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1	·64eda55afc8fcf825aec7169f31b736a·41424608·debug·optional·salmon-dbgsym_1.10.2+ds1-1_arm64.deb	1	·64eda55afc8fcf825aec7169f31b736a·41424608·debug·optional·salmon-dbgsym_1.10.2+ds1-1_arm64.deb
2	·~~d0c~~307b1~~99afd2fe8~~a~~66596251e~~a~~d60d~~·3163220·science·optional·salmon_1.10.2+ds1-1_arm64.deb	2	·986038fb34d679420ad13da01a9a2c57·3163224·science·optional·salmon_1.10.2+ds1-1_arm64.deb


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1	-rw-r--r--···0········0········0········4·2023-08-16·11:09:23.000000·debian-binary	1	-rw-r--r--···0········0········0········4·2023-08-16·11:09:23.000000·debian-binary
2	-rw-r--r--···0········0········0·····2468·2023-08-16·11:09:23.000000·control.tar.xz	2	-rw-r--r--···0········0········0·····2468·2023-08-16·11:09:23.000000·control.tar.xz
3	-rw-r--r--···0········0········0··3160560·2023-08-16·11:09:23.000000·data.tar.xz	3	-rw-r--r--···0········0········0··3160564·2023-08-16·11:09:23.000000·data.tar.xz


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58	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2023-08-16·11:09:23.000000·./usr/share/man/man1/	58	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2023-08-16·11:09:23.000000·./usr/share/man/man1/
59	-rw-r--r--···0·root·········(0)·root·········(0)·····1374·2023-08-16·11:09:23.000000·./usr/share/man/man1/salmon-index.1.gz	59	-rw-r--r--···0·root·········(0)·root·········(0)·····1374·2023-08-16·11:09:23.000000·./usr/share/man/man1/salmon-index.1.gz
60	-rw-r--r--···0·root·········(0)·root·········(0)······530·2023-08-16·11:09:23.000000·./usr/share/man/man1/salmon-quant.1.gz	60	-rw-r--r--···0·root·········(0)·root·········(0)······530·2023-08-16·11:09:23.000000·./usr/share/man/man1/salmon-quant.1.gz
61	-rw-r--r--···0·root·········(0)·root·········(0)······325·2023-08-16·11:09:23.000000·./usr/share/man/man1/salmon-swim.1.gz	61	-rw-r--r--···0·root·········(0)·root·········(0)······325·2023-08-16·11:09:23.000000·./usr/share/man/man1/salmon-swim.1.gz
62	-rw-r--r--···0·root·········(0)·root·········(0)······433·2023-08-16·11:09:23.000000·./usr/share/man/man1/salmon.1.gz	62	-rw-r--r--···0·root·········(0)·root·········(0)······433·2023-08-16·11:09:23.000000·./usr/share/man/man1/salmon.1.gz
63	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2023-08-16·11:09:23.000000·./usr/share/salmon/	63	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2023-08-16·11:09:23.000000·./usr/share/salmon/
64	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2023-08-16·11:09:23.000000·./usr/share/salmon/build-test-logs/	64	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2023-08-16·11:09:23.000000·./usr/share/salmon/build-test-logs/
65	-rw-r--r--···0·root·········(0)·root·········(0)····90934·2023-08-16·11:09:23.000000·./usr/share/salmon/build-test-logs/LastTest.log	65	-rw-r--r--···0·root·········(0)·root·········(0)····90924·2023-08-16·11:09:23.000000·./usr/share/salmon/build-test-logs/LastTest.log
