Skip to content

Commit

Permalink
v0.2.2 - running pre release script
Browse files Browse the repository at this point in the history
  • Loading branch information
bluenote-1577 committed Jul 5, 2024
1 parent 9c5fe00 commit 666894c
Show file tree
Hide file tree
Showing 2 changed files with 123 additions and 70 deletions.
2 changes: 1 addition & 1 deletion scripts/pre_release.sh
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
#!/bin/bash

# Define the expected version
EXPECTED_VERSION="0.2.1"
EXPECTED_VERSION="0.2.2"

# Function to extract the version from Cargo.toml
get_cargo_version() {
Expand Down
191 changes: 122 additions & 69 deletions test_results_versions/0.2.2
Original file line number Diff line number Diff line change
@@ -1,62 +1,113 @@

running 0 tests

successes:

successes:

test result: ok. 0 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s


running 0 tests

successes:

successes:

test result: ok. 0 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s


running 4 tests
test fast_show_degenerate_inputs ... [00:00:00.000] (7f9350a12480) INFO /home/jshaw/software/skani/target/debug/skani dist file_that_doesn't_exist file_that_doesn't_exist
[00:00:00.000] (7f9350a12480) WARN file_that_doesn't_exist is not a valid fasta/fastq file; skipping.
[00:00:00.000] (7f9350a12480) WARN file_that_doesn't_exist is not a valid fasta/fastq file; skipping.
[00:00:00.000] (7f9350a12480) ERROR No reference sketches/genomes or query sketches/genomes found.

[00:00:00.000] (7f1c7513f480) INFO /home/jshaw/software/skani/target/debug/skani dist ./test_files/query_list.txt ./test_files/viruses.fna
[00:00:00.000] (7f1c7513f480) WARN ./test_files/query_list.txt is not a valid fasta/fastq file; skipping.
[00:00:00.000] (7f1c7513f480) ERROR No reference sketches/genomes or query sketches/genomes found.

[00:00:00.000] (7fdb7118d480) INFO /home/jshaw/software/skani/target/debug/skani dist ./test_files/query_list.txt list.txt
[00:00:00.000] (7fdb7118d480) WARN list.txt is not a valid fasta/fastq file; skipping.
[00:00:00.000] (7fdb7118d480) WARN ./test_files/query_list.txt is not a valid fasta/fastq file; skipping.
[00:00:00.000] (7fdb7118d480) ERROR No reference sketches/genomes or query sketches/genomes found.

[00:00:00.000] (7f267177a480) INFO /home/jshaw/software/skani/target/debug/skani dist ./test_files/empty_fasta.fa ./test_files/empty_fasta.fa
[00:00:00.000] (7f267177a480) WARN File ./test_files/empty_fasta.fa consists of only contigs < 500 bp. Skipping this file.
[00:00:00.000] (7f267177a480) WARN File ./test_files/empty_fasta.fa consists of only contigs < 500 bp. Skipping this file.
[00:00:00.000] (7f267177a480) ERROR No reference sketches/genomes or query sketches/genomes found.

[00:00:00.000] (7fb007e27480) INFO /home/jshaw/software/skani/target/debug/skani dist --qi --ri ./test_files/empty_fasta.fa ./test_files/empty_fasta.fa
[00:00:00.000] (7fb007e27480) WARN At least one sequence in file ./test_files/empty_fasta.fa has < 500 bp. These sequences will be skipped.
[00:00:00.000] (7fb007e27480) WARN At least one sequence in file ./test_files/empty_fasta.fa has < 500 bp. These sequences will be skipped.
[00:00:00.000] (7fb007e27480) ERROR No reference sketches/genomes or query sketches/genomes found.

