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geronimp / graftM

GraftM - Rapid community profiles from metagenomes
http://geronimp.github.io/graftM/
GNU General Public License v3.0
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Error with graft command #244

Closed SCarrSuperstar closed 6 years ago

SCarrSuperstar commented 6 years ago

Hi - I'm trying to get graft M up and running and I'm getting an error during the tree step. Any ideas? Thanks!

$ graftM graft --forward G3001R1.fastq --reverse G3001R2.fastq --graftm_package ../4.40.2013_08_greengenes_97_otus.with_euks.gpkg --out put_directory G3001graftM

01/22/2018 06:52:25 PM INFO: Working on G3001R1 01/22/2018 06:52:25 PM INFO: Working on forward reads 01/22/2018 07:00:47 PM INFO: 8758 read(s) detected 01/22/2018 07:00:47 PM INFO: aligning reads to reference package database 01/22/2018 07:03:45 PM INFO: Filtered 1061 short sequences from the alignment 01/22/2018 07:03:45 PM INFO: 7697 sequences remaining 01/22/2018 07:03:45 PM INFO: Working on reverse reads 01/22/2018 07:13:20 PM INFO: 8598 read(s) detected 01/22/2018 07:13:20 PM INFO: aligning reads to reference package database 01/22/2018 07:16:26 PM INFO: Filtered 1027 short sequences from the alignment 01/22/2018 07:16:26 PM INFO: 7571 sequences remaining 01/22/2018 07:16:26 PM INFO: Merging pair G3001R1_forward_hits.aln.fa, G3001R1reverse hits.aln.fa 01/22/2018 07:16:27 PM INFO: Placing reads into phylogenetic tree Traceback (most recent call last): File "/home/shaghaghis/.local/bin/graftM", line 444, in Run(args).main() File "/home/shaghaghis/.local/lib/python2.7/site-packages/graftm/run.py", line 588, i n main self.graft() File "/home/shaghaghis/.local/lib/python2.7/site-packages/graftm/run.py", line 492, i n graft clusterer) File "/home/shaghaghis/.local/lib/python2.7/site-packages/graftm/timeit.py", line 10, in timed result = method(*args, **kw) File "/home/shaghaghis/.local/lib/python2.7/site-packages/graftm/pplacer.py", line 18 1, in place jplace = self.pplacer(files.jplace_output_path(), args.output_directory, files.comb _aln_fa(), args.threads) File "/home/shaghaghis/.local/lib/python2.7/site-packages/graftm/pplacer.py", line 28 , in pplacer extern.run(cmd) File "/home/shaghaghis/.local/lib/python2.7/site-packages/extern/init.py", line 4 6, in run stdout) extern.ExternCalledProcessError: Command pplacer -j 5 --verbosity 0 --out-dir G3001graf tM -c ../4.40.2013_08_greengenes_97_otus.with_euks.gpkg/97_otus_with_euks.gpkg.refpkg G 3001graftM/combined_alignment.aln.fa returned non-zero exit status -9. STDERR was: STDOUT was:

wwood commented 6 years ago

Hi, apologies for the slow response here. There's nothing I can see that might be causing the problem. Can I ask what version of GraftM / pplacer is being used? Also, would you be able to send the contents of the output directory, perhaps via email as detailed at http://ecogenomic.org/personnel/dr-ben-woodcroft so we can have a look? Thanks, ben

SCarrSuperstar commented 6 years ago

Hi Ben!

Sorry, I should have returned to that note, we figured it out!! It was a memory issue - we just didn't have enough. We initiated a larger cloud instance and had no problem. There was a similar issue on the SupportM page, which helped us determine our issue.

What a fun and great tool!

wwood commented 6 years ago

Ah right, glad to you managed to fix it. Thanks for the encouraging comments.