66	lrwxrwxrwx···0·root·········(0)·root·········(0)········0·2023-08-16·11:09:23.000000·./usr/share/doc/salmon/html/_static/doctools.js·->·../../../../javascript/sphinxdoc/1.0/doctools.js	66	lrwxrwxrwx···0·root·········(0)·root·········(0)········0·2023-08-16·11:09:23.000000·./usr/share/doc/salmon/html/_static/doctools.js·->·../../../../javascript/sphinxdoc/1.0/doctools.js
67	lrwxrwxrwx···0·root·········(0)·root·········(0)········0·2023-08-16·11:09:23.000000·./usr/share/doc/salmon/html/_static/language_data.js·->·../../../../javascript/sphinxdoc/1.0/language_data.js	67	lrwxrwxrwx···0·root·········(0)·root·········(0)········0·2023-08-16·11:09:23.000000·./usr/share/doc/salmon/html/_static/language_data.js·->·../../../../javascript/sphinxdoc/1.0/language_data.js
68	lrwxrwxrwx···0·root·········(0)·root·········(0)········0·2023-08-16·11:09:23.000000·./usr/share/doc/salmon/html/_static/searchtools.js·->·../../../../javascript/sphinxdoc/1.0/searchtools.js	68	lrwxrwxrwx···0·root·········(0)·root·········(0)········0·2023-08-16·11:09:23.000000·./usr/share/doc/salmon/html/_static/searchtools.js·->·../../../../javascript/sphinxdoc/1.0/searchtools.js
69	lrwxrwxrwx···0·root·········(0)·root·········(0)········0·2023-08-16·11:09:23.000000·./usr/share/doc/salmon/html/_static/sphinx_highlight.js·->·../../../../javascript/sphinxdoc/1.0/sphinx_highlight.js	69	lrwxrwxrwx···0·root·········(0)·root·········(0)········0·2023-08-16·11:09:23.000000·./usr/share/doc/salmon/html/_static/sphinx_highlight.js·->·../../../../javascript/sphinxdoc/1.0/sphinx_highlight.js


Offset 1, 69 lines modified		Offset 1, 69 lines modified
1	Start·testing:·~~Nov~~·06·00:41·-12	1	Start·testing:·Dec·10·09:21·+14
2	----------------------------------------------------------	2	----------------------------------------------------------
3	1/2·Testing:·unit_tests	3	1/2·Testing:·unit_tests
4	1/2·Test:·unit_tests	4	1/2·Test:·unit_tests
5	Command:·"/usr/bin/cmake"·"-DTOPLEVEL_DIR=/build/reproducible-path/salmon-1.10.2+ds1"·"-P"·"/build/reproducible-path/salmon-1.10.2+ds1/cmake/UnitTests.cmake"	5	Command:·"/usr/bin/cmake"·"-DTOPLEVEL_DIR=/build/reproducible-path/salmon-1.10.2+ds1"·"-P"·"/build/reproducible-path/salmon-1.10.2+ds1/cmake/UnitTests.cmake"
6	Directory:·/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src	6	Directory:·/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src
7	"unit_tests"·start·time:·~~Nov~~·06·00:41·-12	7	"unit_tests"·start·time:·Dec·10·09:21·+14
8	Output:	8	Output:
9	----------------------------------------------------------	9	----------------------------------------------------------
10	--·For·unit·tests,·will·set·working·directory·to·/build/reproducible-path/salmon-1.10.2+ds1/tests	10	--·For·unit·tests,·will·set·working·directory·to·/build/reproducible-path/salmon-1.10.2+ds1/tests
11	===============================================================================	11	===============================================================================
12	All·tests·passed·(~~2006000~~·assertions·in·4·test·cases)	12	All·tests·passed·(1983796·assertions·in·4·test·cases)

13	<end·of·output>	13	<end·of·output>
14	Test·time·=···0.27·sec	14	Test·time·=···0.96·sec
15	----------------------------------------------------------	15	----------------------------------------------------------
