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biocorecrg / allele_specific_RNAseq

Allele Specific RNAseq
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Singularity path error #10

Closed Jacq3lin3 closed 4 years ago

Jacq3lin3 commented 4 years ago

Ciao Luca,

I have the following data that I downloaded as you wrote in the README

> cd /users/bpayer/jseverino/references 

> ls 
VCF
genome
asrnaseq-0.2.simg 

> ls VCF
mgp.v5.merged.indels.dbSNP142.normed.vcf.gz  
mgp.v5.merged.indels.dbSNP142.normed.vcf.gz.tbi

> ls genome
GRCm38_68.fa

And when I run singularity to mask the genome and make the new index file with:

singularity exec -e ./asrnaseq_0.2.simg parseVCF.py -1 CAST_EiJ -2 129S1_SvImJ -i VCF/mgp.v5.merged.snps_all.dbSNP142.vcf.gz -o VCF/CAST_EiJ-129S1_SvImJ.vcf -g genome/GRCm38_68.fa

I get the error:

ERROR  : Image path ./asrnaseq_0.2.simg doesn't exist: No such file or directory
ABORT  : Retval = 255

I believe this is a silly problem with my local PATH or my singularity not understanding where it is or what to do. Could you help me please figure it out? Cause on google I could not find any solution to this problem.

Thanks a lot! Jackie

PS: in your README you wrote singularity exec -e ./asrnaseq_0.2.**sif** but I think you meant simg anyway also with .sif I get the same error.

Jacq3lin3 commented 4 years ago

Extra info when I'm trying to debug:

which singularity
/usr/bin/singularity
Jacq3lin3 commented 4 years ago 
singularity exec -e asrnaseq-0.2.simg parseVCF.py -h
/.singularity.d/actions/exec: line 9: exec: parseVCF.py: not found
Jacq3lin3 commented 4 years ago 
> rm asrnaseq-0.2.simg 

