partis-bcr 1.0.11.post1.dev1__cp312-cp312-manylinux1_x86_64.whl → 1.0.11.post1.dev7__cp312-cp312-manylinux1_x86_64.whl

test/paired/new-results/test/simu/meta.yaml

@@ -0,0 +1 @@
+{"a59a86319d-igh": {"locus": "igh", "paired-uids": []}, "63c1e600bb-igh": {"locus": "igh", "paired-uids": []}, "96f6ea6b59-igh": {"locus": "igh", "paired-uids": ["2d29c65222-igh", "2d29c65222-igl", "96f6ea6b59-igk"]}, "57810cb714-igh": {"locus": "igh", "paired-uids": ["57810cb714-igk"]}, "da88a0f870-igh": {"locus": "igh", "paired-uids": ["da88a0f870-igk"]}, "3659f04e0b-igh": {"locus": "igh", "paired-uids": []}, "962cf676f9-igh": {"locus": "igh", "paired-uids": ["962cf676f9-igk"]}, "8abdecedf6-igh": {"locus": "igh", "paired-uids": ["8abdecedf6-igk"]}, "f9494fc130-igh": {"locus": "igh", "paired-uids": ["f9494fc130-igk"]}, "816fc82f73-igh": {"locus": "igh", "paired-uids": ["816fc82f73-igk"]}, "810f8f7056-igh": {"locus": "igh", "paired-uids": ["810f8f7056-igk", "da96f2c471-igh", "da96f2c471-igl"]}, "997456da00-igh": {"locus": "igh", "paired-uids": ["94040b8e55-igh", "94040b8e55-igl", "997456da00-igk"]}, "047be6c743-igh": {"locus": "igh", "paired-uids": ["047be6c743-igk"]}, "7e90b4242e-igh": {"locus": "igh", "paired-uids": ["7e90b4242e-igk"]}, "14e4ff3a6a-igh": {"locus": "igh", "paired-uids": ["14e4ff3a6a-igk"]}, "5b83db58bc-igh": {"locus": "igh", "paired-uids": ["0e191a1e72-igh", "5b83db58bc-igk"]}, "dde37df0f3-igh": {"locus": "igh", "paired-uids": ["88ea4d6f94-igh", "dde37df0f3-igk"]}, "ceb855766e-igh": {"locus": "igh", "paired-uids": ["ceb855766e-igk"]}, "638b01f2ff-igh": {"locus": "igh", "paired-uids": ["638b01f2ff-igk"]}, "dc03113497-igh": {"locus": "igh", "paired-uids": []}, "42584a044c-igh": {"locus": "igh", "paired-uids": ["42584a044c-igk"]}, "7bfd25e622-igh": {"locus": "igh", "paired-uids": ["7bfd25e622-igk", "f74e482a75-igh", "f74e482a75-igl"]}, "a1f869b08f-igh": {"locus": "igh", "paired-uids": ["02c4dcf740-igh", "02c4dcf740-igl", "a1f869b08f-igk"]}, "626eeaeec5-igh": {"locus": "igh", "paired-uids": ["626eeaeec5-igk", "c022154f42-igh"]}, "7713c8e94f-igh": {"locus": "igh", "paired-uids": ["7713c8e94f-igk"]}, "2e42f5c485-igh": {"locus": "igh", "paired-uids": ["2e42f5c485-igk"]}, "feeff50eb0-igh": {"locus": "igh", "paired-uids": ["feeff50eb0-igk"]}, "cb9b787bf3-igh": {"locus": "igh", "paired-uids": ["cb9b787bf3-igk"]}, "2f6c99db02-igh": {"locus": "igh", "paired-uids": ["2f6c99db02-igk"]}, "6a1829447f-igh": {"locus": "igh", "paired-uids": ["6a1829447f-igk"]}, "d7b2f887dc-igh": {"locus": "igh", "paired-uids": ["d7b2f887dc-igk"]}, "99ec3a50a4-igh": {"locus": "igh", "paired-uids": ["3de3240f4c-igh", "3de3240f4c-igl", "99ec3a50a4-igk"]}, "9b1977f91e-igh": {"locus": "igh", "paired-uids": []}, "475a17c3bd-igh": {"locus": "igh", "paired-uids": ["475a17c3bd-igk", "4e6de5d38d-igh", "4e6de5d38d-igl"]}, "bc72018f26-igh": {"locus": "igh", "paired-uids": []}, "9cfd60a4c8-igh": {"locus": "igh", "paired-uids": ["9cfd60a4c8-igk"]}, "90bc43bbe6-igh": {"locus": "igh", "paired-uids": []}, "83cd33d783-igh": {"locus": "igh", "paired-uids": ["83cd33d783-igl"]}, "24174ebdc9-igh": {"locus": "igh", "paired-uids": ["24174ebdc9-igl", "8828e95dd5-igl"]}, "da96f2c471-igh": {"locus": "igh", "paired-uids": ["810f8f7056-igh", "810f8f7056-igk", "da96f2c471-igl"]}, "2d29c65222-igh": {"locus": "igh", "paired-uids": ["2d29c65222-igl", "96f6ea6b59-igh", "96f6ea6b59-igk"]}, "f74e482a75-igh": {"locus": "igh", "paired-uids": ["7bfd25e622-igh", "7bfd25e622-igk", "f74e482a75-igl"]}, "c022154f42-igh": {"locus": "igh", "paired-uids": ["626eeaeec5-igh", "626eeaeec5-igk"]}, "0e191a1e72-igh": {"locus": "igh", "paired-uids": ["5b83db58bc-igh", "5b83db58bc-igk"]}, "02c4dcf740-igh": {"locus": "igh", "paired-uids": ["02c4dcf740-igl", "a1f869b08f-igh", "a1f869b08f-igk"]}, "4e6de5d38d-igh": {"locus": "igh", "paired-uids": ["475a17c3bd-igh", "475a17c3bd-igk", "4e6de5d38d-igl"]}, "3de3240f4c-igh": {"locus": "igh", "paired-uids": ["3de3240f4c-igl", "99ec3a50a4-igh", "99ec3a50a4-igk"]}, "88ea4d6f94-igh": {"locus": "igh", "paired-uids": ["dde37df0f3-igh", "dde37df0f3-igk"]}, "94040b8e55-igh": {"locus": "igh", "paired-uids": ["94040b8e55-igl", "997456da00-igh", "997456da00-igk"]}, "96f6ea6b59-igk": {"locus": "igk", "paired-uids": ["2d29c65222-igh", "2d29c65222-igl", "96f6ea6b59-igh"]}, "57810cb714-igk": {"locus": "igk", "paired-uids": ["57810cb714-igh"]}, "da88a0f870-igk": {"locus": "igk", "paired-uids": ["da88a0f870-igh"]}, "962cf676f9-igk": {"locus": "igk", "paired-uids": ["962cf676f9-igh"]}, "8abdecedf6-igk": {"locus": "igk", "paired-uids": ["8abdecedf6-igh"]}, "f9494fc130-igk": {"locus": "igk", "paired-uids": ["f9494fc130-igh"]}, "816fc82f73-igk": {"locus": "igk", "paired-uids": ["816fc82f73-igh"]}, "810f8f7056-igk": {"locus": "igk", "paired-uids": ["810f8f7056-igh", "da96f2c471-igh", "da96f2c471-igl"]}, "997456da00-igk": {"locus": "igk", "paired-uids": ["94040b8e55-igh", "94040b8e55-igl", "997456