SUPPA
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comprna
psiPerEvent - "transcript not found"
Dear @EduEyras,
I am having trouble resolving the following issue when generating psiPerEvent. I have ensured that my ioe and expression file follow the guidelines outlined in the tutorial. Upon numerous tries, including the removal of extra tabs/spaces, I'm unable to figure out the issue. I am hoping you might be able to provide some assistance.
Below is the standard error:
INFO:lib.tools:File replacedID.2.txt opened in reading mode.
INFO:psiCalculator:Buffering transcript expression levels.
INFO:lib.tools:File replacedID.2.txt closed.
INFO:lib.tools:File /scratch-cbe/users/kero.guynes/AS_events_SUPPA/illumina/00-Generate_ASevents/00-local/GRCm38.JJ.M25.allevents.ioe opened in reading mode.
INFO:psiCalculator:Calculating PSI from the ioe file.
ERROR:psiCalculator:transcript ENSMUST00000027038.10 not found in the "expression file".
ERROR:psiCalculator:PSI not calculated for event ENSMUSG00000025905.14;A3:chr1:5588663-5589005:5588663-5589035:+.
ERROR:psiCalculator:transcript ENSMUST00000140079.7 not found in the "expression file".
ERROR:psiCalculator:PSI not calculated for event ENSMUSG00000033740.17;A3:chr1:6857443-6858460:6857443-6858988:+.
ERROR:psiCalculator:transcript ENSMUST00000131494.7 not found in the "expression file".
ERROR:psiCalculator:PSI not calculated for event ENSMUSG00000033740.17;A3:chr1:6857443-6858460:6857443-6858988:+.
ERROR:psiCalculator:transcript ENSMUST00000043578.12 not found in the "expression file".
ERROR:psiCalculator:PSI not calculated for event ENSMUSG00000033740.17;A3:chr1:6857443-6858460:6857443-6858988:+.
ERROR:psiCalculator:transcript ENSMUST00000150761.7 not found in the "expression file".
I will enclose an example of my ioe and expression file respectively.
seqname gene_id event_id alternative_transcripts total_transcripts
chr1 ENSMUSG00000025940.6 ENSMUSG00000025940.6;A3:chr1:16665505-16667665:16665505-16667668:+ ENSMUST00000177501.1 ENSMUST00000065373.5,ENSMUST00000177501.1
chr1 ENSMUSG00000025779.10 ENSMUSG00000025779.10;A3:chr1:16691773-16700795:16691773-16700849:+ ENSMUST00000026881.10 ENSMUST00000026881.10,ENSMUST00000190366.1
chr1 ENSMUSG00000041809.5 ENSMUSG00000041809.5;A3:chr1:20951796-20955335:20951796-20955342:+ ENSMUST00000038447.5 ENSMUST00000038447.5,ENSMUST00000160782.1
chr1 ENSMUSG00000025933.15 ENSMUSG00000025933.15;A3:chr1:21226679-21229408:21226679-21229591:+ ENSMUST00000027064.7 ENSMUST00000027064.7,ENSMUST00000027065.11
Zygote-Z1 Zygote-Z10 Zygote-Z11 Zygote-Z12 Zygote-Z13 Zygote-Z2 Zygote-Z3 Zygote-Z4 Zygote-Z5 Zygote-Z6 Zygote-Z7 Zygote-Z8 Zygote-Z9 2cell-e10_1_2 2cell-e10_2_2 2cell-e11_1_2 2cell-e11_2_2 2cell-e12_1_2 2cell-e12_2_2 2cell-e1_1_2 2cell-e1_2_2 2cell-e2_1_2 2cell-e2_2_2 2cell-e3_1_2 2cell-e3_2_2 2cell-e4_1_2 2cell-e4_2_2 2cell-e5_1_2 2cell-e5_2_2 2cell-e6_1_2 2cell-e6_2_2 2cell-e7_1_2 2cell-e7_2_2 2cell-e8_1_2 2cell-e8_2_2 2cell-e9_1_2 2cell-e9_2_2 4cell-e10_1_4 4cell-e10_2_4 4cell-e10_3_4 4cell-e10_4_4 4cell-e11_1_4 4cell-e11_2_4 4cell-e11_3_4 4cell-e11_4_4 4cell-e12_1_4 4cell-e12_2_4 4cell-e12_3_4 4cell-e12_4_4 4cell-e1_1_4 4cell-e1_2_4 4cell-e1_3_4 4cell-e1_4_4 4cell-e2_1_4 4cell-e2_2_4 4cell-e2_3_4 4cell-e2_4_4 4cell-e3_1_4 4cell-e3_2_4 4cell-e3_3_4 4cell-e3_4_4 4cell-e4_1_4 4cell-e4_2_4 4cell-e4_3_4 4cell-e4_4_4 4cell-e5_1_4 4cell-e5_2_4 4cell-e5_3_4 4cell-e6_1_4 4cell-e6_2_4 4cell-e6_3_4 4cell-e6_4_4 4cell-e7_1_4 4cell-e7_2_4 4cell-e7_3_4 4cell-e7_4_4 4cell-e8_1_4 4cell-e8_2_4 4cell-e8_3_4 4cell-e8_4_4 4cell-e9_1_4 4cell-e9_2_4 4cell-e9_3_4 4cell-e9_4_4 Late4cell-e1_1L4 Late4cell-e1_2L4 Late4cell-e1_3L4 Late4cell-e1_4L4 Late4cell-e2_1L4 Late4cell-e2_2L4 Late4cell-e2_3L4 Late4cell-e2_4L4 Late4cell-e3_1L4 Late4cell-e3_2L4 Late4cell-e3_3L4 Late4cell-e3_4L4 Late4cell-e4_1L4 Late4cell-e4_2L4 Late4cell-e4_3L4 Late4cell-e4_4L4 Late4cell-e5_1L4 Late4cell-e5_2L4 Late4cell-e5_3L4 Late4cell-e5_4L4 Late4cell-e6_1L4 Late4cell-e6_2L4 Late4cell-e6_3L4 Late4cell-e6_4L4 8cell-e1_1_8 8cell-e1_2_8 8cell-e1_3_8 8cell-e1_4_8 8cell-e1_5_8 8cell-e1_6_8 8cell-e1_7_8 8cell-e1_8_8 8cell-e2_1_8 8cell-e2_2_8 