16	Test·Passed.	16	Test·Passed.
17	"unit_tests"·end·time:·~~Nov~~·06·00:41·-12	17	"unit_tests"·end·time:·Dec·10·09:21·+14
18	"unit_tests"·time·elapsed:·00:00:00	18	"unit_tests"·time·elapsed:·00:00:00
19	----------------------------------------------------------	19	----------------------------------------------------------

20	2/2·Testing:·salmon_read_test_quasi	20	2/2·Testing:·salmon_read_test_quasi
21	2/2·Test:·salmon_read_test_quasi	21	2/2·Test:·salmon_read_test_quasi
22	Command:·"/usr/bin/cmake"·"-DTOPLEVEL_DIR=/build/reproducible-path/salmon-1.10.2+ds1"·"-P"·"/build/reproducible-path/salmon-1.10.2+ds1/cmake/TestSalmonQuasi.cmake"	22	Command:·"/usr/bin/cmake"·"-DTOPLEVEL_DIR=/build/reproducible-path/salmon-1.10.2+ds1"·"-P"·"/build/reproducible-path/salmon-1.10.2+ds1/cmake/TestSalmonQuasi.cmake"
23	Directory:·/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src	23	Directory:·/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src
24	"salmon_read_test_quasi"·start·time:·~~Nov~~·06·00:41·-12	24	"salmon_read_test_quasi"·start·time:·Dec·10·09:21·+14
25	Output:	25	Output:
26	----------------------------------------------------------	26	----------------------------------------------------------
27	sample_data/	27	sample_data/
28	sample_data/reads_2.fastq	28	sample_data/reads_2.fastq
29	sample_data/sample_alignments.bam	29	sample_data/sample_alignments.bam
30	sample_data/transcripts.fasta	30	sample_data/transcripts.fasta
31	sample_data/reads_1.fastq	31	sample_data/reads_1.fastq
32	index·["sample_salmon_quasi_index"]·did·not·previously·exist··.·.·.·creating·it	32	index·["sample_salmon_quasi_index"]·did·not·previously·exist··.·.·.·creating·it
33	[2024-11-06·00:41:30.~~614~~]·[jLog]·[warning]·The·salmon·index·is·being·built·without·any·decoy·sequences.··It·is·recommended·that·decoy·sequence·(either·computed·auxiliary·decoy·sequence·or·the·genome·of·the·organism)·be·provided·during·indexing.·Further·details·can·be·found·at·https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode.	33	[2025-12-10·09:21:20.188]·[jLog]·[warning]·The·salmon·index·is·being·built·without·any·decoy·sequences.··It·is·recommended·that·decoy·sequence·(either·computed·auxiliary·decoy·sequence·or·the·genome·of·the·organism)·be·provided·during·indexing.·Further·details·can·be·found·at·https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode.
34	[2024-11-06·00:41:30.~~614~~]·[jLog]·[info]·building·index	34	[2025-12-10·09:21:20.188]·[jLog]·[info]·building·index
35	out·:·sample_salmon_quasi_index	35	out·:·sample_salmon_quasi_index
36	[2024-11-06·00:41:30.~~614~~]·[puff::index::jointLog]·[info]·Running·fixFasta	36	[2025-12-10·09:21:20.188]·[puff::index::jointLog]·[info]·Running·fixFasta

37	[Step·1·of·4]·:·counting·k-mers	37	[Step·1·of·4]·:·counting·k-mers

38	[2024-11-06·00:41:30.~~620~~]·[puff::index::jointLog]·[info]·Replaced·0·non-ATCG·nucleotides	38	[2025-12-10·09:21:20.232]·[puff::index::jointLog]·[info]·Replaced·0·non-ATCG·nucleotides
39	[2024-11-06·00:41:30.~~620~~]·[puff::index::jointLog]·[info]·Clipped·poly-A·tails·from·0·transcripts	39	[2025-12-10·09:21:20.232]·[puff::index::jointLog]·[info]·Clipped·poly-A·tails·from·0·transcripts
40	wrote·15·cleaned·references	40	wrote·15·cleaned·references
41	[2024-11-06·00:41:30.~~620~~]·[puff::index::jointLog]·[info]·Filter·size·not·provided;·estimating·from·number·of·distinct·k-mers	41	[2025-12-10·09:21:20.232]·[puff::index::jointLog]·[info]·Filter·size·not·provided;·estimating·from·number·of·distinct·k-mers
42	[2024-11-06·00:41:30.~~622~~]·[puff::index::jointLog]·[info]·ntHll·estimated·54811·distinct·k-mers,·setting·filter·size·to·2^20	42	[2025-12-10·09:21:20.233]·[puff::index::jointLog]·[info]·ntHll·estimated·54811·distinct·k-mers,·setting·filter·size·to·2^20
