DeepGraphGO data.zip extract failure

Hi,

I was trying to extract the data.zip file with unzip data.zip but failed. According to your suggestion, I installed dtrx and tried dtrx data.zip but got error messages as showing below:

ERROR:dtrx-log:Error output from this process: warning [/SAN/orengolab/plm_embeds/DeepGraphGO/data/data.zip]: zipfile claims to be last disk of a multi-part archive; attempting to process anyway, assuming all parts have been concatenated together in order. Expect "errors" and warnings...true multi-part support doesn't exist yet (coming soon). file #1: bad zipfile offset (local header sig): 4 file #2: bad zipfile offset (local header sig): 257014 file #3: bad zipfile offset (local header sig): 796021 file #4: bad zipfile offset (local header sig): 927401 file #5: bad zipfile offset (local header sig): 933560 file #6: bad zipfile offset (local header sig): 1280827 file #7: bad zipfile offset (local header sig): 1327275 file #8: bad zipfile offset (local header sig): 1332097 file #9: bad zipfile offset (local header sig): 24897202 file #10: bad zipfile offset (local header sig): 27849366 file #11: bad zipfile offset (local header sig): 28077466 file #12: bad zipfile offset (local header sig): 28386157 file #13: bad zipfile offset (local header sig): 28418537 file #14: bad zipfile offset (local header sig): 28422186 file #15: bad zipfile offset (local header sig): 28538584 file #16: bad zipfile offset (local header sig): 28550697 file #17: bad zipfile offset (local header sig): 28552456 file #18: bad zipfile offset (local header sig): 44545432 file #19: bad zipfile offset (local header sig): 46371598 file #20: bad zipfile offset (local header sig): 46530173 file #21: bad zipfile offset (local header sig): 46685192 file #22: bad zipfile offset (local header sig): 46699236 file #23: bad zipfile offset (local header sig): 46701245 file #24: bad zipfile offset (local header sig): 22113326 file #25: bad zipfile offset (local header sig): 23462683 file #26: bad zipfile offset (local header sig): 24518807 file #27: bad zipfile offset (lseek): 74645504 file #28: bad zipfile offset (lseek): 77291520 dtrx: ERROR: treating as 7z file failed: could not run 7z ERROR:dtrx-log:treating as 7z file failed: could not run 7z

Then, I tried zip -F data. zip and zip -FF data.zip to fix the zip file, and finally got files such as ppi_mat.npz. However, in the first line of the main function, I got this error: zipfile.BadZipFile: File is not a zip file

Could you please help me to solve this problem? Thank you!

Jun 18 '23 15:06 wlin16

It's strange. I tried dtrx again in my Ubuntu machine and it's work well. Could you please give me more information?

Jun 21 '23 15:06 yourh

If I do unzip data.zip:

Archive: data.zip warning [data.zip]: zipfile claims to be last disk of a multi-part archive; attempting to process anyway, assuming all parts have been concatenated together in order. Expect "errors" and warnings...true multi-part support doesn't exist yet (coming soon). file #1: bad zipfile offset (local header sig): 4 file #2: bad zipfile offset (local header sig): 257014 file #3: bad zipfile offset (local header sig): 796021 file #4: bad zipfile offset (local header sig): 927401 file #5: bad zipfile offset (local header sig): 933560 file #6: bad zipfile offset (local header sig): 1280827 file #7: bad zipfile offset (local header sig): 1327275 file #8: bad zipfile offset (local header sig): 1332097 file #9: bad zipfile offset (local header sig): 24897202 file #10: bad zipfile offset (local header sig): 27849366 file #11: bad zipfile offset (local header sig): 28077466 file #12: bad zipfile offset (local header sig): 28386157 file #13: bad zipfile offset (local header sig): 28418537 file #14: bad zipfile offset (local header sig): 28422186 file #15: bad zipfile offset (local header sig): 28538584 file #16: bad zipfile offset (local header sig): 28550697 file #17: bad zipfile offset (local header sig): 28552456 file #18: bad zipfile offset (local header sig): 44545432 file #19: bad zipfile offset (local header sig): 46371598 file #20: bad zipfile offset (local header sig): 46530173 file #21: bad zipfile offset (local header sig): 46685192 file #22: bad zipfile offset (local header sig): 46699236 file #23: bad zipfile offset (local header sig): 46701245 file #24: bad zipfile offset (local header sig): 22113326 file #25: bad zipfile offset (local header sig): 23462683 file #26: bad zipfile offset (local header sig): 24518807 file #27: bad zipfile offset (lseek): 74645504 file #28: bad zipfile offset (lseek): 77291520 replace ppi_pid_list.txt? [y]es, [n]o, [A]ll, [N]one, [r]ename: A inflating: ppi_pid_list.txt
inflating: bp_test.fasta
inflating: bp_test_go.txt
inflating: bp_test_pid_list.txt
inflating: bp_train.fasta
inflating: bp_train_go.txt