da00-igh"]}, "047be6c743-igk": {"locus": "igk", "paired-uids": ["047be6c743-igh"]}, "8a4877bbfc-igk": {"locus": "igk", "paired-uids": []}, "7e90b4242e-igk": {"locus": "igk", "paired-uids": ["7e90b4242e-igh"]}, "964f9e33e6-igk": {"locus": "igk", "paired-uids": []}, "14e4ff3a6a-igk": {"locus": "igk", "paired-uids": ["14e4ff3a6a-igh"]}, "5b83db58bc-igk": {"locus": "igk", "paired-uids": ["0e191a1e72-igh", "5b83db58bc-igh"]}, "dde37df0f3-igk": {"locus": "igk", "paired-uids": ["88ea4d6f94-igh", "dde37df0f3-igh"]}, "ceb855766e-igk": {"locus": "igk", "paired-uids": ["ceb855766e-igh"]}, "638b01f2ff-igk": {"locus": "igk", "paired-uids": ["638b01f2ff-igh"]}, "42584a044c-igk": {"locus": "igk", "paired-uids": ["42584a044c-igh"]}, "7bfd25e622-igk": {"locus": "igk", "paired-uids": ["7bfd25e622-igh", "f74e482a75-igh", "f74e482a75-igl"]}, "a1f869b08f-igk": {"locus": "igk", "paired-uids": ["02c4dcf740-igh", "02c4dcf740-igl", "a1f869b08f-igh"]}, "626eeaeec5-igk": {"locus": "igk", "paired-uids": ["626eeaeec5-igh", "c022154f42-igh"]}, "7713c8e94f-igk": {"locus": "igk", "paired-uids": ["7713c8e94f-igh"]}, "2e42f5c485-igk": {"locus": "igk", "paired-uids": ["2e42f5c485-igh"]}, "feeff50eb0-igk": {"locus": "igk", "paired-uids": ["feeff50eb0-igh"]}, "cb9b787bf3-igk": {"locus": "igk", "paired-uids": ["cb9b787bf3-igh"]}, "2f6c99db02-igk": {"locus": "igk", "paired-uids": ["2f6c99db02-igh"]}, "6a1829447f-igk": {"locus": "igk", "paired-uids": ["6a1829447f-igh"]}, "d7b2f887dc-igk": {"locus": "igk", "paired-uids": ["d7b2f887dc-igh"]}, "99ec3a50a4-igk": {"locus": "igk", "paired-uids": ["3de3240f4c-igh", "3de3240f4c-igl", "99ec3a50a4-igh"]}, "475a17c3bd-igk": {"locus": "igk", "paired-uids": ["475a17c3bd-igh", "4e6de5d38d-igh", "4e6de5d38d-igl"]}, "9cfd60a4c8-igk": {"locus": "igk", "paired-uids": ["9cfd60a4c8-igh"]}, "83cd33d783-igl": {"locus": "igl", "paired-uids": ["83cd33d783-igh"]}, "24174ebdc9-igl": {"locus": "igl", "paired-uids": ["24174ebdc9-igh", "8828e95dd5-igl"]}, "da96f2c471-igl": {"locus": "igl", "paired-uids": ["810f8f7056-igh", "810f8f7056-igk", "da96f2c471-igh"]}, "2d29c65222-igl": {"locus": "igl", "paired-uids": ["2d29c65222-igh", "96f6ea6b59-igh", "96f6ea6b59-igk"]}, "8828e95dd5-igl": {"locus": "igl", "paired-uids": ["24174ebdc9-igh", "24174ebdc9-igl"]}, "f74e482a75-igl": {"locus": "igl", "paired-uids": ["7bfd25e622-igh", "7bfd25e622-igk", "f74e482a75-igh"]}, "02c4dcf740-igl": {"locus": "igl", "paired-uids": ["02c4dcf740-igh", "a1f869b08f-igh", "a1f869b08f-igk"]}, "4e6de5d38d-igl": {"locus": "igl", "paired-uids": ["475a17c3bd-igh", "475a17c3bd-igk", "4e6de5d38d-igh"]}, "3de3240f4c-igl": {"locus": "igl", "paired-uids": ["3de3240f4c-igh", "99ec3a50a4-igh", "99ec3a50a4-igk"]}, "94040b8e55-igl": {"locus": "igl", "paired-uids": ["94040b8e55-igh", "997456da00-igh", "997456da00-igk"]}}

test/paired/new-results/test.log

@@ -21,19 +21,19 @@ smith-waterman  (writing parameters)
       kept 25 (0.446) unproductive
         writing sw results to test/paired/new-results/test/parameters/simu/igh/sw-cache.yaml
     writing parameters to test/paired/new-results/test/parameters/simu/igh/sw (0.6 sec)
-    water time: 0.7  (ig-sw 0.7  processing 0.0)
+    water time: 0.7  (ig-sw 0.6  processing 0.0)
   writing hmms     removed 16 genes from glfo (leaving v 6  d 18  j 4)
 (0.5 sec)
 hmm
     reading output
         read 56 hmm output lines with 56 sequences in 56 events  (0 failures)
     writing parameters to test/paired/new-results/test/parameters/simu/igh/hmm (0.5 sec)
-    writing parameters to test/paired/new-results/test/parameters/simu/igh/true (0.5 sec)
+    writing parameters to test/paired/new-results/test/parameters/simu/igh/true (0.4 sec)
          infra time: 1.1
       hmm step time: 2.1
   writing hmms     removed 3  genes from glfo (leaving v 6  d 15  j 4)
 (0.3 sec)
-      total time: 4.0
+      total time: 3.9
 cache-parameters igk:
   note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
 run partis cache-parameters --locus igk --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igk --is-simu --random-seed 1 --n-procs 10 --infname test/paired/ref-results/test/simu/igk.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igk/sw-cache.yaml --input-metafnames test/paired/ref-results/test/simu/meta.yaml
@@ -68,8 +68,8 @@ hmm
          infra time: 0.9
       hmm step time: 1.4
   writing hmms     removed 0  genes from glfo (leaving v 5  d 1  j 5)
-(0.3 sec)
-      total time: 2.8
+(0.4 sec)
+      total time: 2.7
 cache-parameters igl:
   note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
 run partis cache-parameters --locus igl --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igl --is-simu --random-seed 1 --n-procs 10 --infname test/paired/ref-results/test/simu/igl.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igl/sw-cache.yaml --input-metafnames test/paired/ref-results/test/simu/meta.yaml
@@ -124,8 +124,8 @@ smith-waterman