43	Threads·=·2	43	Threads·=·2
44	Vertex·length·=·31	44	Vertex·length·=·31
45	Hash·functions·=·5	45	Hash·functions·=·5
46	Filter·size·=·1048576	46	Filter·size·=·1048576
47	Capacity·=·2	47	Capacity·=·2
48	Files:·	48	Files:·
49	sample_salmon_quasi_index/ref_k31_fixed.fa	49	sample_salmon_quasi_index/ref_k31_fixed.fa
50	--------------------------------------------------------------------------------	50	--------------------------------------------------------------------------------
51	Round·0,·0:1048576	51	Round·0,·0:1048576
52	Pass» Filling» Filtering	52	Pass» Filling» Filtering
53	1» 0» 0»	53	1» 0» 0»
54	2» 0» 0	54	2» 0» 0
55	True·junctions·count·=·14	55	True·junctions·count·=·14
56	False·junctions·count·=·18	56	False·junctions·count·=·23
57	Hash·table·size·=·32	57	Hash·table·size·=·37
58	Candidate·marks·count·=·56	58	Candidate·marks·count·=·62
59	--------------------------------------------------------------------------------	59	--------------------------------------------------------------------------------
60	Reallocating·bifurcations·time:·0	60	Reallocating·bifurcations·time:·0
61	True·marks·count:·51	61	True·marks·count:·51
62	Edges·construction·time:·0	62	Edges·construction·time:·0
63	--------------------------------------------------------------------------------	63	--------------------------------------------------------------------------------
64	Distinct·junctions·=·14	64	Distinct·junctions·=·14

Offset 73, 144 lines modified		Offset 73, 144 lines modified
73	Max·Junction·ID:·70	73	Max·Junction·ID:·70
74	seen.size():569·kmerInfo.size():71	74	seen.size():569·kmerInfo.size():71
75	approximateContigTotalLength:·17465	75	approximateContigTotalLength:·17465
76	counters·for·complex·kmers:	76	counters·for·complex·kmers:
77	(prec>1·&·succ>1)=0·\|·(succ>1·&·isStart)=0·\|·(prec>1·&·isEnd)=0·\|·(isStart·&·isEnd)=0	77	(prec>1·&·succ>1)=0·\|·(succ>1·&·isStart)=0·\|·(prec>1·&·isEnd)=0·\|·(isStart·&·isEnd)=0
78	contig·count:·24·element·count:·19592·complex·nodes:·0	78	contig·count:·24·element·count:·19592·complex·nodes:·0
79	#·of·ones·in·rank·vector:·23	79	#·of·ones·in·rank·vector:·23
80	[2024-11-06·00:41:30.659]·[puff::index::jointLog]·[info]·Starting·the·Pufferfish·indexing·by·reading·the·GFA·binary·file.	80	[2025-12-10·09:21:20.353]·[puff::index::jointLog]·[info]·Starting·the·Pufferfish·indexing·by·reading·the·GFA·binary·file.
81	[2024-11-06·00:41:30.659]·[puff::index::jointLog]·[info]·Setting·the·index/BinaryGfa·directory·sample_salmon_quasi_index	81	[2025-12-10·09:21:20.353]·[puff::index::jointLog]·[info]·Setting·the·index/BinaryGfa·directory·sample_salmon_quasi_index
82	size·=·19592	82	size·=·19592
83	-----------------------------------------	83	-----------------------------------------
84	\|·Loading·contigs·\|·Time·=·~~92.~~56·us	84	\|·Loading·contigs·\|·Time·=·50·us
85	-----------------------------------------	85	-----------------------------------------
86	size·=·19592	86	size·=·19592
87	-----------------------------------------	87	-----------------------------------------
88	\|·Loading·contig·boundaries·\|·Time·=·41.241·us	88	\|·Loading·contig·boundaries·\|·Time·=·21.68·us
89	-----------------------------------------	89	-----------------------------------------
90	Number·of·ones:·23	90	Number·of·ones:·23
91	Number·of·ones·per·inventory·item:·512	91	Number·of·ones·per·inventory·item:·512
92	Inventory·entries·filled:·1	92	Inventory·entries·filled:·1
93	23	93	23
94	[2024-11-06·00:41:30.~~660~~]·[puff::index::jointLog]·[info]·Done·wrapping·the·rank·vector·with·a·rank9sel·structure.	94	[2025-12-10·09:21:20.353]·[puff::index::jointLog]·[info]·Done·wrapping·the·rank·vector·with·a·rank9sel·structure.
