xqtl-protocol
xqtl-protocol copied to clipboard
Published
20 hours ago •
cumc
cumc
PSI quantification for alternative splicing events via Psichomics: Execution halted
Script used to run psichomics:
sos run /restricted/projectnb/casa/xqtl-pipeline/pipeline/splicing_calling.ipynb psichomics \
--cwd /restricted/projectnb/casa/skandoi/ROSMAP_DLPFC/psichomics/ \
--samples /restricted/projectnb/casa/skandoi/ROSMAP_DLPFC/psichomics/psichomics_list \
--data-dir /restricted/projectnb/casa/skandoi/ROSMAP_DLPFC/rnaseqc_call/ \
--splicing_annotation /restricted/projectnb/casa/skandoi/ROSMAP_DLPFC/reference_data/hg38_suppa.rds \
--container /restricted/projectnb/casa/xqtl-pipeline/container/singularity/psichomics.sif \
--walltime 100h \
--numThreads 20 \
--mem 128G -J 50 -c csg.yml -q neurology -s build
The error received:
Loading required package: shiny
Loading required package: shinyBS
[0;1;31mSystem has not been booted with systemd as init system (PID 1). Can't operate.[0m
[0;1;31mFailed to create bus connection: Host is down[0m
Registered S3 method overwritten by 'quantmod':
method from
as.zoo.data.frame zoo
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
psichomics 1.22.0: start the visual interface by running psichomics()
Full documentation and tutorials at https://nuno-agostinho.github.io/psichomics
Warning message:
In system("timedatectl", intern = TRUE) :
running command 'timedatectl' had status 1
Attaching package: ‘dplyr’
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
Error: `.x` is empty, and no `.init` supplied
Execution halted
psichomics_junctions.txt file looks like:
Junction ID 01_120405. 02_120405. 03_120405. 04_120405. 05_120405. 07_120410. 08_120410. 100_120417. 101_120418. 102_120418. 103_120418. 104_120418. 108_120418. 109_120418. 111_120418. 112_120418. 113_120418. 115_120418. 116_120418. 118_120418. 119_120418. 11_120410. 120_120418. 121_120418. 122_120418. 124_120419.125_120419. 126_120419. 128_120419. 129_120419. 12_120410. 130_120419. 131_120419. 132_120419. 133_120419. 134_120419. 136_120419. 138_120419. 140_120419. 141_120419. 142_120419. 145_120419. 146_120419. 149_120419. 14_120410. 150_120419. 152_120419. 153_120423. 154_120423. 155_120423. 158_120423. 159_120423. 15_120410. 160_120423. 162_120423. 164_120423. 165_120423. 166_120423. 168_120423. 170_120423. 171_120423. 173_120424. 174_120424. 176_120424. 177_120424. 179_120424. 180_120424. 181_120424. 182_120424. 183_120424. 185_120424. 186_120424. 187_120424. 188_120424. 190_120424. 191_120424. 193_120424. 196_120424. 197_120424. 19_120411. 200_120424. 201_120424. 202_120424. 203_120424. 204_120424. 206_120424. 207_120424. 20_120411. 212_120424. 213_120425. 214_120425. 215_120425. 216_120425. 218_120425. 219_120425. 21_120411. 220_120425. 221_120425. 222_120425. 224_120425. 227_120425. 228_120425. 229_120425. 231_120425. 232_120425. 234_120425. 236_120425.237_120426. 238_120426. 23_120411. 240_120426. 241_120426. 242_120426. 243_120426. 244_120426. 245_120426. 246_120426. 248_120426. 24_120411. 250_120426. 251_120426. 252_120426. 253_120426. 254_120426. 255_120426. 256_120426. 257_120426. 258_120426. 259_120426. 25_120411. 260_120426. 266_120430. 267_120430. 269_120430.26_120411. 270_120430. 271_120430. 272_120430. 273_120430. 274_120430. 276_120430. 277_120430. 279_120430. 280_120430. 281_120430. 283_120430. 284_120430. 285_120430. 286_120430. 287_120430. 288_120430. 289_120430. 28_120411. 290_120430. 291_120430. 292_120430. 294_120430. 296_120430. 298_120430. 299_120430. 29_120416. 300_120430. 302_120430. 303_120430. 304_120430. 305_120430. 306_120430. 307_120430. 309_120430. 30_120416. 310_120430. 312_120430. 314_120501. 315_120501. 316_120501. 318_120501. 321_120501. 322_120501. 323_120501. 325_120501. 326_120501. 327_120501. 328_120501. 329_120501. 32_120416. 331_120501. 332_120501. 334_120501.335_120501. 336_120501. 337_120501. 339_120501. 33_120416. 340_120501. 344_120501. 345_120501. 347_120501. 349_120501. 34_120416. 350_120501. 351_120501. 352_120501. 353_120501. 354_120501. 355_120501. 356_120501. 358_120502. 359_120502. 35_120416. 360_120502. 363_120502. 364_120502. 366_120502. 367_120502. 368_120502.369_120502. 36_120416. 370_120502. 371_120502. 372_120502. 375_120502. 377_120503. 378_120503. 37_120416. 380_120503. 381_120503. 383_120503. 384_120503. 385_120503. 386_120503. 388_120503. 389_120503. 38_120416. 390_120503. 391_120503. 392_120503. 393_120503. 394_120503. 396_120503. 397_120503. 398_120503. 399_120503.39_120416. 402_120503. 403_120503. 405_120503. 406_120503. 407_120503. 408_120503. 40_120416. 410_120503. 411_120503. 412_120503. 413_120503. 414_120503. 