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GMOD / jbrowse-components

Source code for JBrowse 2, a modern React-based genome browser
https://jbrowse.org/jb2
Apache License 2.0
205 stars 61 forks source link

Error when running text indexing on Windows #4581

Closed carolinebridge closed 1 week ago

carolinebridge commented 1 week ago

When populating a tabix gff file on the Windows desktop app, an error occurs during the text indexing step.

To Reproduce

  1. On windows, populate a tabix gff3 file
  2. While running the indexing step, an error occurs
    • track renders fine, just not indexed

image

Version:

JBrowse Windows Desktop v.2.15.3 Windows 10

carolinebridge commented 1 week ago

C:\Users\caroline\Workspace\ixixx-js>yarn test > output.txt FAIL test/index.test.ts × test simple (74 ms) × volvox sans descriptions (72 ms) × volvox with descriptions (62 ms)

● test simple

write EPIPE

   5 |     const [id, ...words] = chunk.toString().split(/\s+/)
   6 |
>  7 |     this.push(words.map(word => `${word.toLowerCase()} ${id}\n`).join(''))
     |          ^
   8 |     done()
   9 |   }
  10 | }

  at TrixInputTransform._transform (src/TrixInputTransform.ts:7:10)
  at push (node_modules/split2/index.js:76:10)
  at Transform.transform [as _transform] (node_modules/split2/index.js:44:7)

● volvox sans descriptions

expect(received).toMatchSnapshot()

