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/srv/reproducible-results/rbuild-debian/r-b-build.bMU0zDvN/b1/salmon_1.10.2+ds1-1_arm64.changes vs.
/srv/reproducible-results/rbuild-debian/r-b-build.bMU0zDvN/b2/salmon_1.10.2+ds1-1_arm64.changes
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1 ·26b9aab1ec99cd883dfe54cee3e58b4c·41439448·debug·optional·salmon-dbgsym_1.10.2+ds1-1_arm64.deb1 ·26b9aab1ec99cd883dfe54cee3e58b4c·41439448·debug·optional·salmon-dbgsym_1.10.2+ds1-1_arm64.deb
2 ·9ef05809c168b10a1bcee984224df300·3162360·science·optional·salmon_1.10.2+ds1-1_arm64.deb2 ·83c4fad1c5dfddc400d02af5796fa85e·3162360·science·optional·salmon_1.10.2+ds1-1_arm64.deb
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salmon_1.10.2+ds1-1_arm64.deb
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control.tar.xz
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control.tar
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./md5sums
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./md5sums
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data.tar.xz
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data.tar
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file list
    
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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.gz59 -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.gz60 -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.gz61 -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.gz62 -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)····90930·2023-08-16·11:09:23.000000·./usr/share/salmon/build-test-logs/LastTest.log65 -rw-r--r--···0·root·········(0)·root·········(0)····90929·2023-08-16·11:09:23.000000·./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.js66 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.js67 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.js68 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.js69 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
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./usr/share/salmon/build-test-logs/LastTest.log
    
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1 Start·testing:·Feb·27·20:15·-121 Start·testing:·Jan·26·16:04·+14
2 ----------------------------------------------------------2 ----------------------------------------------------------
3 1/2·Testing:·unit_tests3 1/2·Testing:·unit_tests
4 1/2·Test:·unit_tests4 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/src6 Directory:·/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src
7 "unit_tests"·start·time:·Feb·27·20:15·-127 "unit_tests"·start·time:·Jan·26·16:04·+14
8 Output:8 Output:
9 ----------------------------------------------------------9 ----------------------------------------------------------
10 --·For·unit·tests,·will·set·working·directory·to·/build/reproducible-path/salmon-1.10.2+ds1/tests10 --·For·unit·tests,·will·set·working·directory·to·/build/reproducible-path/salmon-1.10.2+ds1/tests
11 ===============================================================================11 ===============================================================================
12 All·tests·passed·(2001374·assertions·in·4·test·cases)12 All·tests·passed·(1989111·assertions·in·4·test·cases)
  
13 <end·of·output>13 <end·of·output>
14 Test·time·=···0.26·sec14 Test·time·=···0.70·sec
15 ----------------------------------------------------------15 ----------------------------------------------------------
16 Test·Passed.16 Test·Passed.
17 "unit_tests"·end·time:·Feb·27·20:15·-1217 "unit_tests"·end·time:·Jan·26·16:04·+14
18 "unit_tests"·time·elapsed:·00:00:0018 "unit_tests"·time·elapsed:·00:00:00
19 ----------------------------------------------------------19 ----------------------------------------------------------
  
