partis-bcr 1.0.12.post1.dev4__tar.gz → 1.0.13__tar.gz

partis_bcr-1.0.13/PKG-INFO

@@ -0,0 +1,87 @@
+Metadata-Version: 2.4
+Name: partis-bcr
+Version: 1.0.13
+Summary: B- and T-cell receptor sequence annotation, simulation, clonal family and germline inference
+Home-page: https://github.com/psathyrella/partis
+Author: Duncan Ralph
+Author-email: dkralph@gmail.com
+License: GPL-3.0-or-later
+Project-URL: Bug Reports, https://github.com/psathyrella/partis/issues
+Project-URL: Source, https://github.com/psathyrella/partis
+Project-URL: Documentation, https://github.com/psathyrella/partis/tree/main/docs
+Keywords: immunology bioinformatics bcr tcr antibody sequence-analysis
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.7
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
+License-File: COPYING
+Requires-Dist: biopython
+Requires-Dist: colored-traceback
+Requires-Dist: dendropy
+Requires-Dist: matplotlib
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: psutil
+Requires-Dist: pysam
+Requires-Dist: PyYAML
+Requires-Dist: scikit-learn
+Requires-Dist: scipy
+Requires-Dist: seaborn
+Requires-Dist: six
+Provides-Extra: plotting
+Requires-Dist: circlify; extra == "plotting"
+Requires-Dist: ete3; extra == "plotting"
+Requires-Dist: joypy; extra == "plotting"
+Requires-Dist: matplotlib; extra == "plotting"
+Provides-Extra: full
+Requires-Dist: circlify; extra == "full"
+Requires-Dist: ete3; extra == "full"
+Requires-Dist: joypy; extra == "full"
+Requires-Dist: levenshtein; extra == "full"
+Requires-Dist: matplotlib; extra == "full"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: license-file
+Dynamic: project-url
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+[![](https://img.shields.io/static/v1?label=AIRR-C%20sw-tools%20v1&message=compliant&color=008AFF&labelColor=000000&style=plastic)](https://docs.airr-community.org/en/stable/swtools/airr_swtools_standard.html)
+### partis
+
+Partis is an HMM-based framework for B- and T-cell receptor sequence annotation, simulation, clonal family and germline inference, and affinity prediction.
+It is built on top of the [ham](https://github.com/psathyrella/ham) HMM compiler and [ig-sw](https://github.com/matsengrp/ig-sw) set of Smith-Waterman annotation tools.
+Partis is free software under the GPL v3.
+
+The various components are described in the following papers.
+Since they do quite different things, it's best if you can cite the specific paper(s) that describe the components that you're using.
+
+  * [Paired clustering](https://doi.org/10.1371/journal.pcbi.1010723) Ralph, DK, & Matsen IV, FA (2022). _Inference of B cell clonal families using heavy/light chain pairing information._ PLoS Computational Biology, 18(11), e1010723.
+  * [Selection metrics](https://doi.org/10.1371/journal.pcbi.1008391) Ralph, DK, & Matsen IV, FA (2020). _Using B cell receptor lineage structures to predict affinity._ PLoS Computational Biology, 16(11), e1008391.
+  * [Germline inference](https://doi.org/10.1371/journal.pcbi.1007133) Ralph, DK, & Matsen IV, FA (2019). _Per-sample immunoglobulin germline inference \[...\]._ PLoS Computational Biology, 15(7), e1007133.
+  * [Clonal family inference](http://dx.doi.org/10.1371/journal.pcbi.1005086) Ralph, DK, & Matsen IV, FA (2016). _Likelihood-based Inference of B-cell Clonal Families._ PLoS Computational Biology, 12(10), e1005086.
+  * [HMM framework and BCR annotation](http://doi.org/10.1371/journal.pcbi.1004409) Ralph, DK, & Matsen IV, FA (2016). _Consistency of \[...\] Enables Accurate B Cell Receptor Sequence Annotation._ PLoS Computational Biology, 12(1), e1004409.
+
+The best place to start reading the manual is either [installation](docs/install.md) or [quick start](docs/quick-start.md), but there's also a [table of contents](docs/contents.md).
+Details on the many options not documented there may be found by running each subcommand's help, for instance `partis cache-parameters --help` or `partis simulate --help`.
+
+To ask questions about how to run or how things work, please use the [google group](https://groups.google.com/g/partis).
+For specific issues with the software, e.g. bug reports or feature requests, on the other hand, [submit an issue](https://github.com/psathyrella/partis/issues/new) on github.
+You can also search through past discussion both on the google group and in [closed issues](https://github.com/psathyrella/partis/issues?q=is%3Aissue+is%3Aclosed).
+If you'd like to be notified when something important changes, please subscribe to the google group.