 hmm
   caching all 56 naive sequences (1.0s)
     collapsed 56 queries into 50 clusters with identical naive seqs (0.0 sec)
-  50 clusters with 10 procs (0.6s)
-   44 clusters with 7 procs (0.5s)
+  50 clusters with 10 procs (0.5s)
+   44 clusters with 7 procs (0.6s)
    36 clusters with 5 procs (0.4s)
    31 clusters with 3 procs (0.3s)
    29 clusters with 2 procs (0.5s)
@@ -137,7 +137,7 @@ getting annotations for final partition
     warning skipped annotation performance evaluation on 1 queries with different true and inferred net shm indel lengths: db63559ea9-igh
 (0.0 sec)
 
-    subcluster annotation time 1.0
+    subcluster annotation time 0.9
       total time: 5.0
 partition igk:
   note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
@@ -260,7 +260,7 @@ smith-waterman
 hmm
   subcluster annotating 15 clusters with steps:  (0.3s) (0.1s) 
     subcluster annotation time 0.4
-      total time: 0.4
+      total time: 0.5
 igh+igl: synchronizing heavy and light chain cluster paths
     removing badly + unpaired seqs:  kept 7 total unpaired (i.e. setting aside in order to reintegrate after paired clustering): h 3  l 4
             note: discarding unpaired seqs in families with no (well-)paired seqs (i.e. families that are all either unpaired or paired to the other/wrong light chain), rather than keeping track of them to re-add later
@@ -331,7 +331,7 @@ hmm
         h   20 --> 23   +3
         k    6 --> 15   +9
         l    3 --> 8    +5
-      total time: 20.0
+      total time: 19.8
 subset-partition-new-simu        partis subset-partition --dont-write-git-info --paired-loci --paired-indir test/paired/ref-results/test/simu --max-ccf-fail-frac 0.15 --is-simu --n-subsets 2 --random-seed 1 --n-procs 10 --paired-outdir test/paired/new-results/subset-partition-new-simu
   note: --input-metafnames not specified, so setting to default location test/paired/ref-results/test/simu/meta.yaml
   --input-metafnames: added meta info for 113 sequences from test/paired/ref-results/test/simu/meta.yaml: loci paired-uids
@@ -362,7 +362,7 @@ hmm
     merging parameters from 2 subdirs (e.g. test/paired/new-results/subset-partition-new-simu/isub-0) to test/paired/new-results/subset-partition-new-simu/merged-subsets
 run partis partition --dont-write-git-info --paired-loci --paired-indir test/paired/ref-results/test/simu --max-ccf-fail-frac 0.15 --is-simu --random-seed 1 --n-procs 10 --paired-outdir test/paired/new-results/subset-partition-new-simu --input-metafnames test/paired/new-results/subset-partition-new-simu/merged-subsets/meta.yaml --input-partition-fname test/paired/new-results/subset-partition-new-simu/merged-subsets --continue-from-input-partition --parameter-dir test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters --ignore-sw-pair-info --refuse-to-cache-parameters --ignore-default-input-metafile
         log: test/paired/new-results/subset-partition-new-simu/merged-partition.log
-      total time: 68.1
+      total time: 68.4
 seed-partition-new-simu          partis partition --dont-write-git-info --paired-loci --paired-indir test/paired/ref-results/test/simu --parameter-dir test/paired/new-results/test/parameters/simu --max-ccf-fail-frac 0.10 --is-simu --seed-unique-id 3542bd38d8-igh:3542bd38d8-igk --seed-loci igh:igk --random-seed 1 --n-procs 10 --paired-outdir test/paired/new-results/seed-partition-new-simu
    removing seqs very different from seed seq
                            wrong/no     removed      singly         kept   missing
@@ -400,7 +400,7 @@ getting annotations for final partition
     reading output
         read 12 hmm output lines with 17 sequences in 12 events  (0 failures)
       hmm step time: 0.3
-      total time: 2.0
+      total time: 1.9
 partition igk:
   note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
 run partis partition --locus igk --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igk --max-ccf-fail-frac 0.10 --random-seed 1 --n-procs 10 --refuse-to-cache-parameters --infname test/paired/new-results/seed-partition-new-simu/seeds/3542bd38d8-igh+3542bd38d8-igk/single-chain/input-seqs-igk.fa --outfname test/paired/new-results/seed-partition-new-simu/seeds/3542bd38d8-igh+3542bd38d8-igk/single-chain/partition-igk.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igk/sw-cache.yaml --input-metafnames test/paired/ref-results/test/simu/meta.yaml
@@ -552,7 +552,7 @@ hmm
    N clusters with all seqs:
         h   12 --> 1    -11
         k    2 --> 1    -1
-      total time: 9.4
+      total time: 9.3
 get-selection-metrics-new-simu   partis get-selection-metrics --dont-write-git-info --paired-loci --existing-output-run-cfg paired --min-selection-metric-cluster-size 3 --min-paired-cluster-size-to-read 3 --random-seed 1 --n-procs 10 --paired-outdir test/paired/new-results/partition-new-simu --chosen-ab-fname test/paired/new-results/get-selection-metrics-new-simu-chosen-abs.csv
