Hi everyone! I have been trying to perform beta-rarefaction analyses without success. My efforts to try to debug the error have yielded little success so far. I am using qiime2-amplicon-2024.2 conda version. Please advice after going through the ddescription below.
Here is the code:
qiime diversity beta-rarefaction \
--i-table $QIIME_DENOISE_DIR/data_1_n_2/16S-feature_table_samoles.qza \
--p-metric weighted_unifrac \
--p-clustering-method nj \
--m-metadata-file $METADATA_4_RAREFACTION_DIR/data1_2_metadata.tsv \
--p-sampling-depth 225541 \
--i-phylogeny $PHYLOGENY_OUT_DIR/phylogenetic_tree/rooted_tree.qza \
--o-visualization $RAREFACTION_OUTPUT_DIR/beta_diversity/weighted_unifrac.qzv \
--verbose
Here I use my --p-sampling-depth 225541 as suggested in previous forums about choosing sampling depths. I only have to samples to compare and I chose the lowest sampling depth.
Here is the log :
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command:
ssu -i /var/tmp/pbs.5614058.sched01/qiime2/maloo/data/95c38cb8-7cc0-4570-bd7b-e2d6b31ddde6/data/feature-table.biom -t /var/tmp/pbs.5614058.sched01/qiime2/maloo/data/a912aff9-8f08-4016-b701-9cc6b4ada7b9/data/tree.nwk -m weighted_unnormalized -o /var/tmp/pbs.5614058.sched01/q2-LSMatFormat-30wo7yru
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command:
ssu -i /var/tmp/pbs.5614058.sched01/qiime2/maloo/data/817637c7-b742-488c-b073-9450c94769eb/data/feature-table.biom -t /var/tmp/pbs.5614058.sched01/qiime2/maloo/data/a912aff9-8f08-4016-b701-9cc6b4ada7b9/data/tree.nwk -m weighted_unnormalized -o /var/tmp/pbs.5614058.sched01/q2-LSMatFormat-gmma1vuh
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command:
ssu -i /var/tmp/pbs.5614058.sched01/qiime2/maloo/data/616c400a-6c48-4be7-a7c7-05a4407cfd18/data/feature-table.biom -t /var/tmp/pbs.5614058.sched01/qiime2/maloo/data/a912aff9-8f08-4016-b701-9cc6b4ada7b9/data/tree.nwk -m weighted_unnormalized -o /var/tmp/pbs.5614058.sched01/q2-LSMatFormat-2_aqjx8e
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command:
ssu -i /var/tmp/pbs.5614058.sched01/qiime2/maloo/data/d99ee8a0-7083-4b8b-bbc7-73bb64162eb2/data/feature-table.biom -t /var/tmp/pbs.5614058.sched01/qiime2/maloo/data/a912aff9-8f08-4016-b701-9cc6b4ada7b9/data/tree.nwk -m weighted_unnormalized -o /var/tmp/pbs.5614058.sched01/q2-LSMatFormat-48nrz0n3
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command:
ssu -i /var/tmp/pbs.5614058.sched01/qiime2/maloo/data/b07816b3-3f85-4bb2-b546-61990fe3eb1e/data/feature-table.biom -t /var/tmp/pbs.5614058.sched01/qiime2/maloo/data/a912aff9-8f08-4016-b701-9cc6b4ada7b9/data/tree.nwk -m weighted_unnormalized -o /var/tmp/pbs.5614058.sched01/q2-LSMatFormat-trspsfu0
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command:
ssu -i /var/tmp/pbs.5614058.sched01/qiime2/maloo/data/2ebd55c9-c7a8-4a9d-a5bc-00f507f90b28/data/feature-table.biom -t /var/tmp/pbs.5614058.sched01/qiime2/maloo/data/a912aff9-8f08-4016-b701-9cc6b4ada7b9/data/tree.nwk -m weighted_unnormalized -o /var/tmp/pbs.5614058.sched01/q2-LSMatFormat-l9ow0a6j