8cell-e2_3_8 8cell-e2_4_8 8cell-e2_5_8 8cell-e2_6_8 8cell-e2_7_8 8cell-e2_8_8 8cell-e3_1_8 8cell-e3_2_8 8cell-e3_3_8 8cell-e3_4_8 8cell-e3_5_8 8cell-e3_6_8 8cell-e3_7_8 8cell-e3_8_8 8cell-e4_1_8 8cell-e4_2_8 8cell-e4_3_8 8cell-e4_4_8 8cell-e4_5_8 8cell-e4_6_8 8cell-e4_7_8 8cell-e4_8_8 16cell-e1_1_16 16cell-e1_2_16 16cell-e1_3_16 16cell-e1_4_16 16cell-e1_5_16 16cell-e1_6_16 16cell-e1_7_16 16cell-e1_8_16 16cell-e2_1_16 16cell-e2_2_16 16cell-e2_3_16 16cell-e2_4_16 16cell-e2_5_16 16cell-e2_6_16 16cell-e2_7_16 16cell-e2_8_16 16cell-e3_1_16 16cell-e3_2_16 16cell-e3_3_16 16cell-e3_4_16 16cell-e3_5_16 16cell-e3_6_16 16cell-e3_7_16 16cell-e3_8_16 32cell.ICM-e1_1_32 32cell.TE-e1_2_32 32cell.TE-e1_3_32 32cell.ICM-e1_4_32 32cell.ICM-e1_5_32 32cell.ICM-e1_6_32 32cell.ICM-e1_7_32 32cell.ICM-e1_8_32 32cell.TE-e2_10_32 32cell.TE-e2_1_32 32cell.TE-e2_4_32 32cell.TE-e2_5_32 32cell.TE-e2_7_32 32cell.ICM-e2_8_32 32cell.TE-e2_9_32 32cell.ICM-e3_2_32 32cell.ICM-e3_4_32 32cell.TE-e4_1_32 32cell.TE-e4_2_32 32cell.ICM-e4_3_32 32cell.ICM-e4_4_32 32cell.ICM-e4_5_32 32cell.ICM-e5_3_32 32cell.TE-e5_4_32 32cell.ICM-e5_5_32 32cell.TE-e6_1_32 32cell.ICM-e6_2_32 32cell.ICM-e6_3_32 32cell.ICM-e6_4_32 32cell.ICM-e6_5_32 32cell.ICM-e6_6_32 32cell.ICM-e6_7_32 32cell.ICM-e6_8_32 32cell.ICM-eM_10_32 32cell.TE-eM_11_32 32cell.ICM-eM_12_32 32cell.ICM-eM_13_32 32cell.ICM-eM_14_32 32cell.ICM-eM_15_32 32cell.ICM-eM_16_32 32cell.TE-eM_17_32 32cell.TE-eM_18_32 32cell.TE-eM_19_32 32cell.ICM-eM_1_32 32cell.TE-eM_20_32 32cell.TE-eM_21_32 32cell.TE-eM_22_32 32cell.ICM-eM_23_32 32cell.TE-eM_24_32 32cell.ICM-eM_2_32 32cell.ICM-eM_3_32 32cell.ICM-eM_4_32 32cell.ICM-eM_5_32 32cell.ICM-eM_6_32 32cell.ICM-eM_7_32 32cell.ICM-eM_8_32 32cell.TE-eM_9_32
ENSMUST00000000001.4 23.699801 29.531066 9.373192 28.408768 18.346659 2.903959 31.015459 22.097361 24.368943 17.578748 27.095332 18.107495 26.541401 7.27111 3.282621 12.24435 15.749261 8.774473 13.896691 10.521675 11.431081 8.457218 4.054155 5.060513 6.747456 6.513756 7.37235 6.133776 7.170449 12.358007 8.664183 5.311653 5.010768 8.981175 10.144598 6.880453 8.121582 4.793758 4.376026 6.676918 8.48959 4.468856 3.505609 5.60338 3.238691 5.226141 4.552121 5.871587 7.607344 7.324449 10.336549 7.343999 11.283221 7.099345 4.872275 5.791282 14.589054 11.38145 9.027093 14.689221 8.413332 9.931686 7.855318 9.705259 10.74265 6.890531 8.453856 6.086481 6.958385 7.905544 4.54128 4.756707 5.866568 1.233324 4.53656 2.944799 3.411732 4.614576 3.795896 8.176498 3.724619 4.637435 3.854482 4.233385 6.874941 8.393428 6.532562 7.476727 4.449587 4.738303 4.690767 5.354484 7.515053 6.379646 3.609898 4.113281 6.236357 6.173756 9.437972 8.481441 4.556021 6.95311 5.024506 7.705457 8.29464 7.997389 11.406045 8.33247 9.167994 6.113021 5.674731 5.448893 5.085851 5.9469 6.695142 4.359465 8.590914 5.127503 5.911073 4.992695 3.893009 3.436716 4.198775 4.581969 7.474096 6.029246 2.456529 3.863197 6.363138 5.615331 4.733142 1.271892 7.297295 6.307324 3.084559 6.12322 1.311613 2.504537 3.420215 4.698864 5.651313 5.028374 4.392834 4.631781 3.578765 8.119668 2.945057 3.921662 4.388399 5.267128 3.303975 2.895591 3.037846 1.892419 4.684201 4.474529 4.418258 4.074804 3.106089 1.439385 1.627852 2.48378 1.580571 3.362787 4.386948 3.859264 8.706291 5.214468 0.767522 8.373996 7.024633 12.483276 14.523558 15.132576 13.204651 13.28761 9.732795 8.22582 10.805089 12.017748 7.866661 8.113557 16.030285 9.275673 3.09417 18.216483 8.301265 11.953244 8.816366 10.065319 12.610301 5.578612 8.04173 6.315809 6.986776 7.076559 10.572377 8.84259 13.826717 11.181286 6.889312 7.969009 8.868017 9.146875 8.132292 14.243906 13.227749 9.691322 5.860454 9.280308 6.977942 8.053274 9.439307 11.993553 6.811049 11.54999 10.51758 6.561902 8.369874 11.687409 8.781721
ENSMUST00000000003.15 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 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 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 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 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 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 0 0 0 0 0 0 0 0 0 0 0 0.495437 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 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 0