[00:00:00.000] (7f758d2cd480) INFO /home/jshaw/software/skani/target/debug/skani dist ./test_files/all_ns.fa ./test_files/all_ns.fa
[00:00:00.001] (7f758d2cd480) INFO Learned ANI mode detected. ANI may be adjusted according to a regression model trained on MAGs.
[00:00:00.001] (7f758d2cd480) INFO Generating sketch time: 0.001056513
[00:00:00.001] (7f758d2cd480) INFO ANI calculation time: 0.000024224

ok
test fast_test_screen ... rescue small heuristic with screen 345
test test_diag_triangle ... ok
test fast_show_degenerate_inputs ... ok
test fast_test_small_genomes ... ok
test fast_test_screen ... ok

successes:

---- fast_show_degenerate_inputs stdout ----
[00:00:00.000] (7f9faee12480) INFO /home/jshaw/software/skani/target/debug/skani dist file_that_doesn't_exist file_that_doesn't_exist
[00:00:00.000] (7f9faee12480) WARN file_that_doesn't_exist is not a valid fasta/fastq file; skipping.
[00:00:00.000] (7f9faee12480) WARN file_that_doesn't_exist is not a valid fasta/fastq file; skipping.
[00:00:00.000] (7f9faee12480) ERROR No reference sketches/genomes or query sketches/genomes found.

[00:00:00.000] (7f83fe9df480) INFO /home/jshaw/software/skani/target/debug/skani dist ./test_files/query_list.txt ./test_files/viruses.fna
[00:00:00.000] (7f83fe9df480) WARN ./test_files/query_list.txt is not a valid fasta/fastq file; skipping.
[00:00:00.002] (7f83fe9df480) ERROR No reference sketches/genomes or query sketches/genomes found.

[00:00:00.000] (7f7c2dcdd480) INFO /home/jshaw/software/skani/target/debug/skani dist ./test_files/query_list.txt list.txt
[00:00:00.000] (7f7c2dcdd480) WARN list.txt is not a valid fasta/fastq file; skipping.
[00:00:00.000] (7f7c2dcdd480) WARN ./test_files/query_list.txt is not a valid fasta/fastq file; skipping.
[00:00:00.000] (7f7c2dcdd480) ERROR No reference sketches/genomes or query sketches/genomes found.

[00:00:00.000] (7fc29a04a480) INFO /home/jshaw/software/skani/target/debug/skani dist ./test_files/empty_fasta.fa ./test_files/empty_fasta.fa
[00:00:00.000] (7fc29a04a480) WARN File ./test_files/empty_fasta.fa consists of only contigs < 500 bp. Skipping this file.
[00:00:00.000] (7fc29a04a480) WARN File ./test_files/empty_fasta.fa consists of only contigs < 500 bp. Skipping this file.
[00:00:00.000] (7fc29a04a480) ERROR No reference sketches/genomes or query sketches/genomes found.

[00:00:00.000] (7efcef71c480) INFO /home/jshaw/software/skani/target/debug/skani dist --qi --ri ./test_files/empty_fasta.fa ./test_files/empty_fasta.fa
[00:00:00.000] (7efcef71c480) WARN At least one sequence in file ./test_files/empty_fasta.fa has < 500 bp. These sequences will be skipped.
[00:00:00.000] (7efcef71c480) WARN At least one sequence in file ./test_files/empty_fasta.fa has < 500 bp. These sequences will be skipped.
[00:00:00.000] (7efcef71c480) ERROR No reference sketches/genomes or query sketches/genomes found.

[00:00:00.000] (7f79630d4480) INFO /home/jshaw/software/skani/target/debug/skani dist ./test_files/all_ns.fa ./test_files/all_ns.fa
[00:00:00.001] (7f79630d4480) INFO Learned ANI mode detected. ANI may be adjusted according to a regression model trained on MAGs.
[00:00:00.001] (7f79630d4480) INFO Generating sketch time: 0.001046916
[00:00:00.001] (7f79630d4480) INFO ANI calculation time: 0.000008017


---- fast_test_small_genomes stdout ----
o157_reads, number of results without faster-small: 270
o157_reads, number of results WITH faster-small: 154

