Plugin error from fragment-insertion - CalledProcessError - run-sepp.sh - non-zero exit status 137

qiime fragment-insertion sepp \

–i-representative-sequences ./rep-seqs3.qza
–o-tree ./tree7.qza
–o-placements ./tree_placements7.qza
–p-threads 1
Plugin error from fragment-insertion:

Command ‘[‘run-sepp.sh’, ‘/tmp/qiime2-archive-b7szmydr/ebe47db0-cc01-46ba-a5cd-4728889777a0/data/dna-sequences.fasta’, ‘q2-fragment-insertion’, ‘-x’, ‘1’, ‘-A’, ‘1000’, ‘-P’, ‘5000’]’ returned non-zero exit status 137.

Debug info has been saved to /tmp/qiime2-q2cli-err-f1a1hpfq.log

Hi @Shaminur,

Could you please post the full debug long from your /tmp/qiime2-q2cli-err-f1a1hpfq.log file?

Thanks!
Justine

Thanks for contributing,
Here is the log file…

==> sepp-q2-fragment-insertion-err.log <==
[08:58:26] jobs.py (line 117):     INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp.9UyJ9extIn/sepp-tempssd-kOIp/q2-fragment-insertion.3pxhac5q/root/P_55/pplacer.backbone.h_vd8dpf.fasta, tree_file:/tmp/tmp.9UyJ9extIn/sepp-tempssd-kOIp/q2-fragment-insertion.3pxhac5q/root/P_55/pplacer.tree.bzki6oo1.tre, info_file:/home/qiime2/miniconda/envs/qiime2-2019.7/share/fragment-insertion//ref/RAxML_info-reference-gg-raxml-bl.info, extended alignment:/tmp/tmp.9UyJ9extIn/sepp-tempssd-kOIp/q2-fragment-insertion.3pxhac5q/root/P_55/pplacer.extended.0.lv3j8at4.fasta, output:/tmp/tmp.9UyJ9extIn/sepp-tempssd-kOIp/q2-fragment-insertion.3pxhac5q/root/P_55/pplacer.extended.0.lv3j8at4.jplace
[08:58:58] jobs.py (line 117):     INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp.9UyJ9extIn/sepp-tempssd-kOIp/q2-fragment-insertion.3pxhac5q/root/P_56/pplacer.backbone.qc_bsq3p.fasta, tree_file:/tmp/tmp.9UyJ9extIn/sepp-tempssd-kOIp/q2-fragment-insertion.3pxhac5q/root/P_56/pplacer.tree.4kch79e_.tre, info_file:/home/qiime2/miniconda/envs/qiime2-2019.7/share/fragment-insertion//ref/RAxML_info-reference-gg-raxml-bl.info, extended alignment:/tmp/tmp.9UyJ9extIn/sepp-tempssd-kOIp/q2-fragment-insertion.3pxhac5q/root/P_56/pplacer.extended.0.k6xc08tu.fasta, output:/tmp/tmp.9UyJ9extIn/sepp-tempssd-kOIp/q2-fragment-insertion.3pxhac5q/root/P_56/pplacer.extended.0.k6xc08tu.jplace
[08:59:52] jobs.py (line 117):     INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp.9UyJ9extIn/sepp-tempssd-kOIp/q2-fragment-insertion.3pxhac5q/root/P_57/pplacer.backbone.xlc0ioyl.fasta, tree_file:/tmp/tmp.9UyJ9extIn/sepp-tempssd-kOIp/q2-fragment-insertion.3pxhac5q/root/P_57/pplacer.tree.70ambmfh.tre, info_file:/home/qiime2/miniconda/envs/qiime2-2019.7/share/fragment-insertion//ref/RAxML_info-reference-gg-raxml-bl.info, extended alignment:/tmp/tmp.9UyJ9extIn/sepp-tempssd-kOIp/q2-fragment-insertion.3pxhac5q/root/P_57/pplacer.extended.0.xzk08k6a.fasta, output:/tmp/tmp.9UyJ9extIn/sepp-tempssd-kOIp/q2-fragment-insertion.3pxhac5q/root/P_57/pplacer.extended.0.xzk08k6a.jplace
[09:00:14] jobs.py (line 117):     INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp.9UyJ9extIn/sepp-tempssd-kOIp/q2-fragment-insertion.3pxhac5q/root/P_58/pplacer.backbone.m_6aujez.fasta, tree_file:/tmp/tmp.9UyJ9extIn/sepp-tempssd-kOIp/q2-fragment-insertion.3pxhac5q/root/P_58/pplacer.tree.lnd7k1xi.tre, info_file:/home/qiime2/miniconda/envs/qiime2-2019.7/share/fragment-insertion//ref/RAxML_info-reference-gg-raxml-bl.info, extended alignment:/tmp/tmp.9UyJ9extIn/sepp-tempssd-kOIp/q2-fragment-insertion.3pxhac5q/root/P_58/pplacer.extended.0.ov_3q7vg.fasta, output:/tmp/tmp.9UyJ9extIn/sepp-tempssd-kOIp/q2-fragment-insertion.3pxhac5q/root/P_58/pplacer.extended.0.ov_3q7vg.jplace