partis_bcr-1.0.13/partis_bcr.egg-info/PKG-INFO

@@ -0,0 +1,87 @@
+Metadata-Version: 2.4
+Name: partis-bcr
+Version: 1.0.13
+Summary: B- and T-cell receptor sequence annotation, simulation, clonal family and germline inference
+Home-page: https://github.com/psathyrella/partis
+Author: Duncan Ralph
+Author-email: dkralph@gmail.com
+License: GPL-3.0-or-later
+Project-URL: Bug Reports, https://github.com/psathyrella/partis/issues
+Project-URL: Source, https://github.com/psathyrella/partis
+Project-URL: Documentation, https://github.com/psathyrella/partis/tree/main/docs
+Keywords: immunology bioinformatics bcr tcr antibody sequence-analysis
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.7
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
+License-File: COPYING
+Requires-Dist: biopython
+Requires-Dist: colored-traceback
+Requires-Dist: dendropy
+Requires-Dist: matplotlib
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: psutil
+Requires-Dist: pysam
+Requires-Dist: PyYAML
+Requires-Dist: scikit-learn
+Requires-Dist: scipy
+Requires-Dist: seaborn
+Requires-Dist: six
+Provides-Extra: plotting
+Requires-Dist: circlify; extra == "plotting"
+Requires-Dist: ete3; extra == "plotting"
+Requires-Dist: joypy; extra == "plotting"
+Requires-Dist: matplotlib; extra == "plotting"
+Provides-Extra: full
+Requires-Dist: circlify; extra == "full"
+Requires-Dist: ete3; extra == "full"
+Requires-Dist: joypy; extra == "full"
+Requires-Dist: levenshtein; extra == "full"
+Requires-Dist: matplotlib; extra == "full"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: license-file
+Dynamic: project-url
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+[![](https://img.shields.io/static/v1?label=AIRR-C%20sw-tools%20v1&message=compliant&color=008AFF&labelColor=000000&style=plastic)](https://docs.airr-community.org/en/stable/swtools/airr_swtools_standard.html)
+### partis
+
+Partis is an HMM-based framework for B- and T-cell receptor sequence annotation, simulation, clonal family and germline inference, and affinity prediction.
+It is built on top of the [ham](https://github.com/psathyrella/ham) HMM compiler and [ig-sw](https://github.com/matsengrp/ig-sw) set of Smith-Waterman annotation tools.
+Partis is free software under the GPL v3.
+
+The various components are described in the following papers.
+Since they do quite different things, it's best if you can cite the specific paper(s) that describe the components that you're using.
+
+  * [Paired clustering](https://doi.org/10.1371/journal.pcbi.1010723) Ralph, DK, & Matsen IV, FA (2022). _Inference of B cell clonal families using heavy/light chain pairing information._ PLoS Computational Biology, 18(11), e1010723.
+  * [Selection metrics](https://doi.org/10.1371/journal.pcbi.1008391) Ralph, DK, & Matsen IV, FA (2020). _Using B cell receptor lineage structures to predict affinity._ PLoS Computational Biology, 16(11), e1008391.
+  * [Germline inference](https://doi.org/10.1371/journal.pcbi.1007133) Ralph, DK, & Matsen IV, FA (2019). _Per-sample immunoglobulin germline inference \[...\]._ PLoS Computational Biology, 15(7), e1007133.
+  * [Clonal family inference](http://dx.doi.org/10.1371/journal.pcbi.1005086) Ralph, DK, & Matsen IV, FA (2016). _Likelihood-based Inference of B-cell Clonal Families._ PLoS Computational Biology, 12(10), e1005086.
+  * [HMM framework and BCR annotation](http://doi.org/10.1371/journal.pcbi.1004409) Ralph, DK, & Matsen IV, FA (2016). _Consistency of \[...\] Enables Accurate B Cell Receptor Sequence Annotation._ PLoS Computational Biology, 12(1), e1004409.
+
+The best place to start reading the manual is either [installation](docs/install.md) or [quick start](docs/quick-start.md), but there's also a [table of contents](docs/contents.md).
+Details on the many options not documented there may be found by running each subcommand's help, for instance `partis cache-parameters --help` or `partis simulate --help`.
+
+To ask questions about how to run or how things work, please use the [google group](https://groups.google.com/g/partis).
+For specific issues with the software, e.g. bug reports or feature requests, on the other hand, [submit an issue](https://github.com/psathyrella/partis/issues/new) on github.
+You can also search through past discussion both on the google group and in [closed issues](https://github.com/psathyrella/partis/issues?q=is%3Aissue+is%3Aclosed).
+If you'd like to be notified when something important changes, please subscribe to the google group.