ENSMUST00000000028.15 47.287354 49.644141 17.685213 50.716066 39.853042 3.920077 49.213727 53.602238 39.228201 28.70716 41.569966 29.072961 39.681369 55.767618 101.763093 80.735658 67.189911 23.31336 48.028778 21.297967 28.953399 31.943853 29.243495 34.279608 53.354584 23.743354 16.571281 45.689363 19.5573 56.529155 48.234715 15.999132 13.920245 45.075811 19.561484 80.242835 37.553773 43.90178 36.381608 48.943901 63.919139 51.853761 46.374443 55.221681 29.706866 37.436459 29.174008 39.821919 45.990367 94.914819 93.979019 109.299261 90.550418 89.756933 92.80592 126.963079 127.314566 99.40771 120.032926 120.043174 79.727867 98.109836 74.208857 96.508302 79.758671 75.538617 62.729921 110.122482 83.735922 78.450945 41.758528 58.420319 84.166004 42.766219 40.444327 45.73448 48.311633 55.385348 50.450969 69.442093 74.71438 63.843986 35.421247 43.9383 58.675393 58.833654 55.343101 60.783764 75.703792 72.455805 76.79832 65.211681 75.471254 66.904591 60.136035 63.011135 40.7139 53.012652 43.483533 76.904698 64.667353 58.785229 59.793897 79.742204 73.530047 87.703115 65.71221 103.874636 36.034466 36.172428 36.341309 25.958972 31.731749 24.918847 27.518788 47.038385 28.484236 26.397996 29.820792 31.046573 29.469441 24.92985 28.846256 37.54953 29.206354 33.31462 24.035142 39.307769 32.597044 33.699627 28.656812 25.631481 19.198092 23.448642 27.08588 21.329791 18.604526 15.843903 29.426873 29.155544 24.467047 29.446836 33.360315 17.897125 21.746284 29.335912 32.380652 41.192933 8.395254 11.948721 7.827067 10.193335 9.798004 7.48703 13.018633 9.239254 15.052806 16.01702 9.426014 4.200304 3.703164 10.012569 6.565227 14.915239 10.887732 17.639761 10.791486 18.880859 4.107711 13.06874 5.185026 9.689095 20.103298 7.80463 8.090655 15.447846 31.644158 6.647939 8.90958 7.067004 13.889842 23.062365 29.915087 9.062007 18.381197 16.816003 11.755399 12.511033 38.713467 16.319743 19.701071 17.934028 9.474185 19.105858 27.126112 20.875963 16.225257 10.132076 8.290812 9.258565 5.684479 11.442072 27.940951 16.16369 16.18443 10.550326 13.633867 24.647265 13.866521 17.977808 20.084522 12.819201 26.986037 11.317425 5.930879 20.483479 4.006135 30.082456 3.652945 11.828851 22.926053
ENSMUST00000000031.16 0 0 0.123811 0.936163 0 0 0.103467 0 0 0 0.031687 0.068491 0.603394 0 0.938128 0 0 0 0 1.041091 0.804929 0 0 0 0.21037 0.507824 0 0 0 0.336858 0.907873 0 0 0 0 0 0 0 0 0.166009 0.349755 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.042259 0.253973 0.779035 0.942206 0.026929 0 0 0 0 0 0 0 0 0 0 0.018611 0 0 0 0 0 0.430389 0 0 0 0 0 0 0 0 0 1.102667 0.138387 0 0 0.452975 0 0 0.068913 1.143873 0 0 0 0 0 0 0 0 0.081569 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.342841 0 0 0 0 0 0 0.19409 0.896429 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.49034 0 0 0 0 0 0 0 0 0 0 0 0 0 0.900217 0.935672 0 0.186592 0 0 0.143204 0 0 0 0.232264 0 0 0.059559 0 0 1.287634 0 0 0 0 0 1.350515 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.329225 0 0 0 0 0 0 0 0 0 0 0 0 0 0
ENSMUST00000000037.17 93.489436 81.76692 37.977305 71.756324 57.678214 11.718331 100.212557 81.349296 93.873587 62.142201 91.12093 68.907477 75.627914 40.835748 50.051121 57.889572 61.779187 55.588576 60.046133 65.583237 56.830328 53.537873 46.103594 30.150719 36.627231 57.912446 54.764002 34.883254 34.694436 51.17559 41.660915 54.328928 34.441027 46.297098 50.167459 40.527247 24.126215 5.181628 5.701418 8.317192 9.361625 6.911394 2.867919 6.949731 2.55549 2.252174 4.163168 4.851713 3.251534 15.356784 7.308524 4.989802 3.472203 2.53818 5.545818 1.536429 4.189031 12.853405 6.460353 5.700069 6.746444 8.132782 4.5115 6.012508 6.305973 2.625471 6.546259 17.727472 6.861142 3.743076 7.393494 3.840385 5.081398 2.717532 3.774507 2.021917 4.789885 4.043814 1.9424 4.555117 4.025174 2.298175 2.715958 2.26296 3.870009 2.70052 5.838803 2.700489 10.674344 8.488994 4.736988 8.305241 4.058393 2.930986 4.456863 6.196403 4.658535 2.600115 4.733892 5.629837 3.020004 2.292744 3.292217 1.170996 8.567117 7.860196 6.047172 4.047508 2.058267 