95	[2024-11-06·00:41:30.~~660~~]·[puff::index::jointLog]·[info]·contig·count·for·validation:·23	95	[2025-12-10·09:21:20.353]·[puff::index::jointLog]·[info]·contig·count·for·validation:·23
96	[2024-11-06·00:41:30.~~660~~]·[puff::index::jointLog]·[info]·Total·#·of·Contigs·:·23	96	[2025-12-10·09:21:20.353]·[puff::index::jointLog]·[info]·Total·#·of·Contigs·:·23
97	[2024-11-06·00:41:30.~~660~~]·[puff::index::jointLog]·[info]·Total·#·of·numerical·Contigs·:·23	97	[2025-12-10·09:21:20.353]·[puff::index::jointLog]·[info]·Total·#·of·numerical·Contigs·:·23
98	[2024-11-06·00:41:30.~~660~~]·[puff::index::jointLog]·[info]·Total·#·of·contig·vec·entries:·36	98	[2025-12-10·09:21:20.353]·[puff::index::jointLog]·[info]·Total·#·of·contig·vec·entries:·36
99	[2024-11-06·00:41:30.~~660~~]·[puff::index::jointLog]·[info]·bits·per·offset·entry·6	99	[2025-12-10·09:21:20.353]·[puff::index::jointLog]·[info]·bits·per·offset·entry·6
100	[2024-11-06·00:41:30.~~660~~]·[puff::index::jointLog]·[info]·Done·constructing·the·contig·vector.·24	100	[2025-12-10·09:21:20.353]·[puff::index::jointLog]·[info]·Done·constructing·the·contig·vector.·24
101	[2024-11-06·00:41:30.~~660~~]·[puff::index::jointLog]·[info]·#·segments·=·23	101	[2025-12-10·09:21:20.353]·[puff::index::jointLog]·[info]·#·segments·=·23
102	[2024-11-06·00:41:30.~~660~~]·[puff::index::jointLog]·[info]·total·length·=·19,592	102	[2025-12-10·09:21:20.353]·[puff::index::jointLog]·[info]·total·length·=·19,592
103	[2024-11-06·00:41:30.~~660~~]·[puff::index::jointLog]·[info]·Reading·the·reference·files·...	103	[2025-12-10·09:21:20.353]·[puff::index::jointLog]·[info]·Reading·the·reference·files·...
104	[2024-11-06·00:41:30.~~661~~]·[puff::index::jointLog]·[info]·positional·integer·width·=·15	104	[2025-12-10·09:21:20.376]·[puff::index::jointLog]·[info]·positional·integer·width·=·15
105	[2024-11-06·00:41:30.~~661~~]·[puff::index::jointLog]·[info]·seqSize·=·19,592	105	[2025-12-10·09:21:20.376]·[puff::index::jointLog]·[info]·seqSize·=·19,592
106	[2024-11-06·00:41:30.~~661~~]·[puff::index::jointLog]·[info]·rankSize·=·19,592	106	[2025-12-10·09:21:20.376]·[puff::index::jointLog]·[info]·rankSize·=·19,592
107	[2024-11-06·00:41:30.~~661~~]·[puff::index::jointLog]·[info]·edgeVecSize·=·0	107	[2025-12-10·09:21:20.376]·[puff::index::jointLog]·[info]·edgeVecSize·=·0
108	[2024-11-06·00:41:30.~~661~~]·[puff::index::jointLog]·[info]·num·keys·=·18,902	108	[2025-12-10·09:21:20.376]·[puff::index::jointLog]·[info]·num·keys·=·18,902
109	\xd[Building·BooPHF]··2.32·%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec.[Building·BooPHF]··2.32·%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec.[Building·BooPHF]··2.32·%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec.[Building·BooPHF]··2.32·%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec.[Building[·...·truncated·by·diffoscope;·len:·75774,·SHA:·~~cab~~a2~~e324b3435a~~11~~6874f71d60~~d7b7ac~~5fa4~~f5~~74ddb56b2a~~57~~c74~~47~~8c2~~43d60·...·]·%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec	109	\xd[Building·BooPHF]··2.32·%···elapsed:···0·min·0··sec···remaining:···0·min·1··sec.[Building·BooPHF]··2.32·%···elapsed:···0·min·0··sec···remaining:···0·min·1··sec.[Building·BooPHF]··2.32·%···elapsed:···0·min·0··sec···remaining:···0·min·1··sec.[Building·BooPHF]··2.32·%···elapsed:···0·min·0··sec···remaining:···0·min·1··sec.[Building[·...·truncated·by·diffoscope;·len:·75774,·SHA:·2dca2fa9880010c118c2c545875d74b6bc281efc3be24aee357002f3479774cd·...·]·%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec\xd[Building·BooPHF]··100··%···elapsed:···0·min·0··sec···remaining:···0·min·0··sec