partis_bcr-1.0.13/test/new-results/partition-new-simu/fasttree/iclust-0/log

@@ -0,0 +1,23 @@
+run /home/runner/work/partis/partis/bin/FastTree-linux -gtr -nt -out /home/runner/work/partis/partis/test/new-results/partition-new-simu/fasttree/iclust-0/fasttree.out /home/runner/work/partis/partis/test/new-results/partition-new-simu/fasttree/iclust-0/input-seqs.fa
+FastTree Version 2.1.10 SSE3
+Alignment: /home/runner/work/partis/partis/test/new-results/partition-new-simu/fasttree/iclust-0/input-seqs.fa
+Nucleotide distances: Jukes-Cantor Joins: balanced Support: SH-like 1000
+Search: Normal +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1
+TopHits: 1.00*sqrtN close=default refresh=0.80
+ML Model: Generalized Time-Reversible, CAT approximation with 20 rate categories
+Ignored unknown character X (seen 48 times)
+Initial topology in 0.00 seconds
+Refining topology: 12 rounds ME-NNIs, 2 rounds ME-SPRs, 6 rounds ML-NNIs
+Total branch-length 0.082 after 0.00 sec
+ML-NNI round 1: LogLk = -668.065 NNIs 2 max delta 0.00 Time 0.01
+GTR Frequencies: 0.2215 0.2569 0.3074 0.2143
+GTR rates(ac ag at cg ct gt) 0.9755 0.9620 0.4555 0.6885 0.8030 1.0000
+Switched to using 20 rate categories (CAT approximation)
+Rate categories were divided by 0.641 so that average rate = 1.0
+CAT-based log-likelihoods may not be comparable across runs
+Use -gamma for approximate but comparable Gamma(20) log-likelihoods
+ML-NNI round 2: LogLk = -655.501 NNIs 1 max delta 0.00 Time 0.03
+Turning off heuristics for final round of ML NNIs (converged)
+ML-NNI round 3: LogLk = -655.501 NNIs 1 max delta 0.00 Time 0.04 (final)
+Optimize all lengths: LogLk = -655.501 Time 0.04
+Total time: 0.05 seconds Unique: 8/12 Bad splits: 0/5

partis_bcr-1.0.13/test/new-results/partition-new-simu/fasttree/iclust-2/log

@@ -0,0 +1,22 @@
+run /home/runner/work/partis/partis/bin/FastTree-linux -gtr -nt -out /home/runner/work/partis/partis/test/new-results/partition-new-simu/fasttree/iclust-2/fasttree.out /home/runner/work/partis/partis/test/new-results/partition-new-simu/fasttree/iclust-2/input-seqs.fa
+FastTree Version 2.1.10 SSE3
+Alignment: /home/runner/work/partis/partis/test/new-results/partition-new-simu/fasttree/iclust-2/input-seqs.fa
+Nucleotide distances: Jukes-Cantor Joins: balanced Support: SH-like 1000
+Search: Normal +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1
+TopHits: 1.00*sqrtN close=default refresh=0.80
+ML Model: Generalized Time-Reversible, CAT approximation with 20 rate categories
+Initial topology in 0.00 seconds
+Refining topology: 12 rounds ME-NNIs, 2 rounds ME-SPRs, 6 rounds ML-NNIs
+Total branch-length 0.056 after 0.00 sec
+ML-NNI round 1: LogLk = -675.096 NNIs 1 max delta 0.00 Time 0.01
+GTR Frequencies: 0.2187 0.2796 0.2852 0.2164
+GTR rates(ac ag at cg ct gt) 0.5930 0.1945 0.2547 0.7730 1.2348 1.0000
+Switched to using 20 rate categories (CAT approximation)
+Rate categories were divided by 0.636 so that average rate = 1.0
+CAT-based log-likelihoods may not be comparable across runs
+Use -gamma for approximate but comparable Gamma(20) log-likelihoods
+ML-NNI round 2: LogLk = -662.808 NNIs 2 max delta 0.00 Time 0.03
+Turning off heuristics for final round of ML NNIs (converged)
+ML-NNI round 3: LogLk = -662.808 NNIs 1 max delta 0.00 Time 0.04 (final)
+Optimize all lengths: LogLk = -662.808 Time 0.04
+Total time: 0.04 seconds Unique: 8/8 Bad splits: 0/5

partis_bcr-1.0.13/test/new-results/run-times.csv

@@ -0,0 +1,10 @@
+name,seconds
+cache-parameters-simu,5.5
+annotate-new-simu,2.2
+multi-annotate-new-simu,2.1
+partition-new-simu,3.3
+seed-partition-new-simu,1.8
+vsearch-partition-new-simu,2.1
+get-selection-metrics-new-simu,1.6
+cache-parameters-data,6.5
+simulate,7.8