> singularity pull docker://biocorecrg/asrnaseq:0.2
WARNING: pull for Docker Hub is not guaranteed to produce the
WARNING: same image on repeated pull. Use Singularity Registry
WARNING: (shub://) to pull exactly equivalent images.
Docker image path: index.docker.io/biocorecrg/asrnaseq:0.2
Cache folder set to /nfs/users/bpayer/jseverino/.singularity/docker
Importing: base Singularity environment
Exploding layer: sha256:1e74cf3ea8b17b29912c91cc0ea80b5d3aed0ffe25aa2c8d3d4b24c1454f7052.tar.gz
WARNING: Warning reading tar header: Ignoring malformed pax extended attribute
WARNING: Warning reading tar header: Ignoring malformed pax extended attribute
WARNING: Warning reading tar header: Ignoring malformed pax extended attribute
Exploding layer: sha256:e9092151f7a2491c0d2b42f59c1b8e2bf859ac6e53321eba7bb1017b2b3fe43f.tar.gz
Exploding layer: sha256:276898f99f7b162c4834f6e13978f98bfd5f377635cdc1416d1fe27d38b47820.tar.gz
Exploding layer: sha256:a521508fa11e33da609b8f0480253ef148b68b8beb56c0e409d0d207fda5a363.tar.gz
Exploding layer: sha256:61af738b4846d9ef2e9eea025fb44288da5b8c76e8289a4f9eb62a2beb58626e.tar.gz
Exploding layer: sha256:e518f22d2fe88cb8e3a813783655e7615b90d288ebd5e683e43b14c7769f69de.tar.gz
Exploding layer: sha256:a808f8bcd824acac4d82f9468a5b093eddc46a12468f99bab3c6191e9dd429ac.tar.gz
Exploding layer: sha256:7f4f7d6e8dc6d3bc92ecb3f182a4177c46653fcf4a4e3eaecdebdebd6eebcf5d.tar.gz
Exploding layer: sha256:3762fddd8cf345cbdd4413f62bf112b2a194c330803a1290e4582c26a357a2a6.tar.gz
Exploding layer: sha256:f5624c74d9d1c71e06ad4ca643f473e837b6696d5790a1c8c6c34fdbd1c5a52d.tar.gz
Exploding layer: sha256:047916eec6087fc7002822733b41d8b4f76e06cbfee36edee420f8e19730f858.tar.gz
Exploding layer: sha256:b0c85be337e40513d2c7cdd5760f24f66aa9f4e5b092f8de6ee10fbdd8c2a3bf.tar.gz
Exploding layer: sha256:d5f76c9d11f315a83cab863e8042317dc05769b7bfa9603f7f09428fcd0b0978.tar.gz
Exploding layer: sha256:7a9fddbdb3ca2e07ce37064c5ea6b42c0da570572c6c2580a153e2a6ced82b9d.tar.gz
Exploding layer: sha256:07f993c72f4b1c62324d5d7ce799cef664e8b08c5df1e85c19f5dc4944db92c4.tar.gz
Exploding layer: sha256:9385a7d7f89642d91499350880e6ab2a42bd31620bdce18cc307a10f8037475a.tar.gz
Exploding layer: sha256:d766cc541a45a81ec4823b4522ee7f961b2d2ec98584774410ad992cade39fd9.tar.gz
Exploding layer: sha256:ff4390cdd1a14ee619901d589ed9c24a2e79a58f42edb97ee27aa941357efa6d.tar.gz
Exploding layer: sha256:dbd74f6531c6809f24ba5cf13f151dc94174a9848cbe1d2daacc3702d764a708.tar.gz
Exploding layer: sha256:193e5a425e6baba6bb4d219a908e6e0e94fa4b69f2624446fb7240bc8adb38f6.tar.gz
Exploding layer: sha256:a4d7254676fb442fa47db40c1b7e31bb0a953b3b52729a3b219916d06cbdd11e.tar.gz
WARNING: Warning reading tar header: Ignoring malformed pax extended attribute
WARNING: Warning reading tar header: Ignoring malformed pax extended attribute
Exploding layer: sha256:682c399a9a404d74ee2fb669352db06c0583ba5b9a76f83e9bed0b590dbf7114.tar.gz
Exploding layer: sha256:fa9f9b526b080e6f5c15fc671c80d3b7c3b84ddb57b4fd1db7f27d0368413d7d.tar.gz
Exploding layer: sha256:7e98e8e2e69a1baea5a8e4df1fc657903304ed9cd8a8f84f98b24317bfe9c475.tar.gz
Exploding layer: sha256:2f764843722a65951befd0232dc7c453142a11911667cce6e419ac3dff10fa26.tar.gz
Exploding layer: sha256:23f4f9e84f759a26b8f6619ce5dfc8dc3bf1fd5409c7fb49e0aa69461a27483e.tar.gz
Exploding layer: sha256:af7d7f43af91468f02bd674b094241b28dbd771b43e2ece3443910f4466f9a96.tar.gz
Exploding layer: sha256:4019ac9f5add8089c2d325e5494f79c7003709675a6606b665a4ee2919fe129a.tar.gz
Exploding layer: sha256:659bb129c27e3a94ec86a3573e0151feeaa5b539ee4d330855cc744a45bb7ed2.tar.gz
Exploding layer: sha256:82dc04f02973797054d9342cbf9e76d7b662dd49666fe4392dfdc02db02a2214.tar.gz
Exploding layer: sha256:0ccda971165f6cc04f28e2c5473744e90608052c3efea7f9e41d1c803786dfef.tar.gz
Exploding layer: sha256:c405ff7807f644fbf52e9cc7e1f9be5f93047c8f50969aac47c973128a7233a2.tar.gz
Exploding layer: sha256:1ba0c4ee5bdaa2bd214aa8c19291351133d5b37ded319a4ba1ddf793332f0bca.tar.gz
Exploding layer: sha256:666aa5c4b2379d4a77a72eeb71ff7d339f86789614cb679b251cffd34a005cf8.tar.gz
Exploding layer: sha256:b80deb8653b6ecdff7a0c114b70d5ec3bacb0b2706c386652d7ea05b0efecb1e.tar.gz
Exploding layer: sha256:e9cc5fe1524b77d84efaeddc9f5f2e2c0094f8ce1e4684a3d0a3c678983e4e7b.tar.gz
Exploding layer: sha256:8724f5ad2d658704fdd085a307b5a29d4335ae998645985306e082ca9d3f5b9e.tar.gz
Exploding layer: sha256:64d5fffe30de559d3ea1667911a0b9269503861f9fe9b67343a54acce5b0adab.tar.gz
Exploding layer: sha256:50a9f30cc3de493b12fc5d286d68724759cf00238afdf92a5b51427ad1a4c1b1.tar.gz
Exploding layer: sha256:d025afd49c811f3c85a302cae781e8dae57f953b8bbd65f4ec8703696496b090.tar.gz
Exploding layer: sha256:b91f2e79c31a40a04440f0acad79fea1f3cdef4931d632dcff72f3feb5e0cd21.tar.gz
Exploding layer: sha256:87601171b862f02502065b86e85ba8dc1ffbd83cc94f435f7ea84f169d100604.tar.gz
Exploding layer: sha256:a7a203a6a58ff20dc04c0795b6d91431f69b72673d56d770e4312de72b1a2cb8.tar.gz
Exploding layer: sha256:62c7b653653b5e8512f03e714d794265b33fe717302516e9bd998bb7198d01df.tar.gz
Exploding layer: sha256:59413788692a89bbb1800b1d6a9fafcfe936d56eb27dd44f8951f659ec57b3ba.tar.gz
Exploding layer: sha256:895b58101263039843c13a11ea6e897b0c50c4bd3befd6b71174897d09704aae.tar.gz
Exploding layer: sha256:8980d97e12e17e94b8a7d9ee4fd33ec194ca7acd674bcc6476e9914217a06603.tar.gz
Exploding layer: sha256:78b4e3a92f13d0f7bf9cfba6fcd712ff880b96b2e274cea0a9db68fed21babc1.tar.gz
Exploding layer: sha256:7281e4360df3967a5b8f18bc4cf9c123d32cd04dbc967eeef5d81249d7fe6756.tar.gz
Exploding layer: sha256:5b24f2557431db9f143461d3556ee3301aed8e1f0b2c54d6b2b26b8b196bef50.tar.gz
Exploding layer: sha256:0617b4f4bad6c46f40a06c3c9978bed008dd8cff3315291565241057c0a0df03.tar.gz
Exploding layer: sha256:2f065bb30958dc9d289c75971dcea8912370ec6332fd4295bc1ebc1e47ab8ea7.tar.gz
Exploding layer: sha256:82149bffe93a22dd4f40fd933d984faa1bc31ddfba767d96d43bb41a15e96b7b.tar.gz
Exploding layer: sha256:544b258eb9d75afeeed1d57c780765b9a6d6acc2456d68c28a99a05621b13300.tar.gz
Exploding layer: sha256:58766450bc2b79f34a0330639abb5998feab862f4bd121414bb77916fa57ef22.tar.gz
Exploding layer: sha256:2cd310b8efc86833ab5b69250964e3e53ae520d2ed8d2fb87d5582d28b8dba5f.tar.gz
Exploding layer: sha256:7d47bc10104ea8d4565b1d61956e2495d48c2b3741a56c3cd6dddd7d3dd29fa2.tar.gz
Exploding layer: sha256:354cb08019a1087107b58ed2ca6238cdfebc9b5c02ab0c60e3796e13b93d0449.tar.gz
Exploding layer: sha256:430656ebcfd3e0cfbe473bc25d575f9e915a3361e5ec5a676d85764081336ef7.tar.gz
Exploding layer: sha256:e81604746a57456bee40b9c3aecf644fbdab64252309732006dfd9973d19b492.tar.gz
Exploding layer: sha256:7461dbdae613067f970a5ed88f7d17f1e2010fc7ebb38fbc1eb509e7bae76300.tar.gz
Exploding layer: sha256:0fb33f4109853f844e9fc7ca7c46917b12c48d5feac54deb9fe460371fbb58aa.tar.gz
WARNING: Building container as an unprivileged user. If you run this container as root
WARNING: it may be missing some functionality.
Building Singularity image...
Singularity container built: ./asrnaseq-0.2.simg
Cleaning up...
Done. Container is at: ./asrnaseq-0.2.simg
Jacq3lin3 commented 4 years ago