[09:01:03] jobs.py (line 117):     INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp.9UyJ9extIn/sepp-tempssd-kOIp/q2-fragment-insertion.3pxhac5q/root/P_59/pplacer.backbone.rdby3ho9.fasta, tree_file:/tmp/tmp.9UyJ9extIn/sepp-tempssd-kOIp/q2-fragment-insertion.3pxhac5q/root/P_59/pplacer.tree.e9nv327v.tre, info_file:/home/qiime2/miniconda/envs/qiime2-2019.7/share/fragment-insertion//ref/RAxML_info-reference-gg-raxml-bl.info, extended alignment:/tmp/tmp.9UyJ9extIn/sepp-tempssd-kOIp/q2-fragment-insertion.3pxhac5q/root/P_59/pplacer.extended.0.ljelnqrl.fasta, output:/tmp/tmp.9UyJ9extIn/sepp-tempssd-kOIp/q2-fragment-insertion.3pxhac5q/root/P_59/pplacer.extended.0.ljelnqrl.jplace
[09:01:14] jobs.py (line 117):     INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp.9UyJ9extIn/sepp-tempssd-kOIp/q2-fragment-insertion.3pxhac5q/root/P_60/pplacer.backbone.xwdpxr5e.fasta, tree_file:/tmp/tmp.9UyJ9extIn/sepp-tempssd-kOIp/q2-fragment-insertion.3pxhac5q/root/P_60/pplacer.tree.7ahile2l.tre, info_file:/home/qiime2/miniconda/envs/qiime2-2019.7/share/fragment-insertion//ref/RAxML_info-reference-gg-raxml-bl.info, extended alignment:/tmp/tmp.9UyJ9extIn/sepp-tempssd-kOIp/q2-fragment-insertion.3pxhac5q/root/P_60/pplacer.extended.0.e71mf1gk.fasta, output:/tmp/tmp.9UyJ9extIn/sepp-tempssd-kOIp/q2-fragment-insertion.3pxhac5q/root/P_60/pplacer.extended.0.e71mf1gk.jplace
[09:01:49] jobs.py (line 117):     INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp.9UyJ9extIn/sepp-tempssd-kOIp/q2-fragment-insertion.3pxhac5q/root/P_61/pplacer.backbone.lmxh8cey.fasta, tree_file:/tmp/tmp.9UyJ9extIn/sepp-tempssd-kOIp/q2-fragment-insertion.3pxhac5q/root/P_61/pplacer.tree.she0sl6l.tre, info_file:/home/qiime2/miniconda/envs/qiime2-2019.7/share/fragment-insertion//ref/RAxML_info-reference-gg-raxml-bl.info, extended alignment:/tmp/tmp.9UyJ9extIn/sepp-tempssd-kOIp/q2-fragment-insertion.3pxhac5q/root/P_61/pplacer.extended.0.houq5nkr.fasta, output:/tmp/tmp.9UyJ9extIn/sepp-tempssd-kOIp/q2-fragment-insertion.3pxhac5q/root/P_61/pplacer.extended.0.houq5nkr.jplace
[09:03:20] jobs.py (line 117):     INFO: Finished jsonmerger Job with input: input:pipe output:/tmp/tmp.9UyJ9extIn/sepp-tmp-EbFC8/q2-fragment-insertion_placement.json
[09:03:30] algorithm.py (line 189):     INFO: Current execution Finished in 4252 seconds
[09:03:30] algorithm.py (line 190):     INFO: All checkpointed executions Finished in 4252 cumulative time

==> sepp-q2-fragment-insertion-out.log <==
Removing /tmp/tmp.9UyJ9extIn/sepp-tmp-EbFC8
/home/qiime2/miniconda/envs/qiime2-2019.7/bin/run-sepp.sh: line 36:  5252 Hangup                  $gbin/guppy tog --xml ${name}_placement.json

Hi @Shaminur,
it is hard to debug since information is very limited. However, I am a bit confused by the error message as is, since line 36 of run-sepp.sh has nothing to do with guppy, but points to a function that shall be executed when the script gets terminated. Furthermore, there are two guppy calls:
$gbin/guppy tog ${name}_placement.json and later $gbin/guppy tog --xml ${name}_placement.json. Thus, I wonder why the first passed but the second failed. Might it be a memory issue on your machine?

Would you be willing to share your placement file with me? It should have been computed prior to the error. But arg - the temporary files have been deleted. Could you please re-run your command but add parameters --p-debug --verbose. You should than find a file q2-fragment-insertion_placement.json in the temporary directory.

2 Likes

Dear Stefan,

Thanks for your help, I have increased the RAM 6GB and that worked

1 Like

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