0.692417 1.024385 1.165681 1.097924 1.587094 1.25111 1.778851 1.185968 0.515102 3.683279 2.756023 2.70169 1.039241 0.979897 2.697285 2.589705 5.64951 3.974395 1.761172 2.19261 1.040073 1.927764 4.917901 1.778033 3.905965 1.638823 2.629665 0.133212 1.400547 1.647038 0.138576 0.715257 0.762835 0.861437 0.474078 0.267721 0.152837 0.424976 0.655706 0.276536 0 0.451414 0 0.342016 0.979082 0.685206 0.18318 1.041492 0.204209 0.308678 0.171538 0.037843 0.456383 0 0.666393 0.094747 1.02581 0 0 4.226226 1.265938 0.093635 0.546776 0 0 0 0.527646 0 0 0 0 0.275725 0 0 0 0 0 0 0 0 0 0.803752 0 1.478849 0.267149 0 0 0 0 0 0 0 0 0 0 0 0 0.261909 0 0 0 0 0 0 0 0 0.392536 0 1.27389 0 0 0
ENSMUST00000000049.11 0 0 0 0 0 0 0 0 0 0.094161 0.066553 0 0 1.844433 0 0 0 0.48678 2.113169 0 0 0.159442 0 0 0.172137 2.781913 0.551429 0 0 0 1.014575 1.197547 0 0 0 0 0 0 0 0 0 0 0 0 0.082429 1.097804 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.9848 1.326141 2.386995 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.707816 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0.349952 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2.099105 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 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 0
ENSMUST00000000056.7 17.187512 13.058084 4.291559 9.11523 12.196756 1.371174 14.519641 15.961982 14.54995 11.364278 17.237419 7.636103 11.429688 15.962366 13.482118 4.494861 7.4047 7.379121 11.494511 2.948095 2.235935 4.784682 5.03162 4.629424 6.436491 3.622792 11.237226 6.645275 7.27671 3.333031 2.396052 2.599962 1.742445 2.714846 2.604052 6.996126 6.041317 1.889107 2.109791 0.726275 1.344082 0.391768 0.586408 1.391763 0.561092 1.243266 0.552313 2.33301 1.268324 1.466415 0.86832 5.033286 1.131888 0.768047 5.106209 0.552444 2.122361 1.072117 6.82694 2.97854 0.422183 1.153859 1.883945 3.626643 1.612209 2.596037 2.797803 9.007971 1.000934 0.408824 1.968968 2.240878 1.230686 0.204509 2.032762 0.719276 0.866593 0.593356 0.981222 1.333139 2.721297 3.00614 0.626275 2.649634 0.803929 0.806335 1.39015 6.603095 0.306491 1.528758 2.024114 1.681923 0.2311 0.180091 4.319847 7.957845 0.624883 3.973218 2.438944 2.157658 3.29869 5.317567 0.77714 1.165276 1.484474 6.390725 2.468354 3.261578 0.47389 3.457451 0.170976 0 0.025804 0.347547 0.182796 0 3.069161 0.542874 0.76409 0.830152 3.006962 0.787631 0.921914 0.656929 0.696819 5.955753 2.748242 0.800274 1.69992 0.055446 0.912617 0.246044 0.07241 0 0.523698 0.040831 0.921923 5.309277 2.11425 1.780577 1.341101 1.006866 0.297962 0.211149 0.826585 2.897688 0.115359 2.689669 0.625922 1.37512 0.566299 0.450046 0.471763 0.047284 1.030074 0.736055 1.25303 0.083059 0.61076 1.863088 0.209617 1.685458 0 1.905557 0.241697 0.205425 2.560553 0 1.60621 0.044555 0.192723 0 0.150728 0.06862 0.109628 0 0 0.174565 0.029669 0 1.685689 0.160053 0 1.192529 0 0 0 0.287531 0.521546 0.625429 0.427445 0 0 1.341059 1.01833 0.067062 0.432336 0.335277 0.351064 0.446807 0 0 0.386405 0.157184 0.097316 0 3.299547 0.307102 0 0.105779 0 8.253722 0.292858 0 0 0.191984 0.080827 0 0.751888 0 0.342276
ENSMUST00000000058.6 0.334586 0.581514 0.118006 0.965179 0.423004 0 0.474112 0.959381 0.524554 0.179814 0.594764 0.282361 0.916395 0.140514 0.136942 0.31012 0 0 0 0.537502 0 0 0 0 0.704925 0 0.061858 0 0.744494 0.090307 0.249218 0 0.036042 0.14437 0.079107 0 1.073943 0 0 0 0 0 0 0 0 0 0.049282 0.158349 0 0 0 0.173292 0.038168 0.905395 0 0 0.034135 0 0 0 0 0 1.215849 0 0 0 0 0 0 0 0 0 0 0 0.05925 0.050995 0 0 0 0 0 0.310825 0.284575 0 0.209418 0.138712 0 0 0.031908 0 0 0.208439 0.628426 0 0 0 2.753125 0 0 0 0 0.800573 0.374292 0 0 0 0 0 0.655527 0 2.692298 0.157516 0.085326 0.656848 0.17322 0.191096 0.876312 2.741018 0.299748 2.295354 0.072269 1.450715 0.096213 2.17961 0 0.940804 0.841649 5.71168 0.71971 0 0.445418 0 0 0 0.608075 0.110151 0 0.099234 0.615226 0.844793 1.705237 2.597712 0.659162 2.345665 2.671118 0.098912 0.383492 0.131244 0 0 0.068193 0.033774 0.150698 0.1955 0 0 0.528241 0.192666 0.089953 0 0 0.111242 0 0.816722 0 0 0 0 0 0.961579 0 0 3.459506 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
