTTP server doesn't seem to support byte ranges. Cannot resume."

"Existing file will not tell you if complete or incomplete, which is the cause of the bug. " "It's not the bug explanation but a quick workaround to solve the problem and continue"

CLAIRE-cuhk commented 2 years ago

Hi Véronique,

I just repeated this command make PREFIX=. install-human-annotation, and the package was installed successfully. Thank you so much.

Installation of human annotation:

tar -xf Annotations_Human_3.1.2.tar.gz -C ./share/AnnotSV/ /bin/rm -rf Annotations_Human_3.1.2.tar.gz

--> Human annotation installed

Great thanks.

lgmgeo commented 2 years ago

Great! Have fun with AnnotSV ;o)