20 2/2·Testing:·salmon_read_test_quasi20 2/2·Testing:·salmon_read_test_quasi
21 2/2·Test:·salmon_read_test_quasi21 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/src23 Directory:·/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src
24 "salmon_read_test_quasi"·start·time:·Feb·27·20:15·-1224 "salmon_read_test_quasi"·start·time:·Jan·26·16:04·+14
25 Output:25 Output:
26 ----------------------------------------------------------26 ----------------------------------------------------------
27 sample_data/27 sample_data/
28 sample_data/reads_2.fastq28 sample_data/reads_2.fastq
29 sample_data/sample_alignments.bam29 sample_data/sample_alignments.bam
30 sample_data/transcripts.fasta30 sample_data/transcripts.fasta
31 sample_data/reads_1.fastq31 sample_data/reads_1.fastq
32 index·["sample_salmon_quasi_index"]·did·not·previously·exist··.·.·.·creating·it32 index·["sample_salmon_quasi_index"]·did·not·previously·exist··.·.·.·creating·it
33 [2026-02-27·20:15:50.674]·[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 [2025-01-26·16:04:41.997]·[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 [2026-02-27·20:15:50.674]·[jLog]·[info]·building·index34 [2025-01-26·16:04:41.997]·[jLog]·[info]·building·index
35 out·:·sample_salmon_quasi_index35 out·:·sample_salmon_quasi_index
36 [2026-02-27·20:15:50.675]·[puff::index::jointLog]·[info]·Running·fixFasta36 [2025-01-26·16:04:41.997]·[puff::index::jointLog]·[info]·Running·fixFasta
  
37 [Step·1·of·4]·:·counting·k-mers37 [Step·1·of·4]·:·counting·k-mers
  
38 [2026-02-27·20:15:50.680]·[puff::index::jointLog]·[info]·Replaced·0·non-ATCG·nucleotides38 [2025-01-26·16:04:42.018]·[puff::index::jointLog]·[info]·Replaced·0·non-ATCG·nucleotides
39 [2026-02-27·20:15:50.680]·[puff::index::jointLog]·[info]·Clipped·poly-A·tails·from·0·transcripts39 [2025-01-26·16:04:42.018]·[puff::index::jointLog]·[info]·Clipped·poly-A·tails·from·0·transcripts
40 wrote·15·cleaned·references40 wrote·15·cleaned·references
41 [2026-02-27·20:15:50.681]·[puff::index::jointLog]·[info]·Filter·size·not·provided;·estimating·from·number·of·distinct·k-mers41 [2025-01-26·16:04:42.018]·[puff::index::jointLog]·[info]·Filter·size·not·provided;·estimating·from·number·of·distinct·k-mers
42 [2026-02-27·20:15:50.682]·[puff::index::jointLog]·[info]·ntHll·estimated·54811·distinct·k-mers,·setting·filter·size·to·2^2042 [2025-01-26·16:04:42.019]·[puff::index::jointLog]·[info]·ntHll·estimated·54811·distinct·k-mers,·setting·filter·size·to·2^20
43 Threads·=·243 Threads·=·2
44 Vertex·length·=·3144 Vertex·length·=·31
45 Hash·functions·=·545 Hash·functions·=·5
46 Filter·size·=·104857646 Filter·size·=·1048576
47 Capacity·=·247 Capacity·=·2
48 Files:·48 Files:·
49 sample_salmon_quasi_index/ref_k31_fixed.fa49 sample_salmon_quasi_index/ref_k31_fixed.fa
50 --------------------------------------------------------------------------------50 --------------------------------------------------------------------------------
51 Round·0,·0:104857651 Round·0,·0:1048576
52 Pass»   Filling»    Filtering52 Pass»   Filling»    Filtering
53 1»      0»     0»    53 1»      0»     0»    
54 2»      0»     054 2»      0»     0
55 True·junctions·count·=·1455 True·junctions·count·=·14
56 False·junctions·count·=·1856 False·junctions·count·=·17
57 Hash·table·size·=·3257 Hash·table·size·=·31
58 Candidate·marks·count·=·5558 Candidate·marks·count·=·54
59 --------------------------------------------------------------------------------59 --------------------------------------------------------------------------------
60 Reallocating·bifurcations·time:·060 Reallocating·bifurcations·time:·0
61 True·marks·count:·5161 True·marks·count:·51
62 Edges·construction·time:·062 Edges·construction·time:·0
63 --------------------------------------------------------------------------------63 --------------------------------------------------------------------------------
64 Distinct·junctions·=·1464 Distinct·junctions·=·14
  