ENSMUST00000000078.7 2.789082 0.786019 1.648873 1.111271 3.958626 0.354417 0.533204 0.300765 1.594925 1.227791 0.574214 1.947925 3.196918 2.944017 1.886042 3.194435 0 4.12517 6.041348 0.017456 0.598237 1.112595 1.308569 1.478161 1.613228 2.326362 5.199598 1.755094 2.234203 8.351876 0.849126 5.149227 2.945548 1.791296 2.48624 0.158894 0.182872 0.019692 0.466196 0.141908 0.028705 0 0 0 0.020658 0 0 0 0 0.130467 0.05028 0.027241 0.21176 0.100056 0.027034 0.387896 0.72836 0.048589 0.020815 0.020665 0.052796 0.156881 0.014015 0.053435 0 0.23365 0 0.081903 0.122692 0.091284 0 0.143668 0.017102 0.009687 0.46148 0.207347 0 1.153838 0.025565 0.631703 0 0.084775 0.008477 0 0.026195 0.02894 0 0.373962 0.019972 0.054953 0.020099 0.071668 0 0 0.04495 0 1.228921 0.643451 0.020847 0.14465 0 0 0.022512 0.137435 0 0 0.077661 0 0 0 0 0 0 0 0 0 0 0.018858 0 0.017683 0.014266 0 0 0.035102 0.023424 0.078234 0.025291 0 0 0.346685 0 0.028489 0 0 0 0 0.126013 0 0 0 0.085844 0 0 0 2.716993 2.493614 0.529129 0.049219 7.295619 0.074536 0.119142 0.046107 0.211403 0.156354 1.958608 0.12835 0.112606 0 0.504242 0.159039 0.496361 0.069955 0 7.050469 46.318801 130.820329 76.055336 47.966273 16.220072 9.868566 20.004074 52.562058 36.918618 22.374552 35.859731 28.579825 64.036908 5.631939 50.881748 14.294865 8.591746 41.908902 10.926839 29.729299 12.170858 43.043501 6.126444 181.340477 66.653972 19.120437 34.679719 4.17127 18.037819 0.793591 6.361748 5.397245 5.578454 11.482219 17.836691 12.588418 16.400497 7.213011 13.435379 53.396345 27.518517 32.820368 15.170734 7.772046 74.804985 35.200485 67.525806 24.005462 46.15853 13.196706 16.424238 18.41913 21.684488 16.84778 10.805869 27.133212 25.6408
Please let me know if I can provide anything else. Many thanks for your help in advance!
Edit: attaching the files just in case. I have also tried running the above without the isoform as ENSMUST00000000078 instead of ENSMUST00000000078.7 and still received the same error.
allevents.ioe.gz expression_file.txt.gz
Hello, I have the same error.. it's been two weeks since you've posted the issue, did you find any solution by yourself ?
Thanks in advance for your answer :)
Hi,
Do you get this error for all transcripts or just a few? The ioe will include all events and related transcripts from the annotation, but some transcripts may not have an entry in the expression file if they were not detected in the experiment. Is this a possibility?
E.
On Tue, 12 Mar 2024 at 06:00, bvien24 @.***> wrote:
Dear @EduEyras https://github.com/EduEyras,
I am having trouble resolving the following issue when generating psiPerEvent. I have ensured that my ioe and expression file follow the guidelines outlined in the tutorial. Upon numerous tries, including the removal of extra tabs/spaces, I'm unable to figure out the issue. I am hoping you might be able to provide some assistance.
Below is the standard error:
INFO:lib.tools:File replacedID.2.txt opened in reading mode. INFO:psiCalculator:Buffering transcript expression levels. INFO:lib.tools:File replacedID.2.txt closed. INFO:lib.tools:File /scratch-cbe/users/kero.guynes/AS_events_SUPPA/illumina/00-Generate_ASevents/00-local/GRCm38.JJ.M25.allevents.ioe opened in reading mode. INFO:psiCalculator:Calculating PSI from the ioe file. ERROR:psiCalculator:transcript ENSMUST00000027038.10 not found in the "expression file". ERROR:psiCalculator:PSI not calculated for event ENSMUSG00000025905.14;A3:chr1:5588663-5589005:5588663-5589035:+. ERROR:psiCalculator:transcript ENSMUST00000140079.7 not found in the "expression file". ERROR:psiCalculator:PSI not calculated for event ENSMUSG00000033740.17;A3:chr1:6857443-6858460:6857443-6858988:+. ERROR:psiCalculator:transcript ENSMUST00000131494.7 not found in the "expression file". ERROR:psiCalculator:PSI not calculated for event ENSMUSG00000033740.17;A3:chr1:6857443-6858460:6857443-6858988:+. ERROR:psiCalculator:transcript ENSMUST00000043578.12 not found in the "expression file". ERROR:psiCalculator:PSI not calculated for event ENSMUSG00000033740.17;A3:chr1:6857443-6858460:6857443-6858988:+. ERROR:psiCalculator:transcript ENSMUST00000150761.7 not found in the "expression file".