---- fast_test_screen stdout ----
rescue small heuristic with screen 345
rescue small heuristic no screen 345
dist no rescue, no screen 175
dist rescue, no screen 269
no rescue, screen 87
no rescue, screen, 0 markers 0
ok
test fast_test_small_genomes ... o157_reads, number of results without faster-small: 270
o157_reads, number of results WITH faster-small: 154
ok
test test_diag_triangle ... ok

test result: ok. 4 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.76s

successes:
fast_show_degenerate_inputs
fast_test_screen
fast_test_small_genomes
test_diag_triangle

test result: ok. 4 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.46s


running 3 tests
test full_test_dist ... AAI E.coli test
test full_test_triangle ... ok
test full_test_dist ... ok
test full_test_sketch_and_search ... ok

successes:

---- full_test_triangle stdout ----
4
./test_files/GCF_005706655.1_ASM570665v1_genomic.fna
./test_files/e.coli-EC590.fasta 0.00
./test_files/e.coli-W.fasta.gz 0.00 98.58
./test_files/o157_reads.fastq 0.00 92.81 93.15

[00:00:00.000] (7eff20db7480) INFO /home/jshaw/software/skani/target/debug/skani triangle -l ./test_files/query_list.txt
[00:00:00.073] (7eff20db7480) INFO Learned ANI mode detected. ANI may be adjusted according to a regression model trained on MAGs.
[00:00:00.090] (7eff20db7480) INFO Aligned fraction matrix written to skani_matrix.af
[00:00:00.090] (7eff20db7480) INFO ANI triangle time: 0.09080148

--faster-small TEST

4
./test_files/GCF_005706655.1_ASM570665v1_genomic.fna 100.00 0.00 0.00 0.00
./test_files/e.coli-EC590.fasta 0.00 100.00 98.58 92.81
./test_files/e.coli-W.fasta.gz 0.00 98.58 100.00 93.15
./test_files/o157_reads.fastq 0.00 92.81 93.15 100.00


---- full_test_dist stdout ----
AAI E.coli test
Ref_file Query_file AAI Align_fraction_ref Align_fraction_query Ref_name Query_name
./test_files/e.coli-K12.fasta ./test_files/e.coli-EC590.fasta 98.74 98.25 98.86 NC_007779.1 Escherichia coli str. K-12 substr. W3110, complete sequence NZ_CP016182.2 Escherichia coli strain EC590 chromosome, complete genome

Expand All @@ -73,14 +124,15 @@ ANI E.coli-klebsiella test
Ref_file Query_file ANI Align_fraction_ref Align_fraction_query Ref_name Query_name
./test_files/MN-03.fa ./test_files/e.coli-K12.fasta 79.68 26.21 29.59 NZ_CP081897.1 Klebsiella pneumoniae strain MN-03 chromosome, complete genome NC_007779.1 Escherichia coli str. K-12 substr. W3110, complete sequence

ok
test full_test_sketch_and_search ... ANI search test

---- full_test_sketch_and_search stdout ----
ANI search test
Ref_file Query_file ANI Align_fraction_ref Align_fraction_query Ref_name Query_name
test_files/o157_plasmid.fasta ./test_files/e.coli-o157.fasta 100.00 99.84 1.68 NZ_CP017439.1 Escherichia coli O157:H7 strain 2159 plasmid pO157, complete sequence NZ_CP017438.1 Escherichia coli O157:H7 strain 2159 chromosome, complete genome
test_files/e.coli-o157.fasta ./test_files/e.coli-o157.fasta 100.00 100.00 100.00 NZ_CP017438.1 Escherichia coli O157:H7 strain 2159 chromosome, complete genome NZ_CP017438.1 Escherichia coli O157:H7 strain 2159 chromosome, complete genome
test_files/e.coli-EC590.fasta ./test_files/e.coli-o157.fasta 98.44 87.84 73.62 NZ_CP016182.2 Escherichia coli strain EC590 chromosome, complete genome NZ_CP017438.1 Escherichia coli O157:H7 strain 2159 chromosome, complete genome
test_files/e.coli-K12.fasta ./test_files/e.coli-o157.fasta 98.42 88.04 74.25 NC_007779.1 Escherichia coli str. K-12 substr. W3110, complete sequence NZ_CP017438.1 Escherichia coli O157:H7 strain 2159 chromosome, complete genome
test_files/e.coli-W.fasta.gz ./test_files/e.coli-o157.fasta 98.39 85.46 75.97 NC_017664.1 Escherichia coli W, complete sequence NZ_CP017438.1 Escherichia coli O157:H7 strain 2159 chromosome, complete genome
test_files/e.coli-W.fasta ./test_files/e.coli-o157.fasta 98.39 85.46 75.97 NC_017664.1 Escherichia coli W, complete sequence NZ_CP017438.1 Escherichia coli O157:H7 strain 2159 chromosome, complete genome