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command:
ssu -i /var/tmp/pbs.5614058.sched01/qiime2/maloo/data/67ea7d61-6de0-434d-aa81-a3dc5ad00214/data/feature-table.biom -t /var/tmp/pbs.5614058.sched01/qiime2/maloo/data/a912aff9-8f08-4016-b701-9cc6b4ada7b9/data/tree.nwk -m weighted_unnormalized -o /var/tmp/pbs.5614058.sched01/q2-LSMatFormat-ngj2rlwc
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command:
ssu -i /var/tmp/pbs.5614058.sched01/qiime2/maloo/data/a0434468-092e-46e2-a295-1065414e6f24/data/feature-table.biom -t /var/tmp/pbs.5614058.sched01/qiime2/maloo/data/a912aff9-8f08-4016-b701-9cc6b4ada7b9/data/tree.nwk -m weighted_unnormalized -o /var/tmp/pbs.5614058.sched01/q2-LSMatFormat-bsgwi2s1
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command:
ssu -i /var/tmp/pbs.5614058.sched01/qiime2/maloo/data/eac2df15-a10f-4310-8a9a-c782f2d1f25a/data/feature-table.biom -t /var/tmp/pbs.5614058.sched01/qiime2/maloo/data/a912aff9-8f08-4016-b701-9cc6b4ada7b9/data/tree.nwk -m weighted_unnormalized -o /var/tmp/pbs.5614058.sched01/q2-LSMatFormat-5k5fq4sa
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command:
ssu -i /var/tmp/pbs.5614058.sched01/qiime2/maloo/data/92810a7f-54c9-4d3f-9424-c152a3726a8d/data/feature-table.biom -t /var/tmp/pbs.5614058.sched01/qiime2/maloo/data/a912aff9-8f08-4016-b701-9cc6b4ada7b9/data/tree.nwk -m weighted_unnormalized -o /var/tmp/pbs.5614058.sched01/q2-LSMatFormat-n_h4z4qf
Traceback (most recent call last):
File "/home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2cli/commands.py", line 520, in __call__
results = self._execute_action(
File "/home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2cli/commands.py", line 581, in _execute_action
results = action(**arguments)
File "<decorator-gen-246>", line 2, in beta_rarefaction
File "/home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 342, in bound_callable
outputs = self._callable_executor_(
File "/home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 615, in _callable_executor_
ret_val = self._callable(output_dir=temp_dir, **view_args)
File "/home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2_diversity/_beta/_beta_rarefaction.py", line 67, in beta_rarefaction
heatmap_fig, similarity_df = _make_heatmap(
File "/home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2_diversity/_beta/_beta_rarefaction.py", line 115, in _make_heatmap
sm_df = skbio.stats.distance.pwmantel(
File "/home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/skbio/stats/distance/_mantel.py", line 605, in pwmantel
stat, p_val, n = mantel(x, y, method=method, permutations=permutations,
File "/home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/skbio/stats/distance/_mantel.py", line 278, in mantel
raise ValueError("Distance matrices must have at least 3 matching IDs "
ValueError: Distance matrices must have at least 3 matching IDs between them (i.e., minimum 3x3 in size).
Plugin error from diversity:
Distance matrices must have at least 3 matching IDs between them (i.e., minimum 3x3 in size).