I will enclose an example of my ioe and expression file respectively.
seqname gene_id event_id alternative_transcripts total_transcripts chr1 ENSMUSG00000025940.6 ENSMUSG00000025940.6;A3:chr1:16665505-16667665:16665505-16667668:+ ENSMUST00000177501.1 ENSMUST00000065373.5,ENSMUST00000177501.1 chr1 ENSMUSG00000025779.10 ENSMUSG00000025779.10;A3:chr1:16691773-16700795:16691773-16700849:+ ENSMUST00000026881.10 ENSMUST00000026881.10,ENSMUST00000190366.1 chr1 ENSMUSG00000041809.5 ENSMUSG00000041809.5;A3:chr1:20951796-20955335:20951796-20955342:+ ENSMUST00000038447.5 ENSMUST00000038447.5,ENSMUST00000160782.1 chr1 ENSMUSG00000025933.15 ENSMUSG00000025933.15;A3:chr1:21226679-21229408:21226679-21229591:+ ENSMUST00000027064.7 ENSMUST00000027064.7,ENSMUST00000027065.11
Zygote-Z1 Zygote-Z10 Zygote-Z11 Zygote-Z12 Zygote-Z13 Zygote-Z2 Zygote-Z3 Zygote-Z4 Zygote-Z5 Zygote-Z6 Zygote-Z7 Zygote-Z8 Zygote-Z9 2cell-e10_1_2 2cell-e10_2_2 2cell-e11_1_2 2cell-e11_2_2 2cell-e12_1_2 2cell-e12_2_2 2cell-e1_1_2 2cell-e1_2_2 2cell-e2_1_2 2cell-e2_2_2 2cell-e3_1_2 2cell-e3_2_2 2cell-e4_1_2 2cell-e4_2_2 2cell-e5_1_2 2cell-e5_2_2 2cell-e6_1_2 2cell-e6_2_2 2cell-e7_1_2 2cell-e7_2_2 2cell-e8_1_2 2cell-e8_2_2 2cell-e9_1_2 2cell-e9_2_2 4cell-e10_1_4 4cell-e10_2_4 4cell-e10_3_4 4cell-e10_4_4 4cell-e11_1_4 4cell-e11_2_4 4cell-e11_3_4 4cell-e11_4_4 4cell-e12_1_4 4cell-e12_2_4 4cell-e12_3_4 4cell-e12_4_4 4cell-e1_1_4 4cell-e1_2_4 4cell-e1_3_4 4cell-e1_4_4 4cell-e2_1_4 4cell-e2_2_4 4cell-e2_3_4 4cell-e2_4_4 4cell-e3_1_4 4cell-e3_2_4 4cell-e3_3_4 4cell-e3_4_4 4cell-e4_1_4 4cell-e4_2_4 4cell-e4_3_4 4cell-e4_4_4 4cell-e5_1_4 4cell-e5_2_4 4cell-e5_3_4 4cell-e6_1_4 4cell-e6_2_4 4cell-e6_3_4 4cell-e6_4_4 4cell-e7_1_4 4cell-e7_2_4 4cell-e7_3_4 4cell-e7_4_4 4cell-e8_1_4 4cell-e8_2_4 4cell-e8_3_4 4cell-e8_4_4 4cell-e9_1_4 4cell-e9_2_4 4cell-e9_3_4 4cell-e9_4_4 Late4cell-e1_1L4 Late4cell-e1_2L4 Late4cell-e1_3L4 Late4cell-e1_4L4 Late4cell-e2_1L4 Late4cell-e2_2L4 Late4cell-e2_3L4 Late4cell-e2_4L4 Late4cell-e3_1L4 Late4cell-e3_2L4 Late4cell-e3_3L4 Late4cell-e3_4L4 Late4cell-e4_1L4 Late4cell-e4_2L4 Late4cell-e4_3L4 Late4cell-e4_4L4 Late4cell-e5_1L4 Late4cell-e5_2L4 Late4cell-e5_3L4 Late4cell-e5_4L4 Late4cell-e6_1L4 Late4cell-e6_2L4 Late4cell-e6_3L4 Late4cell-e6_4L4 8cell-e1_1_8 8cell-e1_2_8 8cell-e1_3_8 8cell-e1_4_8 8cell-e1_5_8 8cell-e1_6_8 8cell-e1_7_8 8cell-e1_8_8 8cell-e2_1_8 8cell-e2_2_8 8cell-e2_3_8 8cell-e2_4_8 8cell-e2_5_8 8cell-e2_6_8 8cell-e2_7_8 8cell-e2_8_8 8cell-e3_1_8 8cell-e3_2_8 8cell-e3_3_8 8cell-e3_4_8 8cell-e3_5_8 8cell-e3_6_8 8cell-e3_7_8 8cell-e3_8_8 8cell-e4_1_8 8cell-e4_2_8 8cell-e4_3_8 8cell-e4_4_8 8cell-e4_5_8 8cell-e4_6_8 8cell-e4_7_8 8cell-e4_8_8 16cell-e1_1_16 16cell-e1_2_16 16cell-e1_3_16 16cell-e1_4_16 16cell-e1_5_16 16cell-e1_6_16 16cell-e1_7_16 16cell-e1_8_16 16cell-e2_1_16 16cell-e2_2_16 16cell-e2_3_16 16cell-e2_4_16 16cell-e2_5_16 16cell-e2_6_16 16cell-e2_7_16 16cell-e2_8_16 16cell-e3_1_16 16cell-e3_2_16 16cell-e3_3_16 16cell-e3_4_16 16cell-e3_5_16 16cell-e3_6_16 16cell-e3_7_16 16cell-e3_8_16 32cell.ICM-e1_1_32 32cell.TE-e1_2_32 32cell.TE-e1_3_32 32cell.ICM-e1_4_32 32cell.ICM-e1_5_32 32cell.ICM-e1_6_32 32cell.ICM-e1_7_32 32cell.ICM-e1_8_32 32cell.TE-e2_10_32 32cell.TE-e2_1_32 32cell.TE-e2_4_32 32cell.TE-e2_5_32 32cell.TE-e2_7_32 32cell.ICM-e2_8_32 32cell.TE-e2_9_32 32cell.ICM-e3_2_32 32cell.ICM-e3_4_32 32cell.TE-e4_1_32 32cell.TE-e4_2_32 32cell.ICM-e4_3_32 32cell.ICM-e4_4_32 32cell.ICM-e4_5_32 32cell.ICM-e5_3_32 32cell.TE-e5_4_32 32cell.ICM-e5_5_32 32cell.TE-e6_1_32 32cell.ICM-e6_2_32 32cell.ICM-e6_3_32 32cell.ICM-e6_4_32 32cell.ICM-e6_5_32 32cell.ICM-e6_6_32 32cell.ICM-e6_7_32 