 get-selection-metrics igh+igk: igh
 run partis get-selection-metrics --locus igh --dont-write-git-info --min-selection-metric-cluster-size 3 --min-paired-cluster-size-to-read 3 --random-seed 1 --n-procs 10 --chosen-ab-fname test/paired/new-results/get-selection-metrics-new-simu-chosen-abs.csv --refuse-to-cache-parameters --outfname test/paired/new-results/partition-new-simu/igh+igk/partition-igh.yaml
@@ -673,10 +673,10 @@ hmm
     skipped 1/4 clusters that had no uids in common with tree
   writing selection metrics to test/paired/new-results/partition-new-simu/selection-metrics.yaml
       writing 10 chosen abs to test/paired/new-results/get-selection-metrics-new-simu-chosen-abs.csv
-      total time: 5.6
+      total time: 5.5
 cache-parameters-data            partis cache-parameters --dont-write-git-info --paired-loci --infname test/paired-data/all-seqs.fa --parameter-dir test/paired/new-results/test/parameters/data --n-max-queries 100 --random-seed 1 --n-procs 10
   note: --paired-outdir is not set, so there will be no persistent record of the results (except the parameter directory).
-run extract-pairing-info.py test/paired-data/all-seqs.fa /tmp/runner/hmms/749815/meta.yaml --n-max-queries 100
+run extract-pairing-info.py test/paired-data/all-seqs.fa /tmp/runner/hmms/520265/meta.yaml --n-max-queries 100
   --n-max-queries: chose 48 / 48 droplets (first 100, after random shuffling) which had 100 / 100 seqs
   extract_pairing_info(): read 100 sequences with 48 droplet ids
     droplet id separators (set automatically): _  indices: [0]
@@ -687,9 +687,9 @@ hmm
         2           42     0.875
         3            2     0.042
         4            2     0.042
-run split-loci.py test/paired-data/all-seqs.fa --outdir /tmp/runner/hmms/749815 --input-metafname /tmp/runner/hmms/749815/meta.yaml --n-max-queries 100
+run split-loci.py test/paired-data/all-seqs.fa --outdir /tmp/runner/hmms/520265 --input-metafname /tmp/runner/hmms/520265/meta.yaml --n-max-queries 100
   --n-max-queries: chose 48 / 48 droplets (first 100, after random shuffling) which had 100 / 100 seqs
-  --input-metafnames: added meta info for 100 sequences from /tmp/runner/hmms/749815/meta.yaml: paired-uids
+  --input-metafnames: added meta info for 100 sequences from /tmp/runner/hmms/520265/meta.yaml: paired-uids
     read pairing info for 100 seqs from input meta file
   running vsearch on 100 sequences:
     igh:   49 / 100 v annotations (51 failed) with 28 v genes in 0.1 sec
@@ -712,10 +712,10 @@ totals: igh 48 igk 37 igl 15
                2   0.13   h l
                1   0.07   h k
                1   0.07   h h k
-writing to /tmp/runner/hmms/749815/
-  igh: 48 to 749815/igh.fa
-  igk: 37 to 749815/igk.fa
-  igl: 15 to 749815/igl.fa
+writing to /tmp/runner/hmms/520265/
+  igh: 48 to 520265/igh.fa
+  igk: 37 to 520265/igk.fa
+  igl: 15 to 520265/igl.fa
 writing to paired subdirs
     igh+igk:
       igh: 36 / 48 to igh+igk/igh.fa
@@ -724,8 +724,8 @@ writing to paired subdirs
       igh: 15 / 48 to igh+igl/igh.fa
       igl: 15 / 15 to igh+igl/igl.fa
 cache-parameters igh:
-run partis cache-parameters --locus igh --dont-write-git-info --infname /tmp/runner/hmms/749815/igh.fa --parameter-dir test/paired/new-results/test/parameters/data/igh --random-seed 1 --n-procs 10 --sw-cachefname test/paired/new-results/test/parameters/data/igh/sw-cache.yaml --input-metafnames /tmp/runner/hmms/749815/meta.yaml
-  --input-metafnames: added meta info for 48 sequences from /tmp/runner/hmms/749815/meta.yaml: paired-uids
+run partis cache-parameters --locus igh --dont-write-git-info --infname /tmp/runner/hmms/520265/igh.fa --parameter-dir test/paired/new-results/test/parameters/data/igh --random-seed 1 --n-procs 10 --sw-cachefname test/paired/new-results/test/parameters/data/igh/sw-cache.yaml --input-metafnames /tmp/runner/hmms/520265/meta.yaml
+  --input-metafnames: added meta info for 48 sequences from /tmp/runner/hmms/520265/meta.yaml: paired-uids
 caching parameters
   vsearch: 48 / 48 v annotations (0 failed) with 27 v genes in 0.0 sec
     keeping 23 / 198 v genes
@@ -744,19 +744,19 @@ smith-waterman  (writing parameters)
     writing parameters to test/paired/new-results/test/parameters/data/igh/sw (2.0 sec)
     water time: 2.2  (ig-sw 2.1  processing 0.1)
   writing hmms     removed 13 genes from glfo (leaving v 23  d 19  j 6)
-(0.9 sec)
+(1.0 sec)
 hmm
     reading output
         read 48 hmm output lines with 48 sequences in 48 events  (0 failures)
-    writing parameters to test/paired/new-results/test/parameters/data/igh/hmm (1.9 sec)
+    writing parameters to test/paired/new-results/test/parameters/data/igh/hmm (2.0 sec)
          infra time: 2.0
       hmm step time: 3.0
   writing hmms     removed 1  genes from glfo (leaving v 23  d 18  j 6)
 (0.9 sec)
-      total time: 7.5
+      total time: 7.6
 cache-parameters igk:
-run partis cache-parameters --locus igk --dont-write-git-info --infname /tmp/runner/hmms/749815/igk.fa --parameter-dir test/paired/new-results/test/parameters/data/igk --random-seed 1 --n-procs 10 --sw-cachefname test/paired/new-results/test/parameters/data/igk/sw-cache.yaml --input-metafnames /tmp/runner/hmms/749815/meta.yaml
-  --input-metafnames: added meta info for 37 sequences from /tmp/runner/hmms/749815/meta.yaml: paired-uids
+run partis cache-parameters --locus igk --dont-write-git-info --infname /tmp/runner/hmms/520265/igk.fa --parameter-dir test/paired/new-results/test/parameters/data/igk --random-seed 1 --n-procs 10 --sw-cachefname test/paired/new-results/test/parameters/data/igk/sw-cache.yaml --input-metafnames /tmp/runner/hmms/520265/meta.yaml
+  --input-metafnames: added meta info for 37 sequences from /tmp/runner/hmms/520265/meta.yaml: paired-uids
 caching parameters
   vsearch: 37 / 37 v annotations (0 failed) with 16 v genes in 0.0 sec
     keeping 16 / 64 v genes
@@ -772,7 +772,7 @@ smith-waterman  (writing parameters)
       info for 37 / 37 = 1.000   (removed: 0 failed)
       kept 1 (0.027) unproductive
         writing sw results to test/paired/new-results/test/parameters/data/igk/sw-cache.yaml
-    writing parameters to test/paired/new-results/test/parameters/data/igk/sw (1.4 sec)
+    writing parameters to test/paired/new-results/test/parameters/data/igk/sw (1.3 sec)
     water time: 1.5  (ig-sw 1.4  processing 0.1)
   writing hmms     removed 0  genes from glfo (leaving v 16  d 1  j 7)
 (1.0 sec)
@@ -780,14 +780,14 @@ hmm
     reading output
         read 37 hmm output lines with 37 sequences in 37 events  (0 failures)
     writing parameters to test/paired/new-results/test/parameters/data/igk/hmm (1.3 sec)
-         infra time: 1.4
+         infra time: 1.3
       hmm step time: 1.9
   writing hmms     removed 0  genes from glfo (leaving v 16  d 1  j 7)
 (1.0 sec)
       total time: 5.7
 cache-parameters igl:
-run partis cache-parameters --locus igl --dont-write-git-info --infname /tmp/runner/hmms/749815/igl.fa --parameter-dir test/paired/new-results/test/parameters/data/igl --random-seed 1 --n-procs 10 --sw-cachefname test/paired/new-results/test/parameters/data/igl/sw-cache.yaml --input-metafnames /tmp/runner/hmms/749815/meta.yaml
-  --input-metafnames: added meta info for 15 sequences from /tmp/runner/hmms/749815/meta.yaml: paired-uids
+run partis cache-parameters --locus igl --dont-write-git-info --infname /tmp/runner/hmms/520265/igl.fa --parameter-dir test/paired/new-results/test/parameters/data/igl --random-seed 1 --n-procs 10 --sw-cachefname test/paired/new-results/test/parameters/data/igl/sw-cache.yaml --input-metafnames /tmp/runner/hmms/520265/meta.yaml
+  --input-metafnames: added meta info for 15 sequences from /tmp/runner/hmms/520265/meta.yaml: paired-uids
 caching parameters
   vsearch: 15 / 15 v annotations (0 failed) with 12 v genes in 0.0 sec
     keeping 10 / 80 v genes
@@ -814,5 +814,187 @@ hmm
   writing hmms     removed 0  genes from glfo (leaving v 10  d 1  j 3)
 (0.6 sec)
       total time: 3.5
-      warning expected to remove 1/11 files+dirs that weren't in /tmp/runner/hmms/749815/: failed.fa
+      warning expected to remove 1/11 files+dirs that weren't in /tmp/runner/hmms/520265/: failed.fa
       total time: 21.8
+simulate                         partis simulate --dont-write-git-info --paired-loci --parameter-dir test/paired/new-results/test/parameters/data --n-sim-events 10 --n-trees 10 --n-leaf-distribution geometric --n-leaves 5 --min-observations-per-gene 5 --mean-cells-per-droplet 1.25 --constant-cells-per-droplet --fraction-of-reads-to-remove 0.15 --input-simulation-treefname /home/runner/work/partis/partis/test/trees.nwk --no-per-base-mutation --random-seed 1 --n-procs 10 --paired-outdir test/paired/new-results/test/simu --indel-frequency 0.2
+igh+igk: simulating 7 events
+    warning drawing input simulation trees from --input-simulation-treefname *in order* for both heavy and light (rather than randomly, as for single chain)
+simulate igh+igk: igh
+run partis simulate --locus igh --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/data/igh --n-sim-events 7 --n-trees 10 --n-leaf-distribution geometric --n-leaves 5 --min-observations-per-gene 5 --mean-cells-per-droplet 1.25 --constant-cells-per-droplet --fraction-of-reads-to-remove 0.15 --input-simulation-treefname /home/runner/work/partis/partis/test/trees.nwk --no-per-base-mutation --random-seed 2003260051 --n-procs 10 --indel-frequency 0.2 --choose-trees-in-order --outfname test/paired/new-results/test/simu/igh+igk/igh.yaml
+  note: reducing --n-procs to 7 (was 10) so it isn't bigger than --n-sim-events
+simulating
+      --> proc 0
+    reco params: test/paired/new-results/test/parameters/data/igh/hmm     shm params: test/paired/new-results/test/parameters/data/igh/hmm