Offset 73, 144 lines modifiedOffset 73, 144 lines modified
73 Max·Junction·ID:·7073 Max·Junction·ID:·70
74 seen.size():569·kmerInfo.size():7174 seen.size():569·kmerInfo.size():71
75 approximateContigTotalLength:·1746575 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)=077 (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:·078 contig·count:·24·element·count:·19592·complex·nodes:·0
79 #·of·ones·in·rank·vector:·2379 #·of·ones·in·rank·vector:·23
80 [2026-02-27·20:15:50.720]·[puff::index::jointLog]·[info]·Starting·the·Pufferfish·indexing·by·reading·the·GFA·binary·file.80 [2025-01-26·16:04:42.229]·[puff::index::jointLog]·[info]·Starting·the·Pufferfish·indexing·by·reading·the·GFA·binary·file.
81 [2026-02-27·20:15:50.720]·[puff::index::jointLog]·[info]·Setting·the·index/BinaryGfa·directory·sample_salmon_quasi_index81 [2025-01-26·16:04:42.230]·[puff::index::jointLog]·[info]·Setting·the·index/BinaryGfa·directory·sample_salmon_quasi_index
82 size·=·1959282 size·=·19592
83 -----------------------------------------83 -----------------------------------------
84 |·Loading·contigs·|·Time·=·101.84·us84 |·Loading·contigs·|·Time·=·45.2·us
85 -----------------------------------------85 -----------------------------------------
86 size·=·1959286 size·=·19592
87 -----------------------------------------87 -----------------------------------------
88 |·Loading·contig·boundaries·|·Time·=·44.08·us88 |·Loading·contig·boundaries·|·Time·=·15.801·us
89 -----------------------------------------89 -----------------------------------------
90 Number·of·ones:·2390 Number·of·ones:·23
91 Number·of·ones·per·inventory·item:·51291 Number·of·ones·per·inventory·item:·512
92 Inventory·entries·filled:·192 Inventory·entries·filled:·1
93 2393 23
94 [2026-02-27·20:15:50.720]·[puff::index::jointLog]·[info]·Done·wrapping·the·rank·vector·with·a·rank9sel·structure.94 [2025-01-26·16:04:42.230]·[puff::index::jointLog]·[info]·Done·wrapping·the·rank·vector·with·a·rank9sel·structure.
95 [2026-02-27·20:15:50.720]·[puff::index::jointLog]·[info]·contig·count·for·validation:·2395 [2025-01-26·16:04:42.230]·[puff::index::jointLog]·[info]·contig·count·for·validation:·23
96 [2026-02-27·20:15:50.720]·[puff::index::jointLog]·[info]·Total·#·of·Contigs·:·2396 [2025-01-26·16:04:42.230]·[puff::index::jointLog]·[info]·Total·#·of·Contigs·:·23
97 [2026-02-27·20:15:50.720]·[puff::index::jointLog]·[info]·Total·#·of·numerical·Contigs·:·2397 [2025-01-26·16:04:42.230]·[puff::index::jointLog]·[info]·Total·#·of·numerical·Contigs·:·23
98 [2026-02-27·20:15:50.720]·[puff::index::jointLog]·[info]·Total·#·of·contig·vec·entries:·3698 [2025-01-26·16:04:42.230]·[puff::index::jointLog]·[info]·Total·#·of·contig·vec·entries:·36
99 [2026-02-27·20:15:50.720]·[puff::index::jointLog]·[info]·bits·per·offset·entry·699 [2025-01-26·16:04:42.230]·[puff::index::jointLog]·[info]·bits·per·offset·entry·6
100 [2026-02-27·20:15:50.720]·[puff::index::jointLog]·[info]·Done·constructing·the·contig·vector.·24100 [2025-01-26·16:04:42.230]·[puff::index::jointLog]·[info]·Done·constructing·the·contig·vector.·24