415_120503. 416_120503. 418_120507. 419_120507. 420_120507. 423_120507. 424_120507. 425_120507. 426_120507. 427_120507. 428_120507. 429_120507. 430_120507. 431_120507.433_120507. 434_120507. 435_120507. 437_120507. 438_120507. 440_120507. 443_120507. 444_120507. 445_120507. 448_120507. 449_120507. 44_120416. 450_120507. 451_120507. 452_120507. 453_120507. 456_120507. 458_120507. 459_120514. 45_120416. 460_120514. 461_120514. 462_120514. 463_120514. 464_120514. 466_120514. 468_120514.469_120514. 46_120416. 470_120514. 471_120514. 472_120514. 473_120514. 474_120514. 475_120514. 476_120514. 477_120514. 478_120514. 479_120514. 47_120416. 480_120514. 481_120514. 482_120514. 483_120515. 484_120515. 485_120515. 486_120515. 487_120515. 488_120515. 489_120515. 491_120515. 492_120515. 493_120515. 494_120515.495_120515. 496_120515. 497_120515. 498_120515. 500_120515. 501_120515. 502_120515. 505_120515. 506_120515. 507_120515. 508_120515. 509_120515. 510_120515. 511_120515. 513_120515. 515_120515. 516_120515. 517_120515. 51_120416. 520_120515. 521_120515. 522_120515. 523_120515. 524_120515. 525_120515. 526_120515. 528_120515.52_120416. 530_120515. 531_120516. 532_120516. 533_120516. 534_120516. 535_120516. 536_120516. 537_120516. 538_120516. 539_120516. 53_120417. 540_120516. 541_120516. 542_120516. 543_120516. 544_120516. 545_120516. 547_120516. 548_120516. 549_120517. 54_120417. 550_120517. 551_120517. 553_120517. 554_120517. 555_120517.556_120517. 557_120517. 559_120517. 560_120517. 561_120517. 562_120517. 563_120517. 564_120517. 565_120517. 567_120521. 568_120521. 569_120521. 56_120417. 571_120521. 572_120521. 573_120521. 574_120521. 575_120521. 576_120521. 577_120521. 578_120521. 57_120417. 580_120521. 581_120521. 582_120521. 583_120522. 584_120522.586_120522. 587_120522. 588_120522. 589_120522. 58_120417. 590_120522. 591_120522. 593_120522. 594_120522. 595_120522. 596_120522. 599_120523. 600_120523. 602_120523. 603_120523. 604_120523. 605_120523. 606_120523. 607_120523. 608_120523. 60_120417. 610_120523. 613_120523. 614_120523. 616_120524. 617_120524. 618_120524.619_120524. 620_120524. 624_120524. 625_120524. 626_120524. 628_120524. 629_120524. 630_120524. 631_120524. 632_120524. 633_120524. 634_120524. 635_120524. 636_120524. 637_120524. 638_120524. 641_120524. 643_120524. 644_120524. 646_120524. 647_120529. 648_120529. 649_120529. 64_120417. 653_120529. 654_120529. 656_120529.657_120529. 65_120417. 660_120530. 662_120530. 663_120530. 664_120530. 665_120530. 666_120530. 668_120530. 669_120530. 66_120417. 670_120530. 671_120530. 672_120530. 673_120530. 674_120530. 675_120604. 676_120604. 677_120604. 678_120604. 679_120604. 680_120604. 681_120604. 682_120604. 683_120604. 684_120604. 685_120604.687_120604. 688_120604. 689_120604. 68_120417. 690_120604. 691_120605. 693_120605. 694_120605. 695_120605. 697_120605. 698_120605. 699_120605. 69_120417. 700_120605. 701_120605. 702_120605. 703_120605. 704_120605. 705_120605. 706_120605. 707_120531. 708_120531. 709_120531. 70_120417. 710_120531. 711_120531. 713_120531.714_120531. 715_120531. 716_120531. 718_120531. 720_120531. 721_120531. 722_120531. 724_120605. 72_120417. 73_120417. 74_120417. 75_120417. 763_130520. 764_130520. 767_130523. 768_130523. 769_130523. 76_120417. 770_130523. 775_130528. 776_130528. 777_130528. 778_130528. 77_120417. 781_130528. 786_130530. 787_130530.78_120417. 790_130530. 791_130530. 792_130530. 793_130530. 796_130701. 797_130701. 799_130701. 79_120417. 800_130701. 803_130701. 805_130701. 807_130701. 809_130702. 80_120417. 810_130702. 811_130702. 812_130702. 813_130702. 815_130702. 81_120417. 820_130725. 821_130725. 824_130725. 826_130725. 829_130725. 82_120417. 831_130725. 833_130729. 834_130729. 83_120417. 844_130830. 845_130830. 846_130830. 847_130830. 84_120417. 857_130905. 861_130911. 862_130911. 864_130911. 865_130911. 871_130911. 876_130918. 879_130918. 881_130918. 882_130918. 884_130923. 885_130923. 887_130923. 889_130923. 88_120417. 892_130923. 893_130923. 894_130923.895_130923. 899_131010. 89_120417. 900_131010. 901_131010. 905_131010. 909_131031. 90_120417. 911_131031. 922_131031. 923_131031. 924_131031. 925_131031. 926_131031. 927_131031. 929_131031. 932_131101. 934_131101. 935_131101. 936_131101. 937_131101. 938_131101. 939_131101. 93_120417. 940_131101. 941_131101. 942_131101.943_131101. 944_131107. 945_131107. 946_131107. 949_131107. 94_120417. 950_131107. 951_131107. 952_131107. 954_131107. 956_131107. 957_131107. 958_131107. 96_120417. 97_120417. 98_120417. R24_131017. redo4_140501.
chr1:10029:10379:- 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 00 0 0 0 0 0 0 0 0 0 0 0 0 0