partis_bcr-1.0.13/test/new-results/test.log

@@ -0,0 +1,279 @@
+cache-parameters-simu            partis cache-parameters --dont-write-git-info --infname test/ref-results/test/simu.yaml --parameter-dir test/new-results/test/parameters/simu --sw-cachefname test/new-results/test/parameters/simu/sw-cache.yaml --is-simu --random-seed 1 --n-procs 10
+caching parameters
+  vsearch: 36 / 36 v annotations (0 failed) with 7 v genes in 0.0 sec
+    keeping 7 / 198 v genes
+    missing 8 simulation genes (counts): hv1-202 0  hv2-502 0  hv2-70D04 0  hv3-1104 0  hv3-69-102 0  hv3-902 0  hv4-3401 0  hv4-3909 0
+smith-waterman  (new-allele fitting)
+  vsearch: 36 / 36 v annotations (0 failed) with 7 v genes in 0.0 sec
+  removing old sw cache test/new-results/test/parameters/simu/sw-cache.yaml
+    running 10 procs for 36 seqs
+    running 11 procs for 1 seq
+      info for 36 / 36 = 1.000   (removed: 0 failed)
+      kept 18 (0.500) unproductive
+    water time: 0.1  (ig-sw 0.0  processing 0.0)
+smith-waterman  (writing parameters)
+  vsearch: 36 / 36 v annotations (0 failed) with 7 v genes in 0.0 sec
+    running 10 procs for 36 seqs
+    running 11 procs for 1 seq
+      info for 36 / 36 = 1.000   (removed: 0 failed)
+      kept 18 (0.500) unproductive
+        writing sw results to test/new-results/test/parameters/simu/sw-cache.yaml
+    writing parameters to test/new-results/test/parameters/simu/sw (0.7 sec)
+    water time: 0.8  (ig-sw 0.7  processing 0.0)
+  writing hmms     removed 30 genes from glfo (leaving v 7  d 5  j 3)
+(0.5 sec)
+hmm
+    reading output
+        read 36 hmm output lines with 36 sequences in 36 events  (0 failures)
+    writing parameters to test/new-results/test/parameters/simu/hmm (0.6 sec)
+    writing parameters to test/new-results/test/parameters/simu/true (0.6 sec)
+         infra time: 1.3
+      hmm step time: 1.9
+  writing hmms     removed 0  genes from glfo (leaving v 7  d 5  j 3)
+(0.6 sec)
+      total time: 4.0
+annotate-new-simu                partis annotate --dont-write-git-info --infname test/ref-results/test/simu.yaml --parameter-dir test/new-results/test/parameters/simu --sw-cachefname test/new-results/test/parameters/simu/sw-cache.yaml --plot-annotation-performance --is-simu --plotdir test/new-results/annotate-new-simu-annotation-performance --only-csv-plots --random-seed 1 --n-procs 10 --outfname test/new-results/annotate-new-simu.yaml
+annotating    (with test/new-results/test/parameters/simu/hmm)
+smith-waterman
+  vsearch: 36 / 36 v annotations (0 failed) with 7 v genes in 0.0 sec
+        reading sw results from test/new-results/test/parameters/simu/sw-cache.yaml
+      info for 36 / 36 = 1.000   (removed: 0 failed, 0 duplicates [removed when cache file was written])
+      kept 18 (0.500) unproductive
+  plotting performance 
+    warning skipped annotation performance evaluation on 1 queries with different true and inferred net shm indel lengths: d8761c689a
+(0.0 sec)
+        water time: 0.1
+hmm
+    reading output
+        read 36 hmm output lines with 36 sequences in 36 events  (0 failures)
+  plotting performance 
+    warning skipped annotation performance evaluation on 1 queries with different true and inferred net shm indel lengths: d8761c689a
+(0.0 sec)
+      hmm step time: 0.7
+      total time: 0.8
+multi-annotate-new-simu          partis annotate --dont-write-git-info --infname test/ref-results/test/simu.yaml --parameter-dir test/new-results/test/parameters/simu --sw-cachefname test/new-results/test/parameters/simu/sw-cache.yaml --plot-annotation-performance --simultaneous-true-clonal-seqs --is-simu --plotdir test/new-results/multi-annotate-new-simu-annotation-performance --only-csv-plots --random-seed 1 --n-procs 10 --outfname test/new-results/multi-annotate-new-simu.yaml
+annotating    (with test/new-results/test/parameters/simu/hmm)
+smith-waterman
+  vsearch: 36 / 36 v annotations (0 failed) with 7 v genes in 0.0 sec
+  note: not running msa indel stuff for --simultaneous-true-clonal-seqs, so any families with shm indels within cdr3 will be split up before running the hmm. To fix this you'll either need to run set_msa_info() (which is fine and easy, but slow, and requires deciding whether to make sure to run parameter caching with the arg, or else rerun smith waterman with the msa indels
+        reading sw results from test/new-results/test/parameters/simu/sw-cache.yaml
+      info for 36 / 36 = 1.000   (removed: 0 failed, 0 duplicates [removed when cache file was written])
+      kept 18 (0.500) unproductive
+  plotting performance 
+    warning skipped annotation performance evaluation on 1 queries with different true and inferred net shm indel lengths: d8761c689a
+(0.0 sec)
+        water time: 0.1
+hmm
+  --simultaneous-true-clonal-seqs: grouping seqs according to true partition
+  warning split apart 1 cluster that contained multiple cdr3 lengths (total clusters: 10 --> 11)
+      cluster splits:   8 --> 7 1
+  subcluster annotating 11 clusters with steps:  (0.4s) (0.1s)   plotting performance 
+    warning skipped annotation performance evaluation on 1 queries with different true and inferred net shm indel lengths: d8761c689a
+(0.0 sec)
+
+    subcluster annotation time 0.5
+      total time: 0.6
+partition-new-simu               partis partition --dont-write-git-info --infname test/ref-results/test/simu.yaml --parameter-dir test/new-results/test/parameters/simu --sw-cachefname test/new-results/test/parameters/simu/sw-cache.yaml --plot-annotation-performance --max-ccf-fail-frac 0.10 --is-simu --persistent-cachefname test/new-results/cache-new-partition.csv --plotdir test/new-results/partition-new-simu-annotation-performance --only-csv-plots --no-partition-plots --random-seed 1 --n-procs 10 --outfname test/new-results/partition-new-simu.yaml
+partitioning     (with test/new-results/test/parameters/simu/hmm)
+smith-waterman
+  vsearch: 36 / 36 v annotations (0 failed) with 7 v genes in 0.0 sec
+        reading sw results from test/new-results/test/parameters/simu/sw-cache.yaml
+      info for 36 / 36 = 1.000   (removed: 0 failed, 0 duplicates [removed when cache file was written])
+      kept 18 (0.500) unproductive
+  plotting performance 
+    warning skipped annotation performance evaluation on 1 queries with different true and inferred net shm indel lengths: d8761c689a
+(0.0 sec)
+        water time: 0.1
+hmm
+  --persistent-cachefname: using existing hmm cache file test/new-results/cache-new-partition.csv
+  caching all 36 naive sequences (0.6s)