Snapshot name: `volvox sans descriptions 1`

- Snapshot  - 76
+ Received  +  0

- agt221.3 ["ctgA%3A7500..8000"|"gff3tabix_genes"|"agt221.3"|"Match4"],1
- agt221.5 ["ctgA%3A1050..1500"|"gff3tabix_genes"|"agt221.5"],1 ["ctgA%3A1050..7300"|"gff3tabix_genes"|"agt221.5"|"Match3"],2 ["ctgA%3A5000..5500"|"gff3tabix_genes"|"agt221.5"],3 ["ctgA%3A7000..7300"|"gff3tabix_genes"|"agt221.5"],4
- agt767.3 ["ctgA%3A8000..9000"|"gff3tabix_genes"|"agt767.3"|"Match6"],1
- agt767.5 ["ctgA%3A1150..1500"|"gff3tabix_genes"|"agt767.5"],1 ["ctgA%3A1150..7200"|"gff3tabix_genes"|"agt767.5"|"Match5"],2 ["ctgA%3A5000..5500"|"gff3tabix_genes"|"agt767.5"],3 ["ctgA%3A7000..7200"|"gff3tabix_genes"|"agt767.5"],4
- agt830.3 ["ctgA%3A5410..5500"|"gff3tabix_genes"|"agt830.3"],1 ["ctgA%3A5410..7503"|"gff3tabix_genes"|"agt830.3"|"Match2"],2 ["ctgA%3A7000..7503"|"gff3tabix_genes"|"agt830.3"],3
- agt830.5 ["ctgA%3A1050..1500"|"gff3tabix_genes"|"agt830.5"],1 ["ctgA%3A1050..3202"|"gff3tabix_genes"|"agt830.5"|"Match1"],2 ["ctgA%3A3000..3202"|"gff3tabix_genes"|"agt830.5"],3
- apple2 ["ctgA%3A13000..17200"|"gff3tabix_genes"|"Apple2"|"cds-Apple2"],1
- apple3 ["ctgA%3A17400..23000"|"gff3tabix_genes"|"Apple3"|"rna-Apple3"],1
- b101.2 ["ctgA%3A1000..20000"|"gff3tabix_genes"|"b101.2"|"b101.2"],1
- cds-apple2 ["ctgA%3A13000..17200"|"gff3tabix_genes"|"Apple2"|"cds-Apple2"],1
- ctga ["ctgA%3A1..50001"|"gff3tabix_genes"|"ctgA"],1
- ctgb ["ctgB%3A1..6079"|"gff3tabix_genes"|"ctgB"],1
- eden ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN"|"EDEN"],1
- eden.1 ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN.1"|"EDEN.1"],1
- eden.2 ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN.2"|"EDEN.2"],1
- eden.3 ["ctgA%3A1300..9000"|"gff3tabix_genes"|"EDEN.3"|"EDEN.3"],1
- f01 ["ctgA%3A44705..47713"|"gff3tabix_genes"|"f01"],1
- f02 ["ctgA%3A24562..28338"|"gff3tabix_genes"|"f02"],1
- f03 ["ctgA%3A36649..40440"|"gff3tabix_genes"|"f03"],1
- f04 ["ctgA%3A37242..38653"|"gff3tabix_genes"|"f04"],1
- f05 ["ctgA%3A4715..5968"|"gff3tabix_genes"|"f05"],1 ["ctgB%3A4715..5968"|"gff3tabix_genes"|"f05"],2
- f06 ["ctgA%3A3014..6130"|"gff3tabix_genes"|"f06"],1 ["ctgB%3A3014..6130"|"gff3tabix_genes"|"f06"],2
- f07 ["ctgA%3A1659..1984"|"gff3tabix_genes"|"f07"],1 ["ctgB%3A1659..1984"|"gff3tabix_genes"|"f07"],2
- f08 ["ctgA%3A13280..16394"|"gff3tabix_genes"|"f08"],1
- f09 ["ctgA%3A36034..38167"|"gff3tabix_genes"|"f09"],1
- f10 ["ctgA%3A15329..15533"|"gff3tabix_genes"|"f10"],1
- f11 ["ctgA%3A46990..48410"|"gff3tabix_genes"|"f11"],1
- f12 ["ctgA%3A49758..50000"|"gff3tabix_genes"|"f12"],1
- f13 ["ctgA%3A19157..22915"|"gff3tabix_genes"|"f13"],1
- f14 ["ctgA%3A23072..23185"|"gff3tabix_genes"|"f14"],1
- f15 ["ctgA%3A22132..24633"|"gff3tabix_genes"|"f15"],1
- fakesnp ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"],1
- fakesnp1 ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"],1
- gene:hga ["ctgA%3A1100..2000"|"gff3tabix_genes"|"Gene%3Ahga"],1
- gene:hgb ["ctgA%3A1600..3000"|"gff3tabix_genes"|"Gene%3Ahgb"],1
- m01 ["ctgA%3A48253..48366"|"gff3tabix_genes"|"m01"],1
- m02 ["ctgA%3A28332..30033"|"gff3tabix_genes"|"m02"],1