Running with the highest sampling depth gives a much weirder error:
qiime diversity beta-rarefaction --i-table $QIIME_DENOISE_DIR/data_1_n_2/16S-feature_table_samoles.qza --p-metric weighted_unifrac --p-clustering-method nj --m-metadata-file $METADATA_4_RAREFACTION_DIR/data1_2_metadata.tsv --p-sampling-depth 524879 --i-phylogeny $PHYLOGENY_OUT_DIR/phylogenetic_tree/rooted_tree.qza --o-visualization $RAREFACT
ION_OUTPUT_DIR/beta_diversity/weighted_unifrac.qzv --verbose
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command:
ssu -i /var/tmp/pbs.5614058.sched01/qiime2/maloo/data/3a4da24b-8c74-418c-a130-63d2b26266fa/data/feature-table.biom -t /var/tmp/pbs.5614058.sched01/qiime2/maloo/data/a7098090-fd2b-42cf-a469-3dff8b2f921a/data/tree.nwk -m weighted_unnormalized -o /var/tmp/pbs.5614058.sched01/q2-LSMatFormat-wa80c8p5
*** Error in `/home/maloo/.conda/envs/qiime2-amplicon-2024.2/bin/ssu_nv_avx2': free(): invalid next size (fast): 0x0000000001e6fa80 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x7c503)[0x7ffff4d6e503]
/home/maloo/.conda/envs/qiime2-amplicon-2024.2/bin/ssu_nv_avx2[0x5e68df]
/home/maloo/.conda/envs/qiime2-amplicon-2024.2/bin/ssu_nv_avx2[0x683052]
/home/maloo/.conda/envs/qiime2-amplicon-2024.2/bin/ssu_nv_avx2[0x527918]
/home/maloo/.conda/envs/qiime2-amplicon-2024.2/bin/ssu_nv_avx2[0x518239]
/home/maloo/.conda/envs/qiime2-amplicon-2024.2/bin/ssu_nv_avx2[0x518f95]
/home/maloo/.conda/envs/qiime2-amplicon-2024.2/bin/ssu_nv_avx2[0x519389]
/home/maloo/.conda/envs/qiime2-amplicon-2024.2/bin/ssu_nv_avx2[0x4fd71b]
/home/maloo/.conda/envs/qiime2-amplicon-2024.2/bin/ssu_nv_avx2[0x56cd73]
/home/maloo/.conda/envs/qiime2-amplicon-2024.2/bin/ssu_nv_avx2[0x56f3ac]
/home/maloo/.conda/envs/qiime2-amplicon-2024.2/bin/ssu_nv_avx2[0x605d2d]
/home/maloo/.conda/envs/qiime2-amplicon-2024.2/bin/ssu_nv_avx2[0x539fa8]
/home/maloo/.conda/envs/qiime2-amplicon-2024.2/bin/ssu_nv_avx2[0x73202a]
/home/maloo/.conda/envs/qiime2-amplicon-2024.2/bin/ssu_nv_avx2[0x717e24]
/home/maloo/.conda/envs/qiime2-amplicon-2024.2/bin/ssu_nv_avx2[0x71ee78]
/home/maloo/.conda/envs/qiime2-amplicon-2024.2/bin/ssu_nv_avx2[0x53565b]
/home/maloo/.conda/envs/qiime2-amplicon-2024.2/bin/ssu_nv_avx2[0x5d5128]
/home/maloo/.conda/envs/qiime2-amplicon-2024.2/bin/ssu_nv_avx2[0x5d51e9]
/home/maloo/.conda/envs/qiime2-amplicon-2024.2/bin/ssu_nv_avx2[0x5d52bb]
/home/maloo/.conda/envs/qiime2-amplicon-2024.2/bin/ssu_nv_avx2[0x52d371]
/home/maloo/.conda/envs/qiime2-amplicon-2024.2/bin/ssu_nv_avx2[0x4e728a]
/home/maloo/.conda/envs/qiime2-amplicon-2024.2/bin/ssu_nv_avx2[0x4e7452]
/home/maloo/.conda/envs/qiime2-amplicon-2024.2/bin/ssu_nv_avx2[0x4398ce]
/home/maloo/.conda/envs/qiime2-amplicon-2024.2/bin/ssu_nv_avx2[0x4bf280]
/home/maloo/.conda/envs/qiime2-amplicon-2024.2/bin/ssu_nv_avx2[0x428459]
/home/maloo/.conda/envs/qiime2-amplicon-2024.2/bin/ssu_nv_avx2[0x42dc41]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7ffff4d13b35]
/home/maloo/.conda/envs/qiime2-amplicon-2024.2/bin/ssu_nv_avx2[0x4221f1]
======= Memory map: ========
00400000-011de000 r-xp 00000000 00:28 129206438 /home/maloo/.conda/envs/qiime2-amplicon-2024.2/bin/ssu_nv_avx2
011de000-01213000 r-xp 00ddd000 00:28 129206438 /home/maloo/.conda/envs/qiime2-amplicon-2024.2/bin/ssu_nv_avx2
01213000-0122c000 rwxp 00e12000 00:28 129206438 /home/maloo/.conda/envs/qiime2-amplicon-2024.2/bin/ssu_nv_avx2
01400000-02665000 rwxp 00000000 00:00 0 [heap]
7ffff0000000-7ffff0021000 rwxp 00000000 00:00 0