+    collapsed 36 queries into 12 clusters with identical naive seqs (0.0 sec)
+  12 clusters with 10 procs (0.0s)
+   12 clusters with 7 procs (0.0s)
+   12 clusters with 5 procs (0.0s)
+   12 clusters with 3 procs (0.0s)
+   12 clusters with 2 procs (0.1s)
+   11 clusters with 1 proc (0.3s)
+       partition loop time: 0.6
+getting annotations for final partition
+  subcluster annotating 10 clusters with steps:  (0.3s) (0.1s) (0.1s)   plotting performance 
+    warning skipped annotation performance evaluation on 1 queries with different true and inferred net shm indel lengths: d8761c689a
+(0.0 sec)
+
+    subcluster annotation time 0.5
+      total time: 1.9
+seed-partition-new-simu          partis partition --dont-write-git-info --infname test/ref-results/test/simu.yaml --parameter-dir test/new-results/test/parameters/simu --sw-cachefname test/new-results/test/parameters/simu/sw-cache.yaml --max-ccf-fail-frac 0.10 --is-simu --persistent-cachefname test/new-results/cache-new-partition.csv --seed-unique-id 8024ed1a22 --random-seed 1 --n-procs 10 --outfname test/new-results/seed-partition-new-simu.yaml
+partitioning     (with test/new-results/test/parameters/simu/hmm)
+smith-waterman
+  vsearch: 36 / 36 v annotations (0 failed) with 7 v genes in 0.0 sec
+        reading sw results from test/new-results/test/parameters/simu/sw-cache.yaml
+      info for 36 / 36 = 1.000   (removed: 0 failed, 0 duplicates [removed when cache file was written])
+      kept 18 (0.500) unproductive
+      removed 25 / 36 = 0.69 sequences with cdr3 length different from seed sequence (leaving 11)
+        water time: 0.0
+hmm
+  --persistent-cachefname: using existing hmm cache file test/new-results/cache-new-partition.csv
+   collapsed 11 queries into 2 clusters with identical naive seqs (0.0 sec)
+  reducing n procs to number of clusters: 10 --> 2
+  2 clusters with 2 procs (0.0s)
+       removed 0 sequences in unseeded clusters, split 2 seeded clusters into 11 singletons, and merged these into 2 clusters with identical naive seqs (0.0 sec)
+        new n_procs 1 (initial seqs/proc: 5.50   new seqs/proc: 2.00
+  2 clusters with 1 proc (0.1s)
+       partition loop time: 0.1
+getting annotations for final partition
+  subcluster annotating 1 cluster with steps:  (0.1s) (0.1s) (0.1s) 
+    subcluster annotation time 0.2
+  seed cluster size in best partition: 11, excluding seed seq: 10
+      total time: 0.4
+vsearch-partition-new-simu       partis partition --dont-write-git-info --infname test/ref-results/test/simu.yaml --parameter-dir test/new-results/test/parameters/simu --sw-cachefname test/new-results/test/parameters/simu/sw-cache.yaml --naive-vsearch --is-simu --persistent-cachefname test/new-results/cache-new-partition.csv --random-seed 1 --n-procs 10 --outfname test/new-results/vsearch-partition-new-simu.yaml
+partitioning     (with test/new-results/test/parameters/simu/hmm)
+smith-waterman
+  vsearch: 36 / 36 v annotations (0 failed) with 7 v genes in 0.0 sec
+        reading sw results from test/new-results/test/parameters/simu/sw-cache.yaml
+      info for 36 / 36 = 1.000   (removed: 0 failed, 0 duplicates [removed when cache file was written])
+      kept 18 (0.500) unproductive
+        water time: 0.0
+hmm
+  --persistent-cachefname: using existing hmm cache file test/new-results/cache-new-partition.csv
+        collapsed 36 sequences (36 initial naive seqs/clusters) into 12 unique naive sequences over 9 cdr3 lengths (0.0 sec)
+    using hfrac bound for vsearch 0.013
+    running vsearch 9 times (once for each cdr3 length class): . . . . . . . . . 
+      vsearch time: 0.1
+getting annotations for final partition
+      calculating hmm annotations even though --fast/--naive-vsearch was set (you can set --use-sw-annotations to get faster (but substantially less accurate) annotations, or set --dont-calculate-annotations if you only need the partition)
+  subcluster annotating 10 clusters with steps:  (0.3s) (0.1s) (0.1s) 
+    subcluster annotation time 0.5
+      total time: 0.7
+get-selection-metrics-new-simu   partis get-selection-metrics --dont-write-git-info --existing-output-run-cfg paired --min-selection-metric-cluster-size 3 --min-paired-cluster-size-to-read 3 --random-seed 1 --n-procs 10 --outfname test/new-results/partition-new-simu.yaml --selection-metric-fname test/new-results/get-selection-metrics-new-simu.yaml
+  note: --parameter-dir not set, so using default: x-dummy-x
+  note: By default we print/operate on *all* annotations in the output file, which in general can include annotations from non-best partititons and non-seed clusters (e.g. if --n-final-clusters was set).
+        If you want to restrict to particular annotations, use one of --only-print-best-partition, --only-print-seed-clusters, or --only-print-queries-to-include-clusters (or, if set during partitioning, --n-final-clusters or --min-largest-cluster-size).
+    getting selection metrics (lbi lbr aa-lbi aa-lbr cons-dist-aa) with inferred lines: 4 clusters with sizes 11 7 7 3
+      skipped 6 smaller than 3 (controlled by --min-selection-metric-cluster-size)
+    getting trees for 3 clusters with sizes: 11 7 7
+      starting 3 jobs
+        run /home/runner/work/partis/partis/bin/FastTree-linux -gtr -nt -out /home/runner/work/partis/partis/test/new-results/partition-new-simu/fasttree/iclust-0/fasttree.out /home/runner/work/partis/partis/test/new-results/partition-new-simu/fasttree/iclust-0/input-seqs.fa
+        run /home/runner/work/partis/partis/bin/FastTree-linux -gtr -nt -out /home/runner/work/partis/partis/test/new-results/partition-new-simu/fasttree/iclust-1/fasttree.out /home/runner/work/partis/partis/test/new-results/partition-new-simu/fasttree/iclust-1/input-seqs.fa
+        run /home/runner/work/partis/partis/bin/FastTree-linux -gtr -nt -out /home/runner/work/partis/partis/test/new-results/partition-new-simu/fasttree/iclust-2/fasttree.out /home/runner/work/partis/partis/test/new-results/partition-new-simu/fasttree/iclust-2/input-seqs.fa
+      made 3 fasttree trees (0.1s)
+    tree origins: 3 ran fasttree
+    skipped 1/4 clusters smaller than 4
+      setting default tau to 1 / 352 = 0.0028
+    calculating normalized lb index and lb ratio and lb fraction with tau 0.0028
+      warning get_aa_tree() (AA inf tree, iclust 0): skipped 13/18 edges for which we didn't have sequences for both nodes (i.e. left the original branch length unmodified). Missing nodes: amz bev bnw bop dkn ikm
+      setting default tau to 1 / 352 = 0.0028
