search

wbaopaul / scATAC-pro

A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
MIT License
70 stars 24 forks source link

Cannot pull the singularity #61

Closed Puriney closed 1 year ago

Puriney commented 1 year ago

Hello Wenbao, I cannot pull the singularity (either latest or 1.5.0). It stuck at INFO: Creating SIF file.... It did not generate the SIF file at all.

But I can pull the singularity 1.4.4 singularity pull -F docker://wbaopaul/scatac-pro:1.4.4 and successfully creates the SIF file. 

$ singularity --version
singularity-ce version 3.9.2

Could you try to pull at your side to see if works?

wbaopaul commented 1 year ago

Yes. It works at my side (BTW, my singularity is v3.7.0 and I submitted the pull script as a slurm job).

Puriney commented 1 year ago

How much time does it take you to pull? My server admin also cannot pull it. Very strange.

Puriney commented 1 year ago

Any these log file would help? 

INFO:    Converting OCI blobs to SIF format
INFO:    Starting build...
Getting image source signatures
Copying blob sha256:eaead16dc43bb8811d4ff450935d607f9ba4baffda4fc110cc402fa43f601d83
Copying blob sha256:bd581af1c794265c30e97d59c02f9ef45ca16426bb2df62269a8058ff244a0e7
Copying blob sha256:a2c88c02d9fd51ea4bad3da279a8615619f309dc401882f62386e96240b4a56a
Copying blob sha256:05fb4d365fbbec57d108bcd8a1b67cf215d3b75231f4cf93162739ded082c7af
Copying blob sha256:79b60a1cb68089dce3ee5e31364bedec2eb01166f41ea24bbe6ed1e07d55d541
Copying blob sha256:ad1737219bf9488e2e9f89e4488e41c8f2160c4d6e6f00bbe8d4fd3f79f14f6d
Copying blob sha256:83637e2c4392a38393044f169173206a8af714434a61b2fbc90613cdb46f73d3
Copying blob sha256:7014a12dee7009b90dcaabda3207ec1b218577f37b9756e6f503c74d929fd755
Copying blob sha256:0165958d54c81dbb09f67a501b4625a01e4b425bfc4f2d663256e313118b6d43
Copying blob sha256:b8f6c573b12a49c45a005ea8b1dcd97a8304bc4888b0b9312f55dbcfe1b98263
Copying blob sha256:fd3f59def311ffebdb236cfcd27adb1a299b9d76f7c53d0b3ac85d9083554775
Copying blob sha256:354330e629ba3af1abe08086d5ef68a6cb6c23194e8a86b7421ed7d81739b4ef
Copying blob sha256:2092635e2ae2acb6f0663f1f20d6e399c06acd5fb72796369774e4f122938759
Copying blob sha256:7f881d1f37bb36ab9df508f76456a3295b11f97a283d357518d28a64dc0b8265
Copying blob sha256:f8bab0a9a7444d5dbdc30875b562e2c4d3184d19f56fabca0fd4e89af2b75d93
Copying blob sha256:575095af9c926866e6a3f56007217836942ee326fbc10cb4ccd8d0c7d5eefa6b
Copying blob sha256:32293786da435d70ed25b8c7c4571fe73f1be39f3189dd7d3794c7b157fdbef8
Copying blob sha256:d81f43a0fbca3256ef9d01739d6266b08ae08ee9aa80ddb2932dbcb34f5c3e19
Copying blob sha256:ef416cf9fd9de225161f33532b13ac2d822642fdefe9458757c84d0b90fe0225
Copying blob sha256:c0bf1ef87925e74a56e9422a3e638d39d1390d0566ae7e1488e1dfea8e2b5855
Copying blob sha256:8e058f74494fab1b56bfc6aa2b411865204bb8ddbce9e224b39647b2a55a572b
Copying blob sha256:9c46bbac0bbd5117b31292d3087962973cc783465e30b3b1b2a3028b83a58789
Copying blob sha256:e1b27bad823908d1ed31bd18a7212e313f4492b9c1ad14a04a0bc4d9b701d2c0
Copying blob sha256:bae465a0c55317d4c2987db4895b641d8414103ab5c920abb326af60d1e33da0
Copying blob sha256:8a32451c8268f0249204e30c1dc019e1f5ca316b9b96a0f62361de9175e6b7a6
Copying blob sha256:0263d51cb214210c7ef8c53130c11f41b1bf0693a04c534c7d1dd1b3825fa461