7ffff0021000-7ffff4000000 ---p 00000000 00:00 0
7ffff4a14000-7ffff4c0b000 rwxp 00000000 00:00 0
7ffff4c40000-7ffff4cd7000 rwxp 00000000 00:00 0
7ffff4cd7000-7ffff4cf0000 r-xp 00000000 00:28 146980696 /home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/libgcc_s.so.1
7ffff4cf0000-7ffff4cf1000 r-xp 00019000 00:28 146980696 /home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/libgcc_s.so.1
7ffff4cf1000-7ffff4cf2000 rwxp 0001a000 00:28 146980696 /home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/libgcc_s.so.1
7ffff4cf2000-7ffff4ea8000 r-xp 00000000 00:1c 151142 /usr/lib64/libc-2.17.so
7ffff4ea8000-7ffff50a8000 ---p 001b6000 00:1c 151142 /usr/lib64/libc-2.17.so
7ffff50a8000-7ffff50ac000 r-xp 001b6000 00:1c 151142 /usr/lib64/libc-2.17.so
7ffff50ac000-7ffff50ae000 rwxp 001ba000 00:1c 151142 /usr/lib64/libc-2.17.so
7ffff50ae000-7ffff50b3000 rwxp 00000000 00:00 0
7ffff50b3000-7ffff5283000 r-xp 00000000 00:28 146972935 /home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/libstdc++.so.6.0.32
7ffff5283000-7ffff528e000 r-xp 001cf000 00:28 146972935 /home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/libstdc++.so.6.0.32
7ffff528e000-7ffff5292000 rwxp 001da000 00:28 146972935 /home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/libstdc++.so.6.0.32
7ffff5292000-7ffff5297000 rwxp 00000000 00:00 0
7ffff5297000-7ffff5397000 r-xp 00000000 00:1c 151581 /usr/lib64/libm-2.17.so
7ffff5397000-7ffff5597000 ---p 00100000 00:1c 151581 /usr/lib64/libm-2.17.so
7ffff5597000-7ffff5598000 r-xp 00100000 00:1c 151581 /usr/lib64/libm-2.17.so
7ffff5598000-7ffff5599000 rwxp 00101000 00:1c 151581 /usr/lib64/libm-2.17.so
7ffff5599000-7ffff559b000 r-xp 00000000 00:1c 151201 /usr/lib64/libdl-2.17.so
7ffff559b000-7ffff579b000 ---p 00002000 00:1c 151201 /usr/lib64/libdl-2.17.so
7ffff579b000-7ffff579c000 r-xp 00002000 00:1c 151201 /usr/lib64/libdl-2.17.so
7ffff579c000-7ffff579d000 rwxp 00003000 00:1c 151201 /usr/lib64/libdl-2.17.so
7ffff579d000-7ffff57b6000 r-xp 00000000 00:28 146992527 /home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/libz.so.1.2.13
7ffff57b6000-7ffff57b7000 r-xp 00018000 00:28 146992527 /home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/libz.so.1.2.13
7ffff57b7000-7ffff57b8000 rwxp 00019000 00:28 146992527 /home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/libz.so.1.2.13
7ffff57b8000-7ffff57bf000 r-xp 00000000 00:1c 151737 /usr/lib64/librt-2.17.so
7ffff57bf000-7ffff59be000 ---p 00007000 00:1c 151737 /usr/lib64/librt-2.17.so
7ffff59be000-7ffff59bf000 r-xp 00006000 00:1c 151737 /usr/lib64/librt-2.17.so
7ffff59bf000-7ffff59c0000 rwxp 00007000 00:1c 151737 /usr/lib64/librt-2.17.so
7ffff59c0000-7ffff59d7000 r-xp 00000000 00:1c 151709 /usr/lib64/libpthread-2.17.so
7ffff59d7000-7ffff5bd6000 ---p 00017000 00:1c 151709 /usr/lib64/libpthread-2.17.so
7ffff5bd6000-7ffff5bd7000 r-xp 00016000 00:1c 151709 /usr/lib64/libpthread-2.17.so
7ffff5bd7000-7ffff5bd8000 rwxp 00017000 00:1c 151709 /usr/lib64/libpthread-2.17.so
7ffff5bd8000-7ffff5bdc000 rwxp 00000000 00:00 0
7ffff5bdc000-7ffff5c13000 r-xp 00000000 00:28 146980702 /home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/libquadmath.so.0.0.0
7ffff5c13000-7ffff5c14000 r-xp 00036000 00:28 146980702 /home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/libquadmath.so.0.0.0
7ffff5c14000-7ffff5c15000 rwxp 00037000 00:28 146980702 /home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/libquadmath.so.0.0.0