+    calculating normalized lb index and lb ratio and lb fraction on aa tree with tau 0.0028
+                iclust 1: warning tree depth and mfreq differ by more than 25% for 2/7 nodes (note that this is expected if these are single chain sequences being compared to a paired h+l tree)
+                    mean values:  tree depth 0.001  mfreq 0.001  diff 0.000  abs(frac diff) 25%  ratio 1.3
+          10 with highest abs(diff):
+            tree depth   mfreq      ratio    diff
+              0.0034    0.0027       1.3     0.0007     20a0129b57
+              0.0034    0.0027       1.3     0.0007     97366cf0d8
+          10 with highest+lowest ratios:
+              0.0034    0.0027       1.3     0.0007     20a0129b57
+              0.0034    0.0027       1.3     0.0007     97366cf0d8
+              0.0034    0.0027       1.3     0.0007     20a0129b57
+              0.0034    0.0027       1.3     0.0007     97366cf0d8
+      warning get_aa_tree() (AA inf tree, iclust 1): skipped 3/9 edges for which we didn't have sequences for both nodes (i.e. left the original branch length unmodified). Missing nodes: eov
+      warning get_aa_tree() (AA inf tree, iclust 2): skipped 11/13 edges for which we didn't have sequences for both nodes (i.e. left the original branch length unmodified). Missing nodes: apr dhq fnv nox uvx
+    skipped 1/4 clusters that had no uids in common with tree
+  writing selection metrics to test/new-results/get-selection-metrics-new-simu.yaml
+      total time: 0.2
+cache-parameters-data            partis cache-parameters --dont-write-git-info --infname test/mishmash.fa --parameter-dir test/new-results/test/parameters/data --sw-cachefname test/new-results/test/parameters/data/sw-cache.yaml --n-max-queries 50 --input-metafnames test/input-meta.yaml --random-seed 1 --n-procs 10
+    stopped after reading 50 sequences from test/mishmash.fa
+  --n-max-queries: stopped after reading 50 queries from input file
+  --input-metafnames: added meta info for 4 sequences from test/input-meta.yaml: multiplicities
+caching parameters
+  vsearch: 44 / 50 v annotations (6 failed) with 54 v genes in 0.0 sec
+    keeping 24 / 198 v genes
+smith-waterman  (new-allele fitting)
+  vsearch: 45 / 50 v annotations (5 failed) with 23 v genes in 0.0 sec
+    running 10 procs for 50 seqs
+    running 12 procs for 5 seqs
+      info for 46 / 50 = 0.920   (removed: 4 failed)
+      kept 16 (0.320) unproductive
+    water time: 0.1  (ig-sw 0.0  processing 0.0)
+smith-waterman  (writing parameters)
+  vsearch: 45 / 50 v annotations (5 failed) with 23 v genes in 0.0 sec
+    running 10 procs for 46 seqs
+    running 11 procs for 1 seq
+      info for 46 / 50 = 0.920   (removed: 4 failed)
+      kept 16 (0.320) unproductive
+        writing sw results to test/new-results/test/parameters/data/sw-cache.yaml
+    writing parameters to test/new-results/test/parameters/data/sw (0.8 sec)
+    water time: 1.0  (ig-sw 0.9  processing 0.0)
+  writing hmms     removed 15 genes from glfo (leaving v 18  d 22  j 7)
+(0.8 sec)
+hmm
+    reading output
+        read 46 hmm output lines with 46 sequences in 46 events  (0 failures)
+    writing parameters to test/new-results/test/parameters/data/hmm (0.7 sec)
+         infra time: 0.8
+      hmm step time: 2.3
+  writing hmms     removed 6  genes from glfo (leaving v 15  d 19  j 7)
+(0.7 sec)
+      total time: 5.1
+simulate                         partis simulate --dont-write-git-info --parameter-dir test/new-results/test/parameters/data --n-sim-events 10 --n-trees 10 --n-leaf-distribution geometric --n-leaves 5 --input-simulation-treefname /home/runner/work/partis/partis/test/trees.nwk --no-per-base-mutation --random-seed 1 --n-procs 10 --outfname test/new-results/test/simu.yaml --indel-frequency 0.2
+simulating
+      --> proc 0
+    reco params: test/new-results/test/parameters/data/hmm     shm params: test/new-results/test/parameters/data/hmm
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 6 seqs in 0.2s (0.1s of which was running bppseqgen)
+      total time: 0.3
+
+      --> proc 1
+    reco params: test/new-results/test/parameters/data/hmm     shm params: test/new-results/test/parameters/data/hmm
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 5 seqs in 0.2s (0.1s of which was running bppseqgen)
+      total time: 0.3
+
+      --> proc 2
+    reco params: test/new-results/test/parameters/data/hmm     shm params: test/new-results/test/parameters/data/hmm
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 2 seqs in 0.2s (0.0s of which was running bppseqgen)
+      total time: 0.3
+
+      --> proc 3
+    reco params: test/new-results/test/parameters/data/hmm     shm params: test/new-results/test/parameters/data/hmm
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 11 seqs in 0.3s (0.1s of which was running bppseqgen)
+      total time: 0.4
+
+      --> proc 4
+    reco params: test/new-results/test/parameters/data/hmm     shm params: test/new-results/test/parameters/data/hmm
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 4 seqs in 0.2s (0.1s of which was running bppseqgen)
+      total time: 0.3
+
+      --> proc 5
+    reco params: test/new-results/test/parameters/data/hmm     shm params: test/new-results/test/parameters/data/hmm
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 22 seqs in 0.3s (0.1s of which was running bppseqgen)
+      total time: 0.4
+
+      --> proc 6
+    reco params: test/new-results/test/parameters/data/hmm     shm params: test/new-results/test/parameters/data/hmm
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 12 seqs in 0.2s (0.1s of which was running bppseqgen)
+      total time: 0.3
+
+      --> proc 7
+    reco params: test/new-results/test/parameters/data/hmm     shm params: test/new-results/test/parameters/data/hmm
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 3 seqs in 0.1s (0.1s of which was running bppseqgen)
+      total time: 0.3
+
+      --> proc 8
+    reco params: test/new-results/test/parameters/data/hmm     shm params: test/new-results/test/parameters/data/hmm
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 5 seqs in 0.2s (0.0s of which was running bppseqgen)
+      total time: 0.3
+
+      --> proc 9
+    reco params: test/new-results/test/parameters/data/hmm     shm params: test/new-results/test/parameters/data/hmm
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 4 seqs in 0.1s (0.1s of which was running bppseqgen)
+      total time: 0.2
+
+   read 10 events with 74 seqs from 10 .yaml files
+      total time: 6.4

