PSI quantification for alternative splicing events via Psichomics: Execution halted

[Shrishtee-kandoi]

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