- m03 ["ctgA%3A15396..16159"|"gff3tabix_genes"|"m03"],1
- m04 ["ctgA%3A33325..35791"|"gff3tabix_genes"|"m04"],1
- m05 ["ctgA%3A13801..14007"|"gff3tabix_genes"|"m05"],1
- m06 ["ctgA%3A30578..31748"|"gff3tabix_genes"|"m06"],1
- m07 ["ctgA%3A18048..18552"|"gff3tabix_genes"|"m07"],1
- m08 ["ctgA%3A17023..17675"|"gff3tabix_genes"|"m08"],1
- m09 ["ctgA%3A46012..48851"|"gff3tabix_genes"|"m09"],1
- m10 ["ctgA%3A28342..28447"|"gff3tabix_genes"|"m10"],1
- m11 ["ctgA%3A11911..15561"|"gff3tabix_genes"|"m11"],1
- m12 ["ctgA%3A21748..25612"|"gff3tabix_genes"|"m12"],1
- m13 ["ctgA%3A17667..17690"|"gff3tabix_genes"|"m13"],1
- m14 ["ctgA%3A14731..17239"|"gff3tabix_genes"|"m14"],1
- m15 ["ctgA%3A37497..40559"|"gff3tabix_genes"|"m15"],1
- match1 ["ctgA%3A1050..3202"|"gff3tabix_genes"|"agt830.5"|"Match1"],1
- match2 ["ctgA%3A5410..7503"|"gff3tabix_genes"|"agt830.3"|"Match2"],1
- match3 ["ctgA%3A1050..7300"|"gff3tabix_genes"|"agt221.5"|"Match3"],1
- match4 ["ctgA%3A7500..8000"|"gff3tabix_genes"|"agt221.3"|"Match4"],1
- match5 ["ctgA%3A1150..7200"|"gff3tabix_genes"|"agt767.5"|"Match5"],1
- match6 ["ctgA%3A8000..9000"|"gff3tabix_genes"|"agt767.3"|"Match6"],1
- protein:hga ["ctgA%3A1200..1900"|"gff3tabix_genes"|"Protein%3AHGA"],1
- protein:hgb ["ctgA%3A1800..2900"|"gff3tabix_genes"|"Protein%3AHGB"],1
- remark:hga ["ctgA%3A1000..2000"|"gff3tabix_genes"|"Remark%3Ahga"],1
- rna-apple3 ["ctgA%3A17400..23000"|"gff3tabix_genes"|"Apple3"|"rna-Apple3"],1
- seg01 ["ctgA%3A32329..32359"|"gff3tabix_genes"|"seg01"],1
- seg02 ["ctgA%3A26122..26126"|"gff3tabix_genes"|"seg02"],1 ["ctgA%3A26497..26869"|"gff3tabix_genes"|"seg02"],2 ["ctgA%3A27201..27325"|"gff3tabix_genes"|"seg02"],3 ["ctgA%3A27372..27433"|"gff3tabix_genes"|"seg02"],4 ["ctgA%3A27565..27565"|"gff3tabix_genes"|"seg02"],5 ["ctgA%3A27813..28091"|"gff3tabix_genes"|"seg02"],6 ["ctgA%3A28093..28201"|"gff3tabix_genes"|"seg02"],7 ["ctgA%3A28329..28377"|"gff3tabix_genes"|"seg02"],8 ["ctgA%3A28829..29194"|"gff3tabix_genes"|"seg02"],9 ["ctgA%3A29517..29702"|"gff3tabix_genes"|"seg02"],10 ["ctgA%3A29713..30061"|"gff3tabix_genes"|"seg02"],11 ["ctgA%3A30329..30774"|"gff3tabix_genes"|"seg02"],12 ["ctgA%3A30808..31306"|"gff3tabix_genes"|"seg02"],13 ["ctgA%3A31516..31729"|"gff3tabix_genes"|"seg02"],14 ["ctgA%3A31753..32154"|"gff3tabix_genes"|"seg02"],15 ["ctgA%3A32595..32696"|"gff3tabix_genes"|"seg02"],16 ["ctgA%3A32892..32901"|"gff3tabix_genes"|"seg02"],17 ["ctgA%3A33127..33388"|"gff3tabix_genes"|"seg02"],18 ["ctgA%3A33439..33443"|"gff3tabix_genes"|"seg02"],19 ["ctgA%3A33759..34209"|"gff3tabix_genes"|"seg02"],20 ["ctgA%3A34401..34466"|"gff3tabix_genes"|"seg02"],21
- seg03 ["ctgA%3A6885..7241"|"gff3tabix_genes"|"seg03"],1 ["ctgA%3A7410..7737"|"gff3tabix_genes"|"seg03"],2 ["ctgA%3A8055..8080"|"gff3tabix_genes"|"seg03"],3 ["ctgA%3A8306..8999"|"gff3tabix_genes"|"seg03"],4
- seg04 ["ctgA%3A5233..5302"|"gff3tabix_genes"|"seg04"],1 ["ctgA%3A5800..6101"|"gff3tabix_genes"|"seg04"],2 ["ctgA%3A6442..6854"|"gff3tabix_genes"|"seg04"],3 ["ctgA%3A7106..7211"|"gff3tabix_genes"|"seg04"],4 ["ctgA%3A7695..8177"|"gff3tabix_genes"|"seg04"],5 ["ctgA%3A8545..8783"|"gff3tabix_genes"|"seg04"],6 ["ctgA%3A8869..8935"|"gff3tabix_genes"|"seg04"],7 ["ctgA%3A9404..9825"|"gff3tabix_genes"|"seg04"],8