partis_bcr-1.0.13/test/paired/new-results/partition-new-simu/fasttree/iclust-0/log

@@ -0,0 +1,23 @@
+run /home/runner/work/partis/partis/bin/FastTree-linux -gtr -nt -out test/paired/new-results/partition-new-simu/fasttree/iclust-0/fasttree.out test/paired/new-results/partition-new-simu/fasttree/iclust-0/input-seqs.fa
+FastTree Version 2.1.10 SSE3
+Alignment: test/paired/new-results/partition-new-simu/fasttree/iclust-0/input-seqs.fa
+Nucleotide distances: Jukes-Cantor Joins: balanced Support: SH-like 1000
+Search: Normal +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1
+TopHits: 1.00*sqrtN close=default refresh=0.80
+ML Model: Generalized Time-Reversible, CAT approximation with 20 rate categories
+Ignored unknown character X (seen 32 times)
+Initial topology in 0.00 seconds
+Refining topology: 12 rounds ME-NNIs, 2 rounds ME-SPRs, 6 rounds ML-NNIs
+Total branch-length 0.172 after 0.01 sec
+ML-NNI round 1: LogLk = -1718.413 NNIs 0 max delta 0.00 Time 0.01
+GTR Frequencies: 0.2101 0.3021 0.2760 0.2118
+GTR rates(ac ag at cg ct gt) 1.2877 1.2172 1.4016 0.7474 1.0325 1.0000
+Switched to using 20 rate categories (CAT approximation)
+Rate categories were divided by 0.666 so that average rate = 1.0
+CAT-based log-likelihoods may not be comparable across runs
+Use -gamma for approximate but comparable Gamma(20) log-likelihoods
+ML-NNI round 2: LogLk = -1661.140 NNIs 0 max delta 0.00 Time 0.06
+Turning off heuristics for final round of ML NNIs (converged)
+ML-NNI round 3: LogLk = -1661.140 NNIs 0 max delta 0.00 Time 0.08 (final)
+Optimize all lengths: LogLk = -1661.140 Time 0.08
+Total time: 0.10 seconds Unique: 8/8 Bad splits: 0/5

