Error with gzipped FASTA file in mash.

Question

[Neel]

Hi i am trying to run mashtree to calculate WGS distance and i encountered this error by using following commands. If anyone know anything about this error, please let me know.

## mashtree_bootstrap.pl --reps 100 --numcpus 30 *.fna.gz -- --min-depth 0 > mashtree.bootstrap.dnd##

Use of uninitialized value $dist in concatenation (.) or string at /home/bvs/anaconda3/envs/myenv/lib/site_perl/5.26.2/Mashtree/Db.pm line 263. Use of uninitialized value $dist in concatenation (.) or string at /home/bvs/anaconda3/envs/myenv/lib/site_perl/5.26.2/Mashtree/Db.pm line 263. Use of uninitialized value $dist in concatenation (.) or string at /home/bvs/anaconda3/envs/myenv/lib/site_perl/5.26.2/Mashtree/Db.pm line 263. Use of uninitialized value $dist in concatenation (.) or string at /home/bvs/anaconda3/envs/myenv/lib/site_perl/5.26.2/Mashtree/Db.pm line 263. Use of uninitialized value $dist in concatenation (.) or string at /home/bvs/anaconda3/envs/myenv/lib/site_perl/5.26.2/Mashtree/Db.pm line 263. Use of uninitialized value $dist in concatenation (.) or string at /home/bvs/anaconda3/envs/myenv/lib/site_perl/5.26.2/Mashtree/Db.pm line 263. Use of uninitialized value $dist in concatenation (.) or string at /home/bvs/anaconda3/envs/myenv/lib/site_perl/5.26.2/Mashtree/Db.pm line 263. Use of uninitialized value $dist in concatenation (.) or string at /home/bvs/anaconda3/envs/myenv/lib/site_perl/5.26.2/Mashtree/Db.pm line 263. Use of uninitialized value $dist in concatenation (.) or string at /home/bvs/anaconda3/envs/myenv/lib/site_perl/5.26.2/Mashtree/Db.pm line 263. Use of uninitialized value $dist in concatenation (.) or string at /home/bvs/anaconda3/envs/myenv/lib/site_perl/5.26.2/Mashtree/Db.pm line 263. Use of uninitialized value $dist in concatenation (.) or string at /home/bvs/anaconda3/envs/myenv/lib/site_perl/5.26.2/Mashtree/Db.pm line 263. Use of uninitialized value $dist in concatenation (.) or string at /home/bvs/anaconda3/envs/myenv/lib/site_perl/5.26.2/Mashtree/Db.pm line 263. mashtree_bootstrap.pl: main: Running mashtree single-threaded among 100 replicates using 30 total threads. mashtree_bootstrap.pl: mashtreeRepWorker(TID1): Rep 0 mashtree_bootstrap.pl: mashtreeRepWorker(TID2): Rep 1 mashtree_bootstrap.pl: mashtreeRepWorker(TID3): Rep 2 mashtree_bootstrap.pl: mashtreeRepWorker(TID4): Rep 3 mashtree_bootstrap.pl: mashtreeRepWorker(TID5): Rep 4 mashtree_bootstrap.pl: mashtreeRepWorker(TID6): Rep 5 mashtree_bootstrap.pl: mashtreeRepWorker(TID7): Rep 6 mashtree_bootstrap.pl: mashtreeRepWorker(TID8): Rep 7 mashtree_bootstrap.pl: mashtreeRepWorker(TID9): Rep 8 mashtree_bootstrap.pl: mashtreeRepWorker(TID10): Rep 9 mashtree_bootstrap.pl: mashtreeRepWorker(TID11): Rep 10 Thread 1 terminated abnormally: mashtree_bootstrap.pl: main::mashtreeRepWorker: ERROR on rep 0 mashtree: main: Found mash version 2 - /home/bvs/neelam/mash/mash mashtree: main: Temporary directory will be /tmp/MASHTREE_BOOTSTRAP.il93zT/0 mashtree: main: mashtree on 359 files mashtree: mashSketch(TID1): This thread will work on 359 sketches mashtree: mashSketch(TID1): Working on file 1 out of 359

gzip: P_aeruginosa_12-4-4_59.fna.gz: not in gzip format Thread 1 terminated abnormally: mashtree: main::mashSketch: ERROR with gzip -cd P_aeruginosa_12-4-4_59.fna.gz Stopped at /home/bvs/anaconda3/envs/myenv/bin/mashtree line 236. mashtree: mashDistance: Waiting to join thread (1/1, TID2) mashtree: mashDistance: Databasing distances (1/1, TID2) mashtree: mashDistance: Converting to phylip format into /tmp/MASHTREE_BOOTSTRAP.il93zT/0/distances.phylip mashtree: Mashtree::createTreeFromPhylip: Can't call method "as_text" on an undefined value Stopped

Thank you!

[cpad0112]

Please type file P_aeruginosa_12-4-4_59.fna.gz in gnu-linux OS and post the output here.

[Neel]

Thank you so much for your time...Now it solve.

Answer 1

[Michael]

I have highlighted the significant portion of the error message. It is likely that you simply have to download the fna.gz file. It is likely damaged or not in gzip format. Try to download it again using wget or curl. If you are unsure of its format try to gzip -t it manually.

[Neel]

Thank you it was very helpful. Now it solve.