Hello,
after installing SqueezeMeta and running test_install.pl without any warning or error I have run the test.mock.samples example without problems. However, when running the test.samples case, in STEP 17 I get the following error (reproduced with the --restart option):
Command: SqueezeMeta.pl -m coassembly -p Hadza_real -s test.samples -f raw --restart
SqueezeMeta v1.7.2, June 2025 - (c) J. Tamames, F. Puente-Sánchez CNB-CSIC, Madrid, SPAIN
Please cite: Tamames & Puente-Sánchez, Frontiers in Microbiology 9, 3349 (2019). doi: https://doi.org/10.3389/fmicb.2018.03349
Run started Thu Apr 16 11:42:33 2026 in coassembly mode
2 metagenomes found: SRR1927149 SRR1929485
(all previous steps were skipped since they were already completed in previous executions)
[3 seconds]: STEP17 -> CHECKING BINS: 17.checkbins.pl
Evaluating bins with CheckM2 (Chklovski et al 2023, Nat Met 20, 1203-12)
Error running command: /home/saferr03/miniconda3/envs/SqueezeMeta/SqueezeMeta/bin/checkm2 predict -i /mnt/datos/usuarios/saferr03/db/test/Hadza_real/results/bins -o /mnt/datos/usuarios/saferr03/db/test/Hadza_real/intermediate/checkm2 -t 12 -x fa >> /mnt/datosermediate/checkm2 -t 12 -x fa >> /mnt/datos/usuarios/saferr03/db/test/Hadza_real/syslog 2>&1 at /home/saferr03/miniconda3/envs/SqueezeMeta/SqueezeMeta/scripts/17.checkbins.pl line 62.
Stopping in STEP17 -> 17.checkbins.pl
Died at /home/saferr03/miniconda3/envs/SqueezeMeta/bin/SqueezeMeta.pl line 900.
Hello,
after installing SqueezeMeta and running test_install.pl without any warning or error I have run the test.mock.samples example without problems. However, when running the test.samples case, in STEP 17 I get the following error (reproduced with the --restart option):
Command: SqueezeMeta.pl -m coassembly -p Hadza_real -s test.samples -f raw --restart
SqueezeMeta v1.7.2, June 2025 - (c) J. Tamames, F. Puente-Sánchez CNB-CSIC, Madrid, SPAIN
Please cite: Tamames & Puente-Sánchez, Frontiers in Microbiology 9, 3349 (2019). doi: https://doi.org/10.3389/fmicb.2018.03349
Run started Thu Apr 16 11:42:33 2026 in coassembly mode
2 metagenomes found: SRR1927149 SRR1929485
(all previous steps were skipped since they were already completed in previous executions)
[3 seconds]: STEP17 -> CHECKING BINS: 17.checkbins.pl
Evaluating bins with CheckM2 (Chklovski et al 2023, Nat Met 20, 1203-12)
Error running command: /home/saferr03/miniconda3/envs/SqueezeMeta/SqueezeMeta/bin/checkm2 predict -i /mnt/datos/usuarios/saferr03/db/test/Hadza_real/results/bins -o /mnt/datos/usuarios/saferr03/db/test/Hadza_real/intermediate/checkm2 -t 12 -x fa >> /mnt/datosermediate/checkm2 -t 12 -x fa >> /mnt/datos/usuarios/saferr03/db/test/Hadza_real/syslog 2>&1 at /home/saferr03/miniconda3/envs/SqueezeMeta/SqueezeMeta/scripts/17.checkbins.pl line 62.
Stopping in STEP17 -> 17.checkbins.pl
Died at /home/saferr03/miniconda3/envs/SqueezeMeta/bin/SqueezeMeta.pl line 900.