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/348431/trees-sub-0.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 10 seqs in 0.1s (0.1s of which was running bppseqgen)
+      total time: 0.1
+
+      --> proc 1
+    reco params: test/paired/new-results/test/parameters/data/igh/hmm     shm params: test/paired/new-results/test/parameters/data/igh/hmm
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/348431/trees-sub-1.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 8 seqs in 0.1s (0.0s of which was running bppseqgen)
+      total time: 0.2
+
+      --> proc 2
+    reco params: test/paired/new-results/test/parameters/data/igh/hmm     shm params: test/paired/new-results/test/parameters/data/igh/hmm
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/348431/trees-sub-2.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 1 seqs in 0.1s (0.0s of which was running bppseqgen)
+      total time: 0.2
+
+      --> proc 3
+    reco params: test/paired/new-results/test/parameters/data/igh/hmm     shm params: test/paired/new-results/test/parameters/data/igh/hmm
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/348431/trees-sub-3.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 6 seqs in 0.1s (0.0s of which was running bppseqgen)
+      total time: 0.1
+
+      --> proc 4
+    reco params: test/paired/new-results/test/parameters/data/igh/hmm     shm params: test/paired/new-results/test/parameters/data/igh/hmm
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/348431/trees-sub-4.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 1 seqs in 0.0s (0.0s of which was running bppseqgen)
+      total time: 0.1
+
+      --> proc 5
+    reco params: test/paired/new-results/test/parameters/data/igh/hmm     shm params: test/paired/new-results/test/parameters/data/igh/hmm
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/348431/trees-sub-5.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 1 seqs in 0.1s (0.0s of which was running bppseqgen)
+      total time: 0.1
+
+      --> proc 6
+    reco params: test/paired/new-results/test/parameters/data/igh/hmm     shm params: test/paired/new-results/test/parameters/data/igh/hmm
+    resetting --n-trees from 10 to 16 to match trees read from /tmp/runner/hmms/348431/trees-sub-6.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 13 seqs in 0.1s (0.1s of which was running bppseqgen)
+      total time: 0.2
+
+   read 7 events with 40 seqs from 7 .yaml files
+      total time: 4.1
+simulate igh+igk: igk
+run partis simulate --locus igk --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/data/igk --n-sim-events 7 --n-trees 10 --n-leaf-distribution geometric --n-leaves 5 --min-observations-per-gene 5 --mean-cells-per-droplet 1.25 --constant-cells-per-droplet --fraction-of-reads-to-remove 0.15 --input-simulation-treefname /home/runner/work/partis/partis/test/trees.nwk --no-per-base-mutation --random-seed 2077655082 --n-procs 10 --indel-frequency 0.2 --choose-trees-in-order --outfname test/paired/new-results/test/simu/igh+igk/igk.yaml
+  note: reducing --n-procs to 7 (was 10) so it isn't bigger than --n-sim-events
+simulating
+      --> proc 0
+    reco params: test/paired/new-results/test/parameters/data/igk/hmm     shm params: test/paired/new-results/test/parameters/data/igk/hmm
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/395544/trees-sub-0.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 10 seqs in 0.1s (0.0s of which was running bppseqgen)
+      total time: 0.1
+
+      --> proc 1
+    reco params: test/paired/new-results/test/parameters/data/igk/hmm     shm params: test/paired/new-results/test/parameters/data/igk/hmm
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/395544/trees-sub-1.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 8 seqs in 0.1s (0.0s of which was running bppseqgen)
+      total time: 0.1
+
+      --> proc 2
+    reco params: test/paired/new-results/test/parameters/data/igk/hmm     shm params: test/paired/new-results/test/parameters/data/igk/hmm
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/395544/trees-sub-2.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 1 seqs in 0.0s (0.0s of which was running bppseqgen)
+      total time: 0.1
+
+      --> proc 3
+    reco params: test/paired/new-results/test/parameters/data/igk/hmm     shm params: test/paired/new-results/test/parameters/data/igk/hmm
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/395544/trees-sub-3.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 6 seqs in 0.1s (0.0s of which was running bppseqgen)
+      total time: 0.1
+
+      --> proc 4
+    reco params: test/paired/new-results/test/parameters/data/igk/hmm     shm params: test/paired/new-results/test/parameters/data/igk/hmm
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/395544/trees-sub-4.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 1 seqs in 0.1s (0.0s of which was running bppseqgen)
+      total time: 0.1
+