32cell.ICM-e6_8_32 32cell.ICM-eM_10_32 32cell.TE-eM_11_32 32cell.ICM-eM_12_32 32cell.ICM-eM_13_32 32cell.ICM-eM_14_32 32cell.ICM-eM_15_32 32cell.ICM-eM_16_32 32cell.TE-eM_17_32 32cell.TE-eM_18_32 32cell.TE-eM_19_32 32cell.ICM-eM_1_32 32cell.TE-eM_20_32 32cell.TE-eM_21_32 32cell.TE-eM_22_32 32cell.ICM-eM_23_32 32cell.TE-eM_24_32 32cell.ICM-eM_2_32 32cell.ICM-eM_3_32 32cell.ICM-eM_4_32 32cell.ICM-eM_5_32 32cell.ICM-eM_6_32 32cell.ICM-eM_7_32 32cell.ICM-eM_8_32 32cell.TE-eM_9_32 ENSMUST00000000001.4 23.699801 29.531066 9.373192 28.408768 18.346659 2.903959 31.015459 22.097361 24.368943 17.578748 27.095332 18.107495 26.541401 7.27111 3.282621 12.24435 15.749261 8.774473 13.896691 10.521675 11.431081 8.457218 4.054155 5.060513 6.747456 6.513756 7.37235 6.133776 7.170449 12.358007 8.664183 5.311653 5.010768 8.981175 10.144598 6.880453 8.121582 4.793758 4.376026 6.676918 8.48959 4.468856 3.505609 5.60338 3.238691 5.226141 4.552121 5.871587 7.607344 7.324449 10.336549 7.343999 11.283221 7.099345 4.872275 5.791282 14.589054 11.38145 9.027093 14.689221 8.413332 9.931686 7.855318 9.705259 10.74265 6.890531 8.453856 6.086481 6.958385 7.905544 4.54128 4.756707 5.866568 1.233324 4.53656 2.944799 3.411732 4.614576 3.795896 8.176498 3.724619 4.637435 3.854482 4.233385 6.874941 8.393428 6.532562 7.476727 4.449587 4.738303 4.690767 5.354484 7.515053 6.379646 3.609898 4.113281 6.236357 6.173756 9.437972 8.481441 4.556021 6.95311 5.024506 7.705457 8.29464 7.997389 11.406045 8.33247 9.167994 6.113021 5.674731 5.448893 5.085851 5.9469 6.695142 4.359465 8.590914 5.127503 5.911073 4.992695 3.893009 3.436716 4.198775 4.581969 7.474096 6.029246 2.456529 3.863197 6.363138 5.615331 4.733142 1.271892 7.297295 6.307324 3.084559 6.12322 1.311613 2.504537 3.420215 4.698864 5.651313 5.028374 4.392834 4.631781 3.578765 8.119668 2.945057 3.921662 4.388399 5.267128 3.303975 2.895591 3.037846 1.892419 4.684201 4.474529 4.418258 4.074804 3.106089 1.439385 1.627852 2.48378 1.580571 3.362787 4.386948 3.859264 8.706291 5.214468 0.767522 8.373996 7.024633 12.483276 14.523558 15.132576 13.204651 13.28761 9.732795 8.22582 10.805089 12.017748 7.866661 8.113557 16.030285 9.275673 3.09417 18.216483 8.301265 11.953244 8.816366 10.065319 12.610301 5.578612 8.04173 6.315809 6.986776 7.076559 10.572377 8.84259 13.826717 11.181286 6.889312 7.969009 8.868017 9.146875 8.132292 14.243906 13.227749 9.691322 5.860454 9.280308 6.977942 8.053274 9.439307 11.993553 6.811049 11.54999 10.51758 6.561902 8.369874 11.687409 8.781721 ENSMUST00000000003.15 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 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 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 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 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 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 0 0 0 0 0 0 0 0 0 0 0 0.495437 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 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 0 ENSMUST00000000028.15 47.287354 49.644141 17.685213 50.716066 39.853042 3.920077 49.213727 53.602238 39.228201 28.70716 41.569966 29.072961 39.681369 55.767618 101.763093 80.735658 67.189911 23.31336 48.028778 21.297967 28.953399 31.943853 29.243495 34.279608 53.354584 23.743354 16.571281 45.689363 19.5573 56.529155 48.234715 15.999132 13.920245 45.075811 19.561484 80.242835 37.553773 43.90178 36.381608 48.943901 63.919139 51.853761 46.374443 55.221681 29.706866 37.436459 29.174008 39.821919 45.990367 94.914819 93.979019 109.299261 90.550418 89.756933 92.80592 126.963079 127.314566 99.40771 120.032926 120.043174 