Copying blob sha256:79e7497af3f5f5040fca5886e140cb152a0f0dc21aea5cbd2f2832aa2e282f36
Copying blob sha256:dc0e1945d43349e65d8876157520d770dc1ddc72538d3fa71db6f98f491b0f54
Copying blob sha256:e0a60fa4cb88be4aab1f20842ca328ff514d8bb3436da8ec4e90e0c46730ca29
Copying blob sha256:f3324eccf553d82346fc3f29ea21b5674728f1a6d50ecae25aff611e086644b2
Copying blob sha256:d4b154d9809455a0a7caeebc44f38b8e9c8ed9ab3f1fc618e0450204ee1d9b8e
Copying blob sha256:a20517db962f350ec6a1ad7af66e0e69566895be28dae641ec415ff4adb34f99
Copying blob sha256:11f934fe757b9632e49475380637766bf0f0094a412f687503e840abdaad556d
Copying blob sha256:e8d9ff34c8a57180ba604e7a13e845f780a060138123fe62c50e5c8086635067
Copying blob sha256:2604bd1bd7ce7f333d113264f46f3312aedabbd0771b679d41434baaff1decad
Copying blob sha256:ef4d73ec8d682085eb42c1b22da0e5531e6bf707309b56da8e476680a5925320
Copying blob sha256:1a8aa8e1060b4730a31ba09ab34320eddd5bc2644285f1ed07089024a80dd9b7
Copying blob sha256:601561ff26612653d94e9c3c295e5383a4e4dc2a755f4bdd77a95795a2ccb44b
Copying blob sha256:cc24c7218420f66b5187d09f957f192199a19a7fcf9c08b33443c317565b5221
Copying blob sha256:c08fbfc18fda9953ba06a81a6a9e03990e834201f282948bc7475007d4155bbf
Copying blob sha256:e002dc31ce91da0249481d9124d21487e01a6d55dc13d7dabcfe00bfe9f90f89
Copying blob sha256:66cb227c9c60352372c35aba21fc53d2d4c2f40a3e538a135983728292b61a41
Copying blob sha256:733c2373666cab380f82712b26619c792de76ce7cb63e788fae79eb7076cadd0
Copying blob sha256:c4c4c98f410efc33a6485b98c2ddb9d9642feabd1399250054dd28050a4107ac
Copying blob sha256:f5bf131cd535096cb86f4b96be71a86666335d3b1b3c369abe5b20edff8ef143
Copying blob sha256:cc1ae99e73b3b623a776d2801bf390349552a5abc6b6c73c1ae842c4fdbf9841
Copying blob sha256:ad70759f49827377c2ed06d23121d70014b3baedc73879bbc0a5b9c2a72ec8bf
Copying blob sha256:1422d95fbb5d76b52eb330e4d536bef140e8afab69aeccbeb266945683b52f14
Copying blob sha256:6658743776e2818a7efb2925835ac30f826d84da649b96ad0a8b2438667592ea
Copying config sha256:a95dfda48aeb2c8f6f455d98cec45dd5ea140ee48ceff6a2ab987f466dbcc29f
Writing manifest to image destination
Storing signatures
2022/11/08 11:27:54  info unpack layer: sha256:eaead16dc43bb8811d4ff450935d607f9ba4baffda4fc110cc402fa43f601d83
2022/11/08 11:27:55  info unpack layer: sha256:bd581af1c794265c30e97d59c02f9ef45ca16426bb2df62269a8058ff244a0e7
2022/11/08 11:28:10  info unpack layer: sha256:a2c88c02d9fd51ea4bad3da279a8615619f309dc401882f62386e96240b4a56a
2022/11/08 11:28:13  warn rootless{usr/lib/x86_64-linux-gnu/gstreamer1.0/gstreamer-1.0/gst-ptp-helper} ignoring (usually) harmless EPERM on setxattr "security.capability"
2022/11/08 11:28:15  info unpack layer: sha256:05fb4d365fbbec57d108bcd8a1b67cf215d3b75231f4cf93162739ded082c7af
2022/11/08 11:28:15  info unpack layer: sha256:79b60a1cb68089dce3ee5e31364bedec2eb01166f41ea24bbe6ed1e07d55d541
2022/11/08 11:28:15  info unpack layer: sha256:ad1737219bf9488e2e9f89e4488e41c8f2160c4d6e6f00bbe8d4fd3f79f14f6d
2022/11/08 11:28:15  info unpack layer: sha256:83637e2c4392a38393044f169173206a8af714434a61b2fbc90613cdb46f73d3
2022/11/08 11:29:30  info unpack layer: sha256:7014a12dee7009b90dcaabda3207ec1b218577f37b9756e6f503c74d929fd755