+      --> proc 5
+    reco params: test/paired/new-results/test/parameters/data/igk/hmm     shm params: test/paired/new-results/test/parameters/data/igk/hmm
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/395544/trees-sub-5.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 1 seqs in 0.1s (0.0s of which was running bppseqgen)
+      total time: 0.1
+
+      --> proc 6
+    reco params: test/paired/new-results/test/parameters/data/igk/hmm     shm params: test/paired/new-results/test/parameters/data/igk/hmm
+    resetting --n-trees from 10 to 16 to match trees read from /tmp/runner/hmms/395544/trees-sub-6.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 13 seqs in 0.1s (0.1s of which was running bppseqgen)
+      total time: 0.1
+
+   read 7 events with 40 seqs from 7 .yaml files
+      total time: 4.0
+igh+igl: simulating 3 events
+    warning drawing input simulation trees from --input-simulation-treefname *in order* for both heavy and light (rather than randomly, as for single chain)
+simulate igh+igl: igh
+run partis simulate --locus igh --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/data/igh --n-sim-events 3 --n-trees 10 --n-leaf-distribution geometric --n-leaves 5 --min-observations-per-gene 5 --mean-cells-per-droplet 1.25 --constant-cells-per-droplet --fraction-of-reads-to-remove 0.15 --input-simulation-treefname /home/runner/work/partis/partis/test/trees.nwk --no-per-base-mutation --random-seed 982264879 --n-procs 10 --indel-frequency 0.2 --choose-trees-in-order --outfname test/paired/new-results/test/simu/igh+igl/igh.yaml
+  note: reducing --n-procs to 3 (was 10) so it isn't bigger than --n-sim-events
+simulating
+      --> proc 0
+    reco params: test/paired/new-results/test/parameters/data/igh/hmm     shm params: test/paired/new-results/test/parameters/data/igh/hmm
+    resetting --n-trees from 10 to 33 to match trees read from /tmp/runner/hmms/905323/trees-sub-0.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 10 seqs in 0.1s (0.0s of which was running bppseqgen)
+      total time: 0.1
+
+      --> proc 1
+    reco params: test/paired/new-results/test/parameters/data/igh/hmm     shm params: test/paired/new-results/test/parameters/data/igh/hmm
+    resetting --n-trees from 10 to 33 to match trees read from /tmp/runner/hmms/905323/trees-sub-1.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 2 seqs in 0.0s (0.0s of which was running bppseqgen)
+      total time: 0.1
+
+      --> proc 2
+    reco params: test/paired/new-results/test/parameters/data/igh/hmm     shm params: test/paired/new-results/test/parameters/data/igh/hmm
+    resetting --n-trees from 10 to 34 to match trees read from /tmp/runner/hmms/905323/trees-sub-2.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 1 seqs in 0.0s (0.0s of which was running bppseqgen)
+      total time: 0.1
+
+   read 3 events with 13 seqs from 3 .yaml files
+      total time: 2.0
+simulate igh+igl: igl
+run partis simulate --locus igl --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/data/igl --n-sim-events 3 --n-trees 10 --n-leaf-distribution geometric --n-leaves 5 --min-observations-per-gene 5 --mean-cells-per-droplet 1.25 --constant-cells-per-droplet --fraction-of-reads-to-remove 0.15 --input-simulation-treefname /home/runner/work/partis/partis/test/trees.nwk --no-per-base-mutation --random-seed 1083609742 --n-procs 10 --indel-frequency 0.2 --choose-trees-in-order --outfname test/paired/new-results/test/simu/igh+igl/igl.yaml
+  note: reducing --n-procs to 3 (was 10) so it isn't bigger than --n-sim-events
+simulating
+      --> proc 0
+    reco params: test/paired/new-results/test/parameters/data/igl/hmm     shm params: test/paired/new-results/test/parameters/data/igl/hmm
+    resetting --n-trees from 10 to 33 to match trees read from /tmp/runner/hmms/409067/trees-sub-0.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 10 seqs in 0.0s (0.0s of which was running bppseqgen)
+      total time: 0.1
+
+      --> proc 1
+    reco params: test/paired/new-results/test/parameters/data/igl/hmm     shm params: test/paired/new-results/test/parameters/data/igl/hmm
+    resetting --n-trees from 10 to 33 to match trees read from /tmp/runner/hmms/409067/trees-sub-1.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 2 seqs in 0.0s (0.0s of which was running bppseqgen)
+      total time: 0.1
+
+      --> proc 2
+    reco params: test/paired/new-results/test/parameters/data/igl/hmm     shm params: test/paired/new-results/test/parameters/data/igl/hmm
+    resetting --n-trees from 10 to 34 to match trees read from /tmp/runner/hmms/409067/trees-sub-2.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 1 seqs in 0.0s (0.0s of which was running bppseqgen)
+      total time: 0.1
+
+   read 3 events with 13 seqs from 3 .yaml files
+      total time: 2.1
+igh+igk: synchronizing heavy and light chain simulation trees and rewriting output files in test/paired/new-results/test/simu/igh+igk/