ANI search test learned
Ref_file Query_file ANI Align_fraction_ref Align_fraction_query Ref_name Query_name
Expand All @@ -90,11 +142,11 @@ test_files/e.coli-EC590.fasta ./test_files/e.coli-o157.fasta 98.44 87.84 73.62 N
test_files/e.coli-K12.fasta ./test_files/e.coli-o157.fasta 98.42 88.04 74.25 NC_007779.1 Escherichia coli str. K-12 substr. W3110, complete sequence NZ_CP017438.1 Escherichia coli O157:H7 strain 2159 chromosome, complete genome
test_files/e.coli-W.fasta ./test_files/e.coli-o157.fasta 98.39 85.46 75.97 NC_017664.1 Escherichia coli W, complete sequence NZ_CP017438.1 Escherichia coli O157:H7 strain 2159 chromosome, complete genome

[00:00:00.000] (7fcd35c99480) INFO /home/jshaw/software/skani/target/debug/skani search -d ./tests/results/test_sketch_dir/ ./tests/results/test_sketch_dir/markers.bin ./tests/results/test_sketch_dir/e.coli-EC590.fasta.sketch
[00:00:00.000] (7fcd35c99480) INFO Searching...
[00:00:00.001] (7fcd35c99480) INFO Learned ANI mode detected. ANI may be adjusted according to a regression model trained on MAGs.
[00:00:00.001] (7fcd35c99480) INFO Loading markers time: 0.001559318
[00:00:00.055] (7fcd35c99480) INFO Searching time: 0.054292697
[00:00:00.000] (7f6e247a9480) INFO /home/jshaw/software/skani/target/debug/skani search -d ./tests/results/test_sketch_dir/ ./tests/results/test_sketch_dir/markers.bin ./tests/results/test_sketch_dir/e.coli-EC590.fasta.sketch
[00:00:00.000] (7f6e247a9480) INFO Searching...
[00:00:00.001] (7f6e247a9480) INFO Learned ANI mode detected. ANI may be adjusted according to a regression model trained on MAGs.
[00:00:00.001] (7f6e247a9480) INFO Loading markers time: 0.001559018
[00:00:00.059] (7f6e247a9480) INFO Searching time: 0.058213696

AAI search test
Ref_file Query_file AAI Align_fraction_ref Align_fraction_query Ref_name Query_name
Expand Down Expand Up @@ -375,43 +427,44 @@ Ref_file Query_file ANI Align_fraction_ref Align_fraction_query Ref_name Query_n
./test_files/e.coli-EC590.fasta ./test_files/o157_reads.fastq 93.88 0.37 96.78 NZ_CP016182.2 Escherichia coli strain EC590 chromosome, complete genome fe0cd2ea-fe40-cf0f-d7ab-d0a699dffa0b NZ_CP017438.1,+strand,1378797-1396517 length=17722 error-free_length=17720 read_identity=94.32%
./test_files/e.coli-EC590.fasta ./test_files/o157_reads.fastq 97.90 0.25 94.27 NZ_CP016182.2 Escherichia coli strain EC590 chromosome, complete genome ff0d321f-c9cf-0f8f-e518-538b3ab0e53b NZ_CP017438.1,-strand,1803091-1815087 length=12009 error-free_length=11996 read_identity=99.30%

ok
test full_test_triangle ... 4
./test_files/GCF_005706655.1_ASM570665v1_genomic.fna
./test_files/e.coli-EC590.fasta 0.00
./test_files/e.coli-W.fasta.gz 0.00 98.58
./test_files/o157_reads.fastq 0.00 92.81 93.15