2022/11/08 11:29:30  info unpack layer: sha256:0165958d54c81dbb09f67a501b4625a01e4b425bfc4f2d663256e313118b6d43
2022/11/08 11:29:31  info unpack layer: sha256:b8f6c573b12a49c45a005ea8b1dcd97a8304bc4888b0b9312f55dbcfe1b98263
2022/11/08 11:29:33  info unpack layer: sha256:fd3f59def311ffebdb236cfcd27adb1a299b9d76f7c53d0b3ac85d9083554775
2022/11/08 11:29:33  info unpack layer: sha256:354330e629ba3af1abe08086d5ef68a6cb6c23194e8a86b7421ed7d81739b4ef
2022/11/08 11:29:41  info unpack layer: sha256:2092635e2ae2acb6f0663f1f20d6e399c06acd5fb72796369774e4f122938759
2022/11/08 11:29:41  info unpack layer: sha256:7f881d1f37bb36ab9df508f76456a3295b11f97a283d357518d28a64dc0b8265
2022/11/08 11:29:41  info unpack layer: sha256:f8bab0a9a7444d5dbdc30875b562e2c4d3184d19f56fabca0fd4e89af2b75d93
2022/11/08 11:29:46  info unpack layer: sha256:575095af9c926866e6a3f56007217836942ee326fbc10cb4ccd8d0c7d5eefa6b
2022/11/08 11:29:46  info unpack layer: sha256:32293786da435d70ed25b8c7c4571fe73f1be39f3189dd7d3794c7b157fdbef8
2022/11/08 11:29:46  info unpack layer: sha256:d81f43a0fbca3256ef9d01739d6266b08ae08ee9aa80ddb2932dbcb34f5c3e19
2022/11/08 11:29:46  info unpack layer: sha256:ef416cf9fd9de225161f33532b13ac2d822642fdefe9458757c84d0b90fe0225
2022/11/08 11:29:46  info unpack layer: sha256:c0bf1ef87925e74a56e9422a3e638d39d1390d0566ae7e1488e1dfea8e2b5855
2022/11/08 11:29:46  info unpack layer: sha256:8e058f74494fab1b56bfc6aa2b411865204bb8ddbce9e224b39647b2a55a572b
2022/11/08 11:29:46  info unpack layer: sha256:9c46bbac0bbd5117b31292d3087962973cc783465e30b3b1b2a3028b83a58789
2022/11/08 11:29:50  info unpack layer: sha256:e1b27bad823908d1ed31bd18a7212e313f4492b9c1ad14a04a0bc4d9b701d2c0
2022/11/08 11:29:50  info unpack layer: sha256:bae465a0c55317d4c2987db4895b641d8414103ab5c920abb326af60d1e33da0
2022/11/08 11:29:50  info unpack layer: sha256:8a32451c8268f0249204e30c1dc019e1f5ca316b9b96a0f62361de9175e6b7a6
2022/11/08 11:29:53  info unpack layer: sha256:0263d51cb214210c7ef8c53130c11f41b1bf0693a04c534c7d1dd1b3825fa461
2022/11/08 11:29:53  info unpack layer: sha256:79e7497af3f5f5040fca5886e140cb152a0f0dc21aea5cbd2f2832aa2e282f36
2022/11/08 11:29:53  info unpack layer: sha256:dc0e1945d43349e65d8876157520d770dc1ddc72538d3fa71db6f98f491b0f54
2022/11/08 11:29:58  info unpack layer: sha256:e0a60fa4cb88be4aab1f20842ca328ff514d8bb3436da8ec4e90e0c46730ca29
2022/11/08 11:29:58  info unpack layer: sha256:f3324eccf553d82346fc3f29ea21b5674728f1a6d50ecae25aff611e086644b2
2022/11/08 11:30:00  info unpack layer: sha256:d4b154d9809455a0a7caeebc44f38b8e9c8ed9ab3f1fc618e0450204ee1d9b8e
2022/11/08 11:30:01  info unpack layer: sha256:a20517db962f350ec6a1ad7af66e0e69566895be28dae641ec415ff4adb34f99
2022/11/08 11:30:04  info unpack layer: sha256:11f934fe757b9632e49475380637766bf0f0094a412f687503e840abdaad556d
2022/11/08 11:30:06  info unpack layer: sha256:e8d9ff34c8a57180ba604e7a13e845f780a060138123fe62c50e5c8086635067
2022/11/08 11:30:06  info unpack layer: sha256:2604bd1bd7ce7f333d113264f46f3312aedabbd0771b679d41434baaff1decad
2022/11/08 11:30:06  info unpack layer: sha256:ef4d73ec8d682085eb42c1b22da0e5531e6bf707309b56da8e476680a5925320
2022/11/08 11:30:06  info unpack layer: sha256:1a8aa8e1060b4730a31ba09ab34320eddd5bc2644285f1ed07089024a80dd9b7