+igh+igl: synchronizing heavy and light chain simulation trees and rewriting output files in test/paired/new-results/test/simu/igh+igl/
+  concatenating heavy chain loci:
+      h starting with 7 annotations (40 seqs)
+      k starting with 7 annotations (40 seqs)
+      h adding 3 annotations (13 seqs) for total 7 (40)
+      l starting with 3 annotations (13 seqs)
+    finished with:
+     h: 10 annotations (53 seqs)
+  apportioned 106 seqs among 42 droplets (mean/2 1.3): 2 2 2 4 4 2 4 4 4 4 2 2 2 4 2 2 2 2 2 2 2 2 2 2 4 2 4 2 2 2 2 2 4 4 2 2 2 2 2 2 2 2
+  removed 15 / 106 = 0.14 seqs from outfos (leaving 9 / 91 unpaired)
+    writing combined h/l info to fasta and meta files in test/paired/new-results/test/simu
+      total time: 17.2

test/test.py

@@ -299,6 +299,10 @@ class Tester(object):
 
         if ptest == 'simulate':
             argfo['parameter-dir'] = self.paramdir(input_stype, 'data')
+            if args.no_tree_gen:
+                argfo['extras'] += ['--input-simulation-treefname', '%s/test/trees.nwk'%utils.get_partis_dir()]
+            if args.no_per_base_mutation:
+                argfo['extras'] += ['--no-per-base-mutation']
         else:
             argfo['inpath'] = self.inpath('new' if args.bust_cache else 'ref', input_dtype)
             if ptest.find('subset-') != 0:
@@ -932,6 +936,8 @@ parser.add_argument('--only-bust-current', action='store_true', help='only bust
 parser.add_argument('--paired', action='store_true', help='run paired tests, i.e. with --paired-loci. Note that this doesn\'t test all the things (e.g. seed partitioning) that non-paired does.')
 parser.add_argument('--run-all', action='store_true', help='run all four combinations of tests: paired/non-paired and slow/non-slow (by default only runs one). *Not* for use with --bust-cache, which runs all of them by default.')
 parser.add_argument('--no-simu', action='store_true', help='don\'t run simulation, e.g. if using a minimal install')
+parser.add_argument('--no-tree-gen', action='store_true', help='if set, use the pre-generated newick file instead of generating trees with R/TreeSim (to avoid R installation)')
+parser.add_argument('--no-per-base-mutation', action='store_true', help='use simpler, non-per-base mutation model (to avoid bpp-newlik compilation)')
 parser.add_argument('--ig-or-tr', default='ig')
 parser.add_argument('--print-width', type=int, default=300, help='set to 0 for infinite')
 

test/trees.nwk

@@ -0,0 +1,100 @@
+((((((t5:0.0065205083289372285,t3:0.0065205083289372285):0.00022500931509783387,t7:0.006745517643935062):0.004899701229952831,(t1:0.002825027845972804,(t6:0.0017243288909834001,t10:0.0017243288909834001):0.0011006989559894037):0.008820191027915088):0.0002897695747972105,t2:0.011934988449885104):0.0007992344206923059,(t8:0.010981561979894283,(t4:0.010449007139899408,t9:0.010449007139899408):0.0005325548361948731):0.0017526608909831274):0.0007190526455930778):0.0;
+(((t1:0.0001258970141987568,t2:0.0001258970141987568):0.008179458898919231,t3:0.008305355912917988):0.005147919601949166):0.0;
+(((t7:0.009141959291085274,(t4:0.002603508111024285,t1:0.002603508111024285):0.0065384511800609885):0.00238863691202228,((((t3:0.0007869701168073406,t8:0.0007869701168073406):0.004511602509042083,t2:0.005298572626049423):0.00012755219780118975,t5:0.005426124824050613):0.002271650574021189,t6:0.007697775398071802):0.0038328208050357514):0.001922679312017934):0.0;
+((t1:0.0006977605115867409,t2:0.0006977605115867409):0.012755515003413747):0.0;
+(((t3:0.05287050335052537,(t5:0.026930500450267604,(t2:0.01960187748019478,(t4:0.013062577110129802,t6:0.013062577110129802):0.006539300371064981):0.007328622971072824):0.02594000290025776):0.04450796612044227,t1:0.09737846947096765):0.0022940356280227955):0.0;
+(((((t4:0.021655813878369522,t7:0.021655813878369522):0.00754609737143185,(t9:0.028930954397821774,(t5:0.02595504159804583,(((t10:0.0042205255246822344,t17:0.0042205255246822344):0.0113905359591424,t3:0.015611061478824635):0.009117683045313525,(t13:0.020486598618457554,t14:0.020486598618457554):0.0042421459106806066):0.0012262970749076715):0.002975912793775942):0.0002709568499795995):0.0020096117458486954,t16:0.031211522987650068):0.008580525414353968,((((t1:0.01663197558874777,(t6:0.0062756261115275045,t11:0.0062756261115275045):0.010356349479220265):0.0013316909538997363,(t15:0.0008506675798359528,t8:0.0008506675798359528):0.017112998968711553):0.0024270265108172675,t2:0.020390693058464773):0.007547202862431767,t12:0.02793789591789654):0.011854152489107496):0.0013141289639010585):0.0;
+((((t2:0.011559177998719477,t4:0.011559177998719477):0.011980991178672748,(t1:0.014158793318431492,t5:0.014158793318431492):0.009381375845960735):0.01119591956875972,t3:0.03473608873615194):0.006370088632294323):0.0;
+(t1:0.06981781729950898):0.0;
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