- seg05 ["ctgA%3A26503..26799"|"gff3tabix_genes"|"seg05"],1 ["ctgA%3A27172..27185"|"gff3tabix_genes"|"seg05"],2 ["ctgA%3A27448..27860"|"gff3tabix_genes"|"seg05"],3 ["ctgA%3A27887..28076"|"gff3tabix_genes"|"seg05"],4 ["ctgA%3A28225..28316"|"gff3tabix_genes"|"seg05"],5 ["ctgA%3A28777..29058"|"gff3tabix_genes"|"seg05"],6 ["ctgA%3A29513..29647"|"gff3tabix_genes"|"seg05"],7 ["ctgA%3A30108..30216"|"gff3tabix_genes"|"seg05"],8 ["ctgA%3A30465..30798"|"gff3tabix_genes"|"seg05"],9 ["ctgA%3A31232..31236"|"gff3tabix_genes"|"seg05"],10 ["ctgA%3A31421..31817"|"gff3tabix_genes"|"seg05"],11 ["ctgA%3A32010..32057"|"gff3tabix_genes"|"seg05"],12 ["ctgA%3A32208..32680"|"gff3tabix_genes"|"seg05"],13 ["ctgA%3A33053..33325"|"gff3tabix_genes"|"seg05"],14 ["ctgA%3A33438..33868"|"gff3tabix_genes"|"seg05"],15 ["ctgA%3A34244..34313"|"gff3tabix_genes"|"seg05"],16 ["ctgA%3A34605..34983"|"gff3tabix_genes"|"seg05"],17 ["ctgA%3A35333..35507"|"gff3tabix_genes"|"seg05"],18 ["ctgA%3A35642..35904"|"gff3tabix_genes"|"seg05"],19
- seg06 ["ctgA%3A19249..19559"|"gff3tabix_genes"|"seg06"],1 ["ctgA%3A19975..20260"|"gff3tabix_genes"|"seg06"],2 ["ctgA%3A20379..20491"|"gff3tabix_genes"|"seg06"],3 ["ctgA%3A20533..21005"|"gff3tabix_genes"|"seg06"],4 ["ctgA%3A21122..21331"|"gff3tabix_genes"|"seg06"],5 ["ctgA%3A21682..22176"|"gff3tabix_genes"|"seg06"],6 ["ctgA%3A22374..22570"|"gff3tabix_genes"|"seg06"],7 ["ctgA%3A23025..23427"|"gff3tabix_genes"|"seg06"],8
- seg07 ["ctgA%3A44191..44514"|"gff3tabix_genes"|"seg07"],1 ["ctgA%3A44552..45043"|"gff3tabix_genes"|"seg07"],2 ["ctgA%3A45373..45600"|"gff3tabix_genes"|"seg07"],3 ["ctgA%3A45897..46315"|"gff3tabix_genes"|"seg07"],4 ["ctgA%3A46491..46890"|"gff3tabix_genes"|"seg07"],5 ["ctgA%3A47126..47297"|"gff3tabix_genes"|"seg07"],6 ["ctgA%3A47735..47983"|"gff3tabix_genes"|"seg07"],7 ["ctgA%3A48447..48709"|"gff3tabix_genes"|"seg07"],8 ["ctgA%3A48931..49186"|"gff3tabix_genes"|"seg07"],9 ["ctgA%3A49472..49699"|"gff3tabix_genes"|"seg07"],10 ["ctgA%3A49957..50000"|"gff3tabix_genes"|"seg07"],11 ["ctgA%3A49957..50000"|"gff3tabix_genes"|"seg07"],12
- seg08 ["ctgA%3A18509..18985"|"gff3tabix_genes"|"seg08"],1 ["ctgA%3A18989..19388"|"gff3tabix_genes"|"seg08"],2 ["ctgA%3A19496..19962"|"gff3tabix_genes"|"seg08"],3 ["ctgA%3A20093..20580"|"gff3tabix_genes"|"seg08"],4 ["ctgA%3A20970..21052"|"gff3tabix_genes"|"seg08"],5 ["ctgA%3A21270..21277"|"gff3tabix_genes"|"seg08"],6 ["ctgA%3A21685..22168"|"gff3tabix_genes"|"seg08"],7 ["ctgA%3A22564..22869"|"gff3tabix_genes"|"seg08"],8 ["ctgA%3A22958..23298"|"gff3tabix_genes"|"seg08"],9 ["ctgA%3A23412..23469"|"gff3tabix_genes"|"seg08"],10 ["ctgA%3A23932..23932"|"gff3tabix_genes"|"seg08"],11 ["ctgA%3A24328..24787"|"gff3tabix_genes"|"seg08"],12 ["ctgA%3A25228..25367"|"gff3tabix_genes"|"seg08"],13
- seg09 ["ctgA%3A36616..37057"|"gff3tabix_genes"|"seg09"],1 ["ctgA%3A37208..37227"|"gff3tabix_genes"|"seg09"],2
- seg10 ["ctgA%3A29771..29942"|"gff3tabix_genes"|"seg10"],1 ["ctgA%3A30042..30340"|"gff3tabix_genes"|"seg10"],2 ["ctgA%3A30810..31307"|"gff3tabix_genes"|"seg10"],3 ["ctgA%3A31761..31984"|"gff3tabix_genes"|"seg10"],4 ["ctgA%3A32374..32937"|"gff3tabix_genes"|"seg10"],5