101 [2026-02-27·20:15:50.720]·[puff::index::jointLog]·[info]·#·segments·=·23101 [2025-01-26·16:04:42.230]·[puff::index::jointLog]·[info]·#·segments·=·23
102 [2026-02-27·20:15:50.720]·[puff::index::jointLog]·[info]·total·length·=·19,592102 [2025-01-26·16:04:42.230]·[puff::index::jointLog]·[info]·total·length·=·19,592
103 [2026-02-27·20:15:50.720]·[puff::index::jointLog]·[info]·Reading·the·reference·files·...103 [2025-01-26·16:04:42.230]·[puff::index::jointLog]·[info]·Reading·the·reference·files·...
104 [2026-02-27·20:15:50.722]·[puff::index::jointLog]·[info]·positional·integer·width·=·15104 [2025-01-26·16:04:42.290]·[puff::index::jointLog]·[info]·positional·integer·width·=·15
105 [2026-02-27·20:15:50.722]·[puff::index::jointLog]·[info]·seqSize·=·19,592105 [2025-01-26·16:04:42.290]·[puff::index::jointLog]·[info]·seqSize·=·19,592
106 [2026-02-27·20:15:50.722]·[puff::index::jointLog]·[info]·rankSize·=·19,592106 [2025-01-26·16:04:42.290]·[puff::index::jointLog]·[info]·rankSize·=·19,592
107 [2026-02-27·20:15:50.722]·[puff::index::jointLog]·[info]·edgeVecSize·=·0107 [2025-01-26·16:04:42.290]·[puff::index::jointLog]·[info]·edgeVecSize·=·0
108 [2026-02-27·20:15:50.722]·[puff::index::jointLog]·[info]·num·keys·=·18,902108 [2025-01-26·16:04:42.290]·[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:·79637,·SHA:·e2804fd677384ec11419c8e46f5a34640aa853a405f6eb2aefb2122b685b65a7·...·]··sec···remaining:···0·min·0··sec109 \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:·79637,·SHA:·f2748d65abeb2da282781f09c224b9a0633db58d259beaea41543eaf541e1ef2·...·]··sec···remaining:···0·min·0··sec
110 [2026-02-27·20:15:50.739]·[puff::index::jointLog]·[info]·mphf·size·=·0.0125198·MB110 [2025-01-26·16:04:42.807]·[puff::index::jointLog]·[info]·mphf·size·=·0.0125198·MB
111 [2026-02-27·20:15:50.739]·[puff::index::jointLog]·[info]·chunk·size·=·9,796111 [2025-01-26·16:04:42.807]·[puff::index::jointLog]·[info]·chunk·size·=·9,796
112 [2026-02-27·20:15:50.739]·[puff::index::jointLog]·[info]·chunk·0·=·[0,·9,796)112 [2025-01-26·16:04:42.807]·[puff::index::jointLog]·[info]·chunk·0·=·[0,·9,796)
113 [2026-02-27·20:15:50.739]·[puff::index::jointLog]·[info]·chunk·1·=·[9,796,·19,562)113 [2025-01-26·16:04:42.807]·[puff::index::jointLog]·[info]·chunk·1·=·[9,796,·19,562)
114 [2026-02-27·20:15:50.742]·[puff::index::jointLog]·[info]·finished·populating·pos·vector114 [2025-01-26·16:04:42.827]·[puff::index::jointLog]·[info]·finished·populating·pos·vector
115 [2026-02-27·20:15:50.742]·[puff::index::jointLog]·[info]·writing·index·components115 [2025-01-26·16:04:42.827]·[puff::index::jointLog]·[info]·writing·index·components
116 [2026-02-27·20:15:50.742]·[puff::index::jointLog]·[info]·finished·writing·dense·pufferfish·index116 [2025-01-26·16:04:42.827]·[puff::index::jointLog]·[info]·finished·writing·dense·pufferfish·index
117 [2026-02-27·20:15:50.742]·[jLog]·[info]·done·building·index117 [2025-01-26·16:04:42.827]·[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)·v1.10.2121 ###·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/logs129 Logs·will·be·written·to·sample_salmon_quasi_quant/logs
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