SQMtools: loadSQM Error

[megberryman]

Hey guys!

I have successfully run SqueezeMeta in coassembly mode. I ran sqm2tables.py with /path/to/project/results/tables.

However, I am still getting "does not seem to contain a valid SqueezeMeta project"

Attached is the SqueezeMeta log file serial_test_58095398.log

I cannot find anything wrong. Any ideas?

[megberryman]

I am running R version 4.2.1 (2022-06-23) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Ventura 13.2.1 other attached packages: SQMtools_1.6.0

[fpusan]

What command are you using to load the project exactly? What files did you copy to your Mac computer?

[megberryman]

I copied the entire output squeezemeta output folder into two different external hard drives

I have tried: coassem = loadSQM("/Volumes/Berryman/coassembly_first20_0223") and coassem1 = loadSQM("/Volumes/easystore/coassembly_first20_0223/")

[fpusan]

So what happens if you do run ls /Volumes/Berryman/coassembly_first20_0223 in the terminal? How about ls /Volumes/easystore/coassembly_first20_0223/?

[megberryman]

ls -l /Volumes/Berryman/coassembly_first20_0223 total 5632 -rwxrwxrwx 1 meghanberryman staff 2582 Feb 23 09:32 SqueezeMeta_conf.pl.gz drwxrwxrwx 1 meghanberryman staff 131072 Feb 25 14:28 data drwxrwxrwx 1 meghanberryman staff 131072 Feb 27 10:28 ext_tables drwxrwxrwx 1 meghanberryman staff 131072 Feb 27 10:28 intermediate -rwxrwxrwx 1 meghanberryman staff 867 Feb 25 17:51 methods.txt.gz -rwxrwxrwx 1 meghanberryman staff 3289 Feb 23 09:32 parameters.pl -rwxrwxrwx@ 1 meghanberryman staff 384 Mar 3 12:07 progress -rwxrwxrwx@ 1 meghanberryman staff 274 Feb 25 17:52 progress.gz drwxrwxrwx 1 meghanberryman staff 131072 Feb 27 09:34 results -rwxrwxrwx@ 1 meghanberryman staff 1108884 Mar 3 12:05 syslog -rwxrwxrwx@ 1 meghanberryman staff 36060 Feb 25 17:52 syslog.gz drwxrwxrwx 1 meghanberryman staff 393216 Feb 25 17:51 temp

ls -l /Volumes/easystore/coassembly_first20_0223 total 128 -rwxr-xr-x 1 meghanberryman staff 2582 Mar 3 13:04 SqueezeMeta_conf.pl.gz drwxr-xr-x 1 meghanberryman staff 4096 Mar 7 21:16 data drwxr-xr-x 1 meghanberryman staff 0 Mar 3 13:04 ext_tables drwxr-xr-x 1 meghanberryman staff 4096 Mar 3 13:04 intermediate -rwxr-xr-x 1 meghanberryman staff 867 Mar 8 22:17 methods.txt.gz -rwxr-xr-x 1 meghanberryman staff 3289 Mar 7 21:16 parameters.pl -rwxr-xr-x 1 meghanberryman staff 274 Mar 3 13:04 progress.gz drwxr-xr-x 1 meghanberryman staff 4096 Mar 7 21:48 results -rwxr-xr-x 1 meghanberryman staff 36060 Mar 8 22:17 syslog.gz drwxr-xr-x 1 meghanberryman staff 626688 Mar 8 22:17 temp

*** I had some trouble transfer the files to /Berryman, which is why I tried to transfer to the other /easystore

[fpusan]

SqueezeMeta_conf.pl.gz this file is compressed, and it shouldn't be. That's why SQMtools is not detecting the project.

[megberryman]

Agh! Thank you!

[megberryman]

I am getting this error now:

Error in file(file, "rt") : cannot open the connection In addition: Warning message: In file(file, "rt") : cannot open file '/Volumes/Berryman/coassembly_first20_0223/intermediate/18.coassembly_first20_0223.contigsinbins': No such file or directory

[megberryman]

It looks like everything in /intermediate/ is gzipped

[fpusan]

Yeah no files should be gzipped

El jue., 16 mar. 2023 17:19, megberryman @.***> escribió:

It looks like everything in /intermediate/ is gzipped

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[fpusan]

We have just released v1.6.2, which greatly simplifies transferring SqueezeMeta projects between different computers and installing SQMtools locally.

[fpusan]

Closing due to lack of activity, feel free to reopen!