partis_bcr-1.0.13/test/paired/new-results/partition-new-simu/fasttree/iclust-1/log

@@ -0,0 +1,23 @@
+run /home/runner/work/partis/partis/bin/FastTree-linux -gtr -nt -out test/paired/new-results/partition-new-simu/fasttree/iclust-1/fasttree.out test/paired/new-results/partition-new-simu/fasttree/iclust-1/input-seqs.fa
+FastTree Version 2.1.10 SSE3
+Alignment: test/paired/new-results/partition-new-simu/fasttree/iclust-1/input-seqs.fa
+Nucleotide distances: Jukes-Cantor Joins: balanced Support: SH-like 1000
+Search: Normal +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1
+TopHits: 1.00*sqrtN close=default refresh=0.80
+ML Model: Generalized Time-Reversible, CAT approximation with 20 rate categories
+Ignored unknown character X (seen 176 times)
+Initial topology in 0.00 seconds
+Refining topology: 12 rounds ME-NNIs, 2 rounds ME-SPRs, 6 rounds ML-NNIs
+Total branch-length 0.116 after 0.01 sec
+ML-NNI round 1: LogLk = -1516.977 NNIs 0 max delta 0.00 Time 0.02
+GTR Frequencies: 0.2498 0.2482 0.2788 0.2231
+GTR rates(ac ag at cg ct gt) 0.7186 0.4400 0.9760 0.8085 0.8107 1.0000
+Switched to using 20 rate categories (CAT approximation)
+Rate categories were divided by 0.652 so that average rate = 1.0
+CAT-based log-likelihoods may not be comparable across runs
+Use -gamma for approximate but comparable Gamma(20) log-likelihoods
+ML-NNI round 2: LogLk = -1478.013 NNIs 0 max delta 0.00 Time 0.06
+Turning off heuristics for final round of ML NNIs (converged)
+ML-NNI round 3: LogLk = -1478.012 NNIs 0 max delta 0.00 Time 0.07 (final)
+Optimize all lengths: LogLk = -1478.012 Time 0.07
+Total time: 0.08 seconds Unique: 8/8 Bad splits: 0/5

partis_bcr-1.0.13/test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/log

@@ -0,0 +1,23 @@
+run /home/runner/work/partis/partis/bin/FastTree-linux -gtr -nt -out /home/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/fasttree.out /home/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/input-seqs.fa
+FastTree Version 2.1.10 SSE3
+Alignment: /home/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/input-seqs.fa
+Nucleotide distances: Jukes-Cantor Joins: balanced Support: SH-like 1000
+Search: Normal +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1
+TopHits: 1.00*sqrtN close=default refresh=0.80
+ML Model: Generalized Time-Reversible, CAT approximation with 20 rate categories
+Ignored unknown character X (seen 21 times)
+Initial topology in 0.00 seconds
+Refining topology: 11 rounds ME-NNIs, 2 rounds ME-SPRs, 6 rounds ML-NNIs
+Total branch-length 0.133 after 0.00 sec
+ML-NNI round 1: LogLk = -824.239 NNIs 0 max delta 0.00 Time 0.01
+GTR Frequencies: 0.2278 0.2456 0.3207 0.2059
+GTR rates(ac ag at cg ct gt) 1.1229 1.2867 0.8408 1.1118 0.5795 1.0000
+Switched to using 20 rate categories (CAT approximation)
+Rate categories were divided by 0.658 so that average rate = 1.0
+CAT-based log-likelihoods may not be comparable across runs
+Use -gamma for approximate but comparable Gamma(20) log-likelihoods
+ML-NNI round 2: LogLk = -794.522 NNIs 0 max delta 0.00 Time 0.03
+Turning off heuristics for final round of ML NNIs (converged)
+ML-NNI round 3: LogLk = -794.513 NNIs 0 max delta 0.00 Time 0.03 (final)
+Optimize all lengths: LogLk = -794.513 Time 0.03
+Total time: 0.04 seconds Unique: 7/7 Bad splits: 0/4