- seg11 ["ctgA%3A24228..24510"|"gff3tabix_genes"|"seg11"],1 ["ctgA%3A24868..25012"|"gff3tabix_genes"|"seg11"],2 ["ctgA%3A25212..25426"|"gff3tabix_genes"|"seg11"],3 ["ctgA%3A25794..25874"|"gff3tabix_genes"|"seg11"],4 ["ctgA%3A26075..26519"|"gff3tabix_genes"|"seg11"],5 ["ctgA%3A26930..26940"|"gff3tabix_genes"|"seg11"],6 ["ctgA%3A26975..27063"|"gff3tabix_genes"|"seg11"],7 ["ctgA%3A27415..27799"|"gff3tabix_genes"|"seg11"],8 ["ctgA%3A27880..27943"|"gff3tabix_genes"|"seg11"],9 ["ctgA%3A28225..28346"|"gff3tabix_genes"|"seg11"],10 ["ctgA%3A28375..28570"|"gff3tabix_genes"|"seg11"],11 ["ctgA%3A28758..29041"|"gff3tabix_genes"|"seg11"],12 ["ctgA%3A29101..29302"|"gff3tabix_genes"|"seg11"],13 ["ctgA%3A29604..29702"|"gff3tabix_genes"|"seg11"],14 ["ctgA%3A29867..29885"|"gff3tabix_genes"|"seg11"],15 ["ctgA%3A30241..30246"|"gff3tabix_genes"|"seg11"],16 ["ctgA%3A30575..30738"|"gff3tabix_genes"|"seg11"],17
- seg12 ["ctgA%3A12531..12895"|"gff3tabix_genes"|"seg12"],1 ["ctgA%3A13122..13449"|"gff3tabix_genes"|"seg12"],2 ["ctgA%3A13452..13745"|"gff3tabix_genes"|"seg12"],3 ["ctgA%3A13908..13965"|"gff3tabix_genes"|"seg12"],4 ["ctgA%3A13998..14488"|"gff3tabix_genes"|"seg12"],5 ["ctgA%3A14564..14899"|"gff3tabix_genes"|"seg12"],6 ["ctgA%3A15185..15276"|"gff3tabix_genes"|"seg12"],7 ["ctgA%3A15639..15736"|"gff3tabix_genes"|"seg12"],8 ["ctgA%3A15745..15870"|"gff3tabix_genes"|"seg12"],9
- seg13 ["ctgA%3A49406..49476"|"gff3tabix_genes"|"seg13"],1 ["ctgA%3A49762..50000"|"gff3tabix_genes"|"seg13"],2
- seg14 ["ctgA%3A41137..41318"|"gff3tabix_genes"|"seg14"],1 ["ctgA%3A41754..41948"|"gff3tabix_genes"|"seg14"],2 ["ctgA%3A42057..42474"|"gff3tabix_genes"|"seg14"],3 ["ctgA%3A42890..43270"|"gff3tabix_genes"|"seg14"],4 ["ctgA%3A43395..43811"|"gff3tabix_genes"|"seg14"],5 ["ctgA%3A44065..44556"|"gff3tabix_genes"|"seg14"],6 ["ctgA%3A44763..45030"|"gff3tabix_genes"|"seg14"],7 ["ctgA%3A45231..45488"|"gff3tabix_genes"|"seg14"],8 ["ctgA%3A45790..46022"|"gff3tabix_genes"|"seg14"],9 ["ctgA%3A46092..46318"|"gff3tabix_genes"|"seg14"],10 ["ctgA%3A46816..46992"|"gff3tabix_genes"|"seg14"],11 ["ctgA%3A47449..47829"|"gff3tabix_genes"|"seg14"],12
- seg15 ["ctgA%3A39265..39361"|"gff3tabix_genes"|"seg15"],1 ["ctgA%3A39753..40034"|"gff3tabix_genes"|"seg15"],2 ["ctgA%3A40515..40954"|"gff3tabix_genes"|"seg15"],3 ["ctgA%3A41252..41365"|"gff3tabix_genes"|"seg15"],4 ["ctgA%3A41492..41504"|"gff3tabix_genes"|"seg15"],5 ["ctgA%3A41941..42377"|"gff3tabix_genes"|"seg15"],6 ["ctgA%3A42748..42954"|"gff3tabix_genes"|"seg15"],7 ["ctgA%3A43401..43897"|"gff3tabix_genes"|"seg15"],8 ["ctgA%3A44043..44113"|"gff3tabix_genes"|"seg15"],9 ["ctgA%3A44399..44888"|"gff3tabix_genes"|"seg15"],10 ["ctgA%3A45281..45375"|"gff3tabix_genes"|"seg15"],11 ["ctgA%3A45711..46041"|"gff3tabix_genes"|"seg15"],12 ["ctgA%3A46425..46564"|"gff3tabix_genes"|"seg15"],13 ["ctgA%3A46738..47087"|"gff3tabix_genes"|"seg15"],14 ["ctgA%3A47329..47595"|"gff3tabix_genes"|"seg15"],15 ["ctgA%3A47858..47979"|"gff3tabix_genes"|"seg15"],16 ["ctgA%3A48169..48453"|"gff3tabix_genes"|"seg15"],17
-