If I do dtrx data.zip dtrx: ERROR: could not handle data.zip ERROR:dtrx-log:could not handle data.zip dtrx: ERROR: treating as Zip file failed: extraction error: 'unzip -q home/DeepGraphGO/data/data.zip' returned status code 3 ERROR:dtrx-log:treating as Zip file failed: extraction error: 'unzip -q home/DeepGraphGO/data/data.zip' returned status code 3 dtrx: ERROR: Error output from this process: warning [home/DeepGraphGO/data/data.zip]: zipfile claims to be last disk of a multi-part archive; attempting to process anyway, assuming all parts have been concatenated together in order. Expect "errors" and warnings...true multi-part support doesn't exist yet (coming soon). file #1: bad zipfile offset (local header sig): 4 file #2: bad zipfile offset (local header sig): 257014 file #3: bad zipfile offset (local header sig): 796021 file #4: bad zipfile offset (local header sig): 927401 file #5: bad zipfile offset (local header sig): 933560 file #6: bad zipfile offset (local header sig): 1280827 file #7: bad zipfile offset (local header sig): 1327275 file #8: bad zipfile offset (local header sig): 1332097 file #9: bad zipfile offset (local header sig): 24897202 file #10: bad zipfile offset (local header sig): 27849366 file #11: bad zipfile offset (local header sig): 28077466 file #12: bad zipfile offset (local header sig): 28386157 file #13: bad zipfile offset (local header sig): 28418537 file #14: bad zipfile offset (local header sig): 28422186 file #15: bad zipfile offset (local header sig): 28538584 file #16: bad zipfile offset (local header sig): 28550697 file #17: bad zipfile offset (local header sig): 28552456 file #18: bad zipfile offset (local header sig): 44545432 file #19: bad zipfile offset (local header sig): 46371598 file #20: bad zipfile offset (local header sig): 46530173 file #21: bad zipfile offset (local header sig): 46685192 file #22: bad zipfile offset (local header sig): 46699236 file #23: bad zipfile offset (local header sig): 46701245 file #24: bad zipfile offset (local header sig): 22113326 file #25: bad zipfile offset (local header sig): 23462683 file #26: bad zipfile offset (local header sig): 24518807 file #27: bad zipfile offset (lseek): 74645504 file #28: bad zipfile offset (lseek): 77291520 ERROR:dtrx-log:Error output from this process: warning [home/DeepGraphGO/data/data.zip]: zipfile claims to be last disk of a multi-part archive; attempting to process anyway, assuming all parts have been concatenated together in order. Expect "errors" and warnings...true multi-part support doesn't exist yet (coming soon). file #1: bad zipfile offset (local header sig): 4 file #2: bad zipfile offset (local header sig): 257014 file #3: bad zipfile offset (local header sig): 796021 file #4: bad zipfile offset (local header sig): 927401 file #5: bad zipfile offset (local header sig): 933560 file #6: bad zipfile offset (local header sig): 1280827 file #7: bad zipfile offset (local header sig): 1327275 file #8: bad zipfile offset (local header sig): 1332097 file #9: bad zipfile offset (local header sig): 24897202 file #10: bad zipfile offset (local header sig): 27849366 file #11: bad zipfile offset (local header sig): 28077466 file #12: bad zipfile offset (local header sig): 28386157 file #13: bad zipfile offset (local header sig): 28418537 file #14: bad zipfile offset (local header sig): 28422186 file #15: bad zipfile offset (local header sig): 28538584 file #16: bad zipfile offset (local header sig): 28550697 file #17: bad zipfile offset (local header sig): 28552456 file #18: bad zipfile offset (local header sig): 44545432 file #19: bad zipfile offset (local header sig): 46371598 file #20: bad zipfile offset (local header sig): 46530173 file #21: bad zipfile offset (local header sig): 46685192 file #22: bad zipfile offset (local header sig): 46699236 file #23: bad zipfile offset (local header sig): 46701245 file #24: bad zipfile offset (local header sig): 22113326 file #25: bad zipfile offset (local header sig): 23462683 file #26: bad zipfile offset (local header sig): 24518807 file #27: bad zipfile offset (lseek): 74645504 file #28: bad zipfile offset (lseek): 77291520 dtrx: ERROR: treating as 7z file failed: could not run 7z ERROR:dtrx-log:treating as 7z file failed: could not run 7z

If it is possible, could you please send me the data in a data.tar.gz format?

Jun 21 '23 15:06 wlin16

OK, give me your e-mail address, but I'm not sure I can send a such large auxiliary.

Jun 22 '23 17:06 yourh

OK, give me your e-mail address, but I'm not sure I can send a such large auxiliary.

Thank you for your help! My email address is [email protected]. If a large auxiliary is not able to be sent via email, can you please send me your WeChat ID (if you have one) via email, then we can discuss other methods?

Jun 25 '23 11:06 wlin16

Hi, I have the same issue, have you update the data somewhere? Could you please share the data via any public path for data downloading or email? Thanks in advance

Sep 18 '23 10:09 KexinNiu