110	[2024-11-06·00:41:30.~~679~~]·[puff::index::jointLog]·[info]·mphf·size·=·0.0125198·MB	110	[2025-12-10·09:21:20.855]·[puff::index::jointLog]·[info]·mphf·size·=·0.0125198·MB
111	[2024-11-06·00:41:30.~~679~~]·[puff::index::jointLog]·[info]·chunk·size·=·9,796	111	[2025-12-10·09:21:20.855]·[puff::index::jointLog]·[info]·chunk·size·=·9,796
112	[2024-11-06·00:41:30.~~679~~]·[puff::index::jointLog]·[info]·chunk·0·=·[0,·9,796)	112	[2025-12-10·09:21:20.855]·[puff::index::jointLog]·[info]·chunk·0·=·[0,·9,796)
113	[2024-11-06·00:41:30.~~679~~]·[puff::index::jointLog]·[info]·chunk·1·=·[9,796,·19,562)	113	[2025-12-10·09:21:20.855]·[puff::index::jointLog]·[info]·chunk·1·=·[9,796,·19,562)
114	[2024-11-06·00:41:30.~~682~~]·[puff::index::jointLog]·[info]·finished·populating·pos·vector	114	[2025-12-10·09:21:20.875]·[puff::index::jointLog]·[info]·finished·populating·pos·vector
115	[2024-11-06·00:41:30.~~682~~]·[puff::index::jointLog]·[info]·writing·index·components	115	[2025-12-10·09:21:20.875]·[puff::index::jointLog]·[info]·writing·index·components
116	[2024-11-06·00:41:30.~~682~~]·[puff::index::jointLog]·[info]·finished·writing·dense·pufferfish·index	116	[2025-12-10·09:21:20.875]·[puff::index::jointLog]·[info]·finished·writing·dense·pufferfish·index
117	[2024-11-06·00:41:30.~~682~~]·[jLog]·[info]·done·building·index	117	[2025-12-10·09:21:20.875]·[jLog]·[info]·done·building·index
118	for·info,·total·work·write·each··:·2.331····total·work·inram·from·level·3·:·4.322··total·work·raw·:·25.000·	118	for·info,·total·work·write·each··:·2.331····total·work·inram·from·level·3·:·4.322··total·work·raw·:·25.000·
119	Bitarray··········105024··bits·(100.00·%)···(array·+·ranks·)	119	Bitarray··········105024··bits·(100.00·%)···(array·+·ranks·)
120	final·hash·············0··bits·(0.00·%)·(nb·in·final·hash·0)	120	final·hash·············0··bits·(0.00·%)·(nb·in·final·hash·0)
121	###·salmon·(selective-alignment-based)·v1.10.2	121	###·salmon·(selective-alignment-based)·v1.10.2
122	###·[·program·]·=>·salmon·	122	###·[·program·]·=>·salmon·
123	###·[·command·]·=>·quant·	123	###·[·command·]·=>·quant·
124	###·[·index·]·=>·{·sample_salmon_quasi_index·}	124	###·[·index·]·=>·{·sample_salmon_quasi_index·}
125	###·[·libType·]·=>·{·IU·}	125	###·[·libType·]·=>·{·IU·}
126	###·[·mates1·]·=>·{·reads_1.fastq·}	126	###·[·mates1·]·=>·{·reads_1.fastq·}
127	###·[·mates2·]·=>·{·reads_2.fastq·}	127	###·[·mates2·]·=>·{·reads_2.fastq·}
128	###·[·output·]·=>·{·sample_salmon_quasi_quant·}	128	###·[·output·]·=>·{·sample_salmon_quasi_quant·}
129	Logs·will·be·written·to·sample_salmon_quasi_quant/logs	129	Logs·will·be·written·to·sample_salmon_quasi_quant/logs
Max diff block lines reached; 6298/177502 bytes (3.55%) of diff not shown.