2022/11/08 11:30:08  info unpack layer: sha256:601561ff26612653d94e9c3c295e5383a4e4dc2a755f4bdd77a95795a2ccb44b
2022/11/08 11:30:10  info unpack layer: sha256:cc24c7218420f66b5187d09f957f192199a19a7fcf9c08b33443c317565b5221
2022/11/08 11:30:10  info unpack layer: sha256:c08fbfc18fda9953ba06a81a6a9e03990e834201f282948bc7475007d4155bbf
2022/11/08 11:30:11  info unpack layer: sha256:e002dc31ce91da0249481d9124d21487e01a6d55dc13d7dabcfe00bfe9f90f89
2022/11/08 11:30:11  info unpack layer: sha256:66cb227c9c60352372c35aba21fc53d2d4c2f40a3e538a135983728292b61a41
2022/11/08 11:31:08  warn rootless{usr/local/bin/bedops/bin/bam2bed} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/08 11:31:08  warn rootless{usr/local/bin/bedops/bin/bam2bed_gnuParallel} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/08 11:31:08  warn rootless{usr/local/bin/bedops/bin/bam2bed_sge} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/08 11:31:08  warn rootless{usr/local/bin/bedops/bin/bam2bed_slurm} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/08 11:31:08  warn rootless{usr/local/bin/bedops/bin/bam2starch} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/08 11:31:08  warn rootless{usr/local/bin/bedops/bin/bam2starch_gnuParallel} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/08 11:31:08  warn rootless{usr/local/bin/bedops/bin/bam2starch_sge} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/08 11:31:08  warn rootless{usr/local/bin/bedops/bin/bam2starch_slurm} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/08 11:31:08  warn rootless{usr/local/bin/bedops/bin/bedextract} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/08 11:31:08  warn rootless{usr/local/bin/bedops/bin/bedmap} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/08 11:31:08  warn rootless{usr/local/bin/bedops/bin/bedops} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/08 11:31:09  warn rootless{usr/local/bin/bedops/bin/closest-features} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/08 11:31:09  warn rootless{usr/local/bin/bedops/bin/convert2bed} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/08 11:31:09  warn rootless{usr/local/bin/bedops/bin/gff2bed} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/08 11:31:09  warn rootless{usr/local/bin/bedops/bin/gff2starch} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/08 11:31:09  warn rootless{usr/local/bin/bedops/bin/gtf2bed} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/08 11:31:09  warn rootless{usr/local/bin/bedops/bin/gtf2starch} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/08 11:31:09  warn rootless{usr/local/bin/bedops/bin/gvf2bed} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/08 11:31:09  warn rootless{usr/local/bin/bedops/bin/gvf2starch} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/08 11:31:09  warn rootless{usr/local/bin/bedops/bin/psl2bed} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/08 11:31:09  warn rootless{usr/local/bin/bedops/bin/psl2starch} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/08 11:31:09  warn rootless{usr/local/bin/bedops/bin/rmsk2bed} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/08 11:31:09  warn rootless{usr/local/bin/bedops/bin/rmsk2starch} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/08 