[00:00:00.000] (7eff99792480) INFO /home/jshaw/software/skani/target/debug/skani triangle -l ./test_files/query_list.txt
[00:00:00.052] (7eff99792480) INFO Learned ANI mode detected. ANI may be adjusted according to a regression model trained on MAGs.
[00:00:00.065] (7eff99792480) INFO Aligned fraction matrix written to skani_matrix.af
[00:00:00.065] (7eff99792480) INFO ANI triangle time: 0.065410115

--faster-small TEST

4
./test_files/GCF_005706655.1_ASM570665v1_genomic.fna 100.00 0.00 0.00 0.00
./test_files/e.coli-EC590.fasta 0.00 100.00 98.58 92.81
./test_files/e.coli-W.fasta.gz 0.00 98.58 100.00 93.15
./test_files/o157_reads.fastq 0.00 92.81 93.15 100.00
successes:
full_test_dist
full_test_sketch_and_search
full_test_triangle

ok

test result: ok. 3 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 7.82s
test result: ok. 3 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 4.62s


running 5 tests
test fast_NNN_test_code ... ok
test fast_avx2_vs_normal_code ... ok
test fast_ecoli_plasmid_test ... ok
test fast_ecoli_test_simple ... ok
test fast_eukaryote_test ... AniEstResult { ani: 0.9898663, align_fraction_query: 0.60535073, align_fraction_ref: 0.74593395, ref_file: "./test_files/TOPAZ_IOD1_E001.fna.gz", query_file: "./test_files/TOPAZ_RSS1_E007.fna.gz", query_contig: "RS-all-SRF-0-8-5-00_k119_3692", ref_contig: "IO-all-DCM-0-8-5-00_k119_2678", ci_upper: 0.9900135, ci_lower: 0.9897283, aai: false, quant_90_contig_len_q: 9095.0, quant_90_contig_len_r: 7016.0, quant_50_contig_len_q: 4276.0, quant_50_contig_len_r: 3761.0, quant_10_contig_len_q: 2759.0, quant_10_contig_len_r: 2688.0, std: 0.007433527, num_contigs_q: 8559, num_contigs_r: 8377, avg_chain_int_len: 3187, total_bases_covered: 27655368 }
ok
test fast_eukaryote_test ... ok

successes:

---- fast_eukaryote_test stdout ----
AniEstResult { ani: 0.9898663, align_fraction_query: 0.60535073, align_fraction_ref: 0.74593395, ref_file: "./test_files/TOPAZ_IOD1_E001.fna.gz", query_file: "./test_files/TOPAZ_RSS1_E007.fna.gz", query_contig: "RS-all-SRF-0-8-5-00_k119_3692", ref_contig: "IO-all-DCM-0-8-5-00_k119_2678", ci_upper: 0.9900135, ci_lower: 0.9897283, aai: false, quant_90_contig_len_q: 9095.0, quant_90_contig_len_r: 7016.0, quant_50_contig_len_q: 4276.0, quant_50_contig_len_r: 3761.0, quant_10_contig_len_q: 2759.0, quant_10_contig_len_r: 2688.0, std: 0.007433527, num_contigs_q: 8559, num_contigs_r: 8377, avg_chain_int_len: 3187, total_bases_covered: 27655368 }


test result: ok. 5 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 1.17s
successes:
fast_NNN_test_code
fast_avx2_vs_normal_code
fast_ecoli_plasmid_test
fast_ecoli_test_simple
fast_eukaryote_test

test result: ok. 5 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 1.09s


running 0 tests

successes:

successes:

test result: ok. 0 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s

0 comments on commit 666894c

Please sign in to comment.