search

lskatz / mashtree

:deciduous_tree: Create a tree using Mash distances
GNU General Public License v3.0
148 stars 21 forks source link

mashtree: Mashtree::createTreeFromPhylip: Can't call method "as_text" on an undefined value #75

Open angeladelvalle opened 1 year ago

angeladelvalle commented 1 year ago

Hello, I am trying to use mashtree running the following command: mashtree --numcpus 4 *.fasta > mashtree.dnd

But I get this error:

mashtree: main: Found mash version 2 - /home/angelagarcia/mambaforge/envs/mashtree/bin/mash mashtree: main: Temporary directory will be /tmp/MASHTREE.TaArRu mashtree: main: mashtree on 2207 files mashtree: mashSketch(TID1): This thread will work on 552 sketches mashtree: mashSketch(TID1): Working on file 1 out of 552 sh: 1: Syntax error: "(" unexpected mashtree: mashSketch(TID1): ERROR running mash sketch -S 42 -k 21 -s 10000 -o /tmp/MASHTREE.TaArRu/PG-N1-014-CTX-21sta_02_1308_Col(KPHS6).fasta PG-N1-014-CTX-21sta_02_1308_Col(KPHS6).fasta 2>&1!

Thread 1 terminated abnormally: mashtree: main::mashSketch: Died Stopped at /home/angelagarcia/mambaforge/envs/mashtree/bin/mashtree line 320. mashtree: mashSketch(TID2): This thread will work on 552 sketches mashtree: mashSketch(TID2): Working on file 1 out of 552 sh: 1: Syntax error: "(" unexpected mashtree: mashSketch(TID2): ERROR running mash sketch -S 42 -k 21 -s 10000 -o /tmp/MASHTREE.TaArRu/2337sta_02_1433_Col(MG828).fasta 2337sta_02_1433_Col(MG828).fasta 2>&1!

Thread 2 terminated abnormally: mashtree: main::mashSketch: Died Stopped at /home/angelagarcia/mambaforge/envs/mashtree/bin/mashtree line 320. mashtree: mashSketch(TID3): This thread will work on 552 sketches mashtree: mashSketch(TID3): Working on file 1 out of 552 sh: 1: Syntax error: "(" unexpected mashtree: mashSketch(TID3): ERROR running mash sketch -S 42 -k 21 -s 10000 -o /tmp/MASHTREE.TaArRu/2455sta_02_1433_Col(MG828).fasta 2455sta_02_1433_Col(MG828).fasta 2>&1!

Thread 3 terminated abnormally: mashtree: main::mashSketch: Died Stopped at /home/angelagarcia/mambaforge/envs/mashtree/bin/mashtree line 320. mashtree: mashSketch(TID4): This thread will work on 551 sketches mashtree: mashSketch(TID4): Working on file 1 out of 551 sh: 1: Syntax error: "(" unexpected mashtree: mashSketch(TID4): ERROR running mash sketch -S 42 -k 21 -s 10000 -o /tmp/MASHTREE.TaArRu/2456sta_02_1433_Col(MG828).fasta 2456sta_02_1433_Col(MG828).fasta 2>&1!

Thread 4 terminated abnormally: mashtree: main::mashSketch: Died Stopped at /home/angelagarcia/mambaforge/envs/mashtree/bin/mashtree line 320. mashtree: mashDistance: Waiting to join thread (1/4, TID5) mashtree: mashDistance: Databasing distances (1/4, TID5) mashtree: mashDistance: Waiting to join thread (2/4, TID6) mashtree: mashDistance: Databasing distances (2/4, TID6) mashtree: mashDistance: Waiting to join thread (3/4, TID7) mashtree: mashDistance: Databasing distances (3/4, TID7) mashtree: mashDistance: Waiting to join thread (4/4, TID8) mashtree: mashDistance: Databasing distances (4/4, TID8) mashtree: mashDistance: Converting to phylip format into /tmp/MASHTREE.TaArRu/distances.phylip mashtree: Mashtree::createTreeFromPhylip: Can't call method "as_text" on an undefined value Stopped at /home/angelagarcia/mambaforge/envs/mashtree/lib/perl5/site_perl/Mashtree.pm line 217.

Could someone help me with it?

lskatz commented 10 months ago

Hi, please let me know if this is fixed with the newest version of Mashtree