11:31:09  warn rootless{usr/local/bin/bedops/bin/sam2bed} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/08 11:31:09  warn rootless{usr/local/bin/bedops/bin/sam2starch} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/08 11:31:09  warn rootless{usr/local/bin/bedops/bin/sort-bed} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/08 11:31:09  warn rootless{usr/local/bin/bedops/bin/starch} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/08 11:31:09  warn rootless{usr/local/bin/bedops/bin/starch-diff} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/08 11:31:09  warn rootless{usr/local/bin/bedops/bin/starchcat} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/08 11:31:09  warn rootless{usr/local/bin/bedops/bin/starchcluster_gnuParallel} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/08 11:31:09  warn rootless{usr/local/bin/bedops/bin/starchcluster_sge} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/08 11:31:09  warn rootless{usr/local/bin/bedops/bin/starchcluster_slurm} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/08 11:31:09  warn rootless{usr/local/bin/bedops/bin/starchstrip} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/08 11:31:09  warn rootless{usr/local/bin/bedops/bin/unstarch} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/08 11:31:09  warn rootless{usr/local/bin/bedops/bin/update-sort-bed-migrate-candidates} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/08 11:31:09  warn rootless{usr/local/bin/bedops/bin/update-sort-bed-slurm} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/08 11:31:09  warn rootless{usr/local/bin/bedops/bin/update-sort-bed-starch-slurm} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/08 11:31:09  warn rootless{usr/local/bin/bedops/bin/vcf2bed} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/08 11:31:09  warn rootless{usr/local/bin/bedops/bin/vcf2starch} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/08 11:31:09  warn rootless{usr/local/bin/bedops/bin/wig2bed} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/08 11:31:09  warn rootless{usr/local/bin/bedops/bin/wig2starch} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2022/11/08 11:31:14  info unpack layer: sha256:733c2373666cab380f82712b26619c792de76ce7cb63e788fae79eb7076cadd0
2022/11/08 11:31:15  info unpack layer: sha256:c4c4c98f410efc33a6485b98c2ddb9d9642feabd1399250054dd28050a4107ac
2022/11/08 11:31:15  info unpack layer: sha256:f5bf131cd535096cb86f4b96be71a86666335d3b1b3c369abe5b20edff8ef143
2022/11/08 11:31:18  info unpack layer: sha256:cc1ae99e73b3b623a776d2801bf390349552a5abc6b6c73c1ae842c4fdbf9841
2022/11/08 11:31:21  info unpack layer: sha256:ad70759f49827377c2ed06d23121d70014b3baedc73879bbc0a5b9c2a72ec8bf
2022/11/08 11:31:22  info unpack layer: sha256:1422d95fbb5d76b52eb330e4d536bef140e8afab69aeccbeb266945683b52f14
2022/11/08 11:31:22  info unpack layer: sha256:6658743776e2818a7efb2925835ac30f826d84da649b96ad0a8b2438667592ea
INFO:    Creating SIF file...
wbaopaul commented 1 year ago

It took me 48 minutes and 10Gb memory. My log is similar to yours but I was able to generate the correct .sif file.

Puriney commented 1 year ago

Still cannot work.