I think the parseVCF.py executable is not present inside the asrnaseq-0.2 image. Can it be possible?

singularity exec -e asrnaseq-0.2.sif python par [_TAB autocomplete_]
parallel   parted     partprobe  partx
Jacq3lin3 commented 4 years ago

Hi again,

I tried to launch the python parseVCF.py executable from the bin folder of this repo, but it can't find bedtools so I tried with my conda environment where I have bedtools-2.29.2 and execute again. I still get an error that it cannot find the output file CAST_EiJ-129S1_SvImJ.vcf, it crashes. I tried all my tricks to run this VCF parser, but I have no more ideas.

Is this step necessary anyway? The file CAST_EiJ-129S1_SvImJ.vcf it will be used in the variants parameter in the params.config file?

Thanks, Jackie

lucacozzuto commented 4 years ago

Hi Jackie, so first of all there is a problem of singularity version :). We should stick with one (and I'll put it in the README). I recommend the 3.2.1, you can load it using modules in your bash profile. The parseVCF.py file is inside the bin folder:

allele_specific_RNAseq/bin
Jacq3lin3 commented 4 years ago

SOLUTION to singluarity version problem

In my ~/.bashrcadd:

#use the new version of singularity

module use /software/as/el7.2/EasyBuild/CRG/modules/all
module load Singularity/3.2.1
> singularity --version
singularity version 3.2.1-640.gcde5d98

Re-donwload singularity image file

> singularity pull docker://biocorecrg/asrnaseq:0.2
> ls
VCF  asrnaseq_0.2.sif  cas  genome  mus

Thanks Luca!