  30 |   const r1 = fs.readFileSync(l1.name, 'utf8')
  31 |   const r2 = fs.readFileSync(l2.name, 'utf8')
> 32 |   expect(r1).toMatchSnapshot()
     |              ^
  33 |   expect(r2).toMatchSnapshot()
  34 | })
  35 |

  at test/index.test.ts:32:14
  at fulfilled (test/index.test.ts:5:58)

● volvox sans descriptions

expect(received).toMatchSnapshot()

Snapshot name: `volvox sans descriptions 2`

- Snapshot  - 2
+ Received  + 0

- agt220000000000
-

  31 |   const r2 = fs.readFileSync(l2.name, 'utf8')
  32 |   expect(r1).toMatchSnapshot()
> 33 |   expect(r2).toMatchSnapshot()
     |              ^
  34 | })
  35 |
  36 | test('volvox with descriptions', async () => {

  at test/index.test.ts:33:14
  at fulfilled (test/index.test.ts:5:58)

● volvox with descriptions

write EPIPE

› 2 snapshots failed. Snapshot Summary › 2 snapshots failed from 1 test suite. Inspect your code changes or run yarn test -u to update them.

Test Suites: 1 failed, 1 total Tests: 3 failed, 3 total Snapshots: 2 failed, 2 total Time: 1.281 s, estimated 2 s Ran all test suites. error Command failed with exit code 1.