7ffff5c15000-7ffff5d36000 r-xp 00000000 00:28 147002066 /home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/libopenblasp-r0.3.25.so
7ffff5d36000-7ffff5d3d000 ---p 00121000 00:28 147002066 /home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/libopenblasp-r0.3.25.so
7ffff5d3d000-7ffff7dac000 r-xp 00128000 00:28 147002066 /home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/libopenblasp-r0.3.25.so
7ffff7dac000-7ffff7dba000 r-xp 02197000 00:28 147002066 /home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/libopenblasp-r0.3.25.so
7ffff7dba000-7ffff7dcc000 rwxp 021a5000 00:28 147002066 /home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/libopenblasp-r0.3.25.so
7ffff7dcc000-7ffff7ddd000 rwxp 00000000 00:00 0
7ffff7ddd000-7ffff7dfd000 r-xp 00000000 00:1c 150999 /usr/lib64/ld-2.17.so
7ffff7dfd000-7ffff7dfe000 rwxp 00000000 00:00 0
7ffff7dfe000-7ffff7e09000 r-xp 00000000 00:28 94888172 /home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/libsz.so.2.0.1
7ffff7e09000-7ffff7e0a000 r-xp 0000a000 00:28 94888172 /home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/libsz.so.2.0.1
7ffff7e0a000-7ffff7e0b000 rwxp 0000b000 00:28 94888172 /home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/libsz.so.2.0.1
7ffff7e0b000-7ffff7e0c000 rwxp 00000000 00:00 0
7ffff7e21000-7ffff7e22000 rwxp 00000000 00:00 0
7ffff7e22000-7ffff7fca000 r-xp 00000000 00:28 146991959 /home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/libgfortran.so.5.0.0
7ffff7fca000-7ffff7fcb000 r-xp 001a8000 00:28 146991959 /home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/libgfortran.so.5.0.0
7ffff7fcb000-7ffff7fcd000 rwxp 001a9000 00:28 146991959 /home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/libgfortran.so.5.0.0
7ffff7fcd000-7ffff7fce000 rwxp 00000000 00:00 0
7ffff7fce000-7ffff7ff7000 r-xp 00000000 00:28 146992538 /home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/liblz4.so.1.9.4
7ffff7ff7000-7ffff7ff8000 r-xp 00028000 00:28 146992538 /home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/liblz4.so.1.9.4
7ffff7ff8000-7ffff7ff9000 rwxp 00029000 00:28 146992538 /home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/liblz4.so.1.9.4
7ffff7ff9000-7ffff7ffa000 rwxp 00000000 00:00 0
7ffff7ffa000-7ffff7ffc000 r-xp 00000000 00:00 0 [vdso]
7ffff7ffc000-7ffff7ffd000 r-xp 0001f000 00:1c 150999 /usr/lib64/ld-2.17.so
7ffff7ffd000-7ffff7ffe000 rwxp 00020000 00:1c 150999 /usr/lib64/ld-2.17.so
7ffff7ffe000-7ffff7fff000 rwxp 00000000 00:00 0
7ffffffdb000-7ffffffff000 rwxp 00000000 00:00 0 [stack]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
Traceback (most recent call last):
File "/home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2cli/commands.py", line 520, in __call__
results = self._execute_action(
File "/home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2cli/commands.py", line 581, in _execute_action
results = action(**arguments)
File "<decorator-gen-246>", line 2, in beta_rarefaction
File "/home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 342, in bound_callable
outputs = self._callable_executor_(
File "/home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 615, in _callable_executor_
ret_val = self._callable(output_dir=temp_dir, **view_args)
File "/home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2_diversity/_beta/_beta_rarefaction.py", line 61, in beta_rarefaction
distance_matrices = _get_multiple_rarefaction(
File "/home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2_diversity/_beta/_beta_rarefaction.py", line 107, in _get_multiple_rarefaction
distance_matrix, = beta_func(table=rarefied_table, metric=metric)
File "<decorator-gen-819>", line 2, in beta_phylogenetic
File "/home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/context.py", line 143, in deferred_action
return action_obj._bind(
File "<decorator-gen-823>", line 2, in beta_phylogenetic
File "/home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 342, in bound_callable
outputs = self._callable_executor_(
File "/home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 647, in _callable_executor_
outputs = self._callable(scope.ctx, **view_args)
File "/home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2_diversity/_beta/_pipeline.py", line 31, in beta_phylogenetic
dm, = action(table, phylogeny, threads=threads,
File "<decorator-gen-824>", line 2, in weighted_unifrac
File "/home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/context.py", line 143, in deferred_action
return action_obj._bind(
File "<decorator-gen-825>", line 2, in weighted_unifrac
File "/home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 342, in bound_callable
outputs = self._callable_executor_(
File "/home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 566, in _callable_executor_
output_views = self._callable(**view_args)
File "<decorator-gen-145>", line 2, in weighted_unifrac
File "/home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2_diversity_lib/_util.py", line 75, in _validate_tables
return wrapped_function(*args, **kwargs)
File "<decorator-gen-144>", line 2, in weighted_unifrac
File "/home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2_diversity_lib/_util.py", line 118, in _validate_requested_cpus
return wrapped_function(*bound_arguments.args, **bound_arguments.kwargs)
File "/home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2_diversity_lib/beta.py", line 243, in weighted_unifrac
_omp_cmd_wrapper(threads, cmd)
File "/home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2_diversity_lib/_util.py", line 134, in _omp_cmd_wrapper
return _run_external_cmd(cmd, verbose=verbose, env=env)
File "/home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2_diversity_lib/_util.py", line 128, in _run_external_cmd
return subprocess.run(cmd, check=True, env=env)
File "/home/maloo/.conda/envs/qiime2-amplicon-2024.2/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['ssu', '-i', '/var/tmp/pbs.5614058.sched01/qiime2/maloo/data/3a4da24b-8c74-418c-a130-63d2b26266fa/data/feature-table.biom', '-t', '/var/tmp/pbs.5614058.sched01/qiime2/maloo/data/a7098090-fd2b-42cf-a469-3dff8b2f921a/data/tree.nwk', '-m', 'weighted_unnormalized', '-o', '/var/tmp/pbs.5614058.sched01/q2-LSMatFormat-wa80c8p5']' died with <Signals.SIGABRT: 6>.
Plugin error from diversity:
Command '['ssu', '-i', '/var/tmp/pbs.5614058.sched01/qiime2/maloo/data/3a4da24b-8c74-418c-a130-63d2b26266fa/data/feature-table.biom', '-t', '/var/tmp/pbs.5614058.sched01/qiime2/maloo/data/a7098090-fd2b-42cf-a469-3dff8b2f921a/data/tree.nwk', '-m', 'weighted_unnormalized', '-o', '/var/tmp/pbs.5614058.sched01/q2-LSMatFormat-wa80c8p5']' died with <Signals.SIGABRT: 6>.
See above for debug info.
Here is my featuretable qzv:
16S-feature_table_samoles2.qzv (586.6 KB)
Here is my metadata
sample-id source subCounty studySIte fertiliserUsage
S1-S1-L001-001 soil Gatundu-North Gituamba Yes
S2-S1-L001-001 soil Gatundu-North Mangu No