79.727867 98.109836 74.208857 96.508302 79.758671 75.538617 62.729921 110.122482 83.735922 78.450945 41.758528 58.420319 84.166004 42.766219 40.444327 45.73448 48.311633 55.385348 50.450969 69.442093 74.71438 63.843986 35.421247 43.9383 58.675393 58.833654 55.343101 60.783764 75.703792 72.455805 76.79832 65.211681 75.471254 66.904591 60.136035 63.011135 40.7139 53.012652 43.483533 76.904698 64.667353 58.785229 59.793897 79.742204 73.530047 87.703115 65.71221 103.874636 36.034466 36.172428 36.341309 25.958972 31.731749 24.918847 27.518788 47.038385 28.484236 26.397996 29.820792 31.046573 29.469441 24.92985 28.846256 37.54953 29.206354 33.31462 24.035142 39.307769 32.597044 33.699627 28.656812 25.631481 19.198092 23.448642 27.08588 21.329791 18.604526 15.843903 29.426873 29.155544 24.467047 29.446836 33.360315 17.897125 21.746284 29.335912 32.380652 41.192933 8.395254 11.948721 7.827067 10.193335 9.798004 7.48703 13.018633 9.239254 15.052806 16.01702 9.426014 4.200304 3.703164 10.012569 6.565227 14.915239 10.887732 17.639761 10.791486 18.880859 4.107711 13.06874 5.185026 9.689095 20.103298 7.80463 8.090655 15.447846 31.644158 6.647939 8.90958 7.067004 13.889842 23.062365 29.915087 9.062007 18.381197 16.816003 11.755399 12.511033 38.713467 16.319743 19.701071 17.934028 9.474185 19.105858 27.126112 20.875963 16.225257 10.132076 8.290812 9.258565 5.684479 11.442072 27.940951 16.16369 16.18443 10.550326 13.633867 24.647265 13.866521 17.977808 20.084522 12.819201 26.986037 11.317425 5.930879 20.483479 4.006135 30.082456 3.652945 11.828851 22.926053 ENSMUST00000000031.16 0 0 0.123811 0.936163 0 0 0.103467 0 0 0 0.031687 0.068491 0.603394 0 0.938128 0 0 0 0 1.041091 0.804929 0 0 0 0.21037 0.507824 0 0 0 0.336858 0.907873 0 0 0 0 0 0 0 0 0.166009 0.349755 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.042259 0.253973 0.779035 0.942206 0.026929 0 0 0 0 0 0 0 0 0 0 0.018611 0 0 0 0 0 0.430389 0 0 0 0 0 0 0 0 0 1.102667 0.138387 0 0 0.452975 0 0 0.068913 1.143873 0 0 0 0 0 0 0 0 0.081569 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.342841 0 0 0 0 0 0 0.19409 0.896429 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.49034 0 0 0 0 0 0 0 0 0 0 0 0 0 0.900217 0.935672 0 0.186592 0 0 0.143204 0 0 0 0.232264 0 0 0.059559 0 0 1.287634 0 0 0 0 0 1.350515 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.329225 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ENSMUST00000000037.17 93.489436 81.76692 37.977305 71.756324 57.678214 11.718331 100.212557 81.349296 93.873587 62.142201 91.12093 68.907477 75.627914 40.835748 50.051121 57.889572 61.779187 55.588576 60.046133 65.583237 56.830328 53.537873 46.103594 30.150719 36.627231 57.912446 54.764002 34.883254 34.694436 51.17559 41.660915 54.328928 34.441027 46.297098 50.167459 40.527247 24.126215 5.181628 5.701418 8.317192 9.361625 6.911394 2.867919 6.949731 2.55549 2.252174 4.163168 4.851713 3.251534 15.356784 7.308524 4.989802 3.472203 2.53818 5.545818 1.536429 4.189031 12.853405 6.460353 5.700069 6.746444 8.132782 4.5115 6.012508 6.305973 2.625471 6.546259 17.727472 6.861142 3.743076 7.393494 3.840385 5.081398 2.717532 3.774507 2.021917 4.789885 4.043814 1.9424 4.555117 4.025174 2.298175 2.715958 2.26296 3.870009 2.70052 5.838803 2.700489 10.674344 8.488994 4.736988 8.305241 4.058393 2.930986 4.456863 6.196403 4.658535 2.600115 4.733892 5.629837 3.020004 2.292744 3.292217 1.170996 8.567117 7.860196 6.047172 4.047508 2.058267 0.692417 1.024385 1.165681 1.097924 1.587094 1.25111 1.778851 1.185968 0.515102 3.683279 2.756023 2.70169 1.039241 0.979897 2.697285 2.589705 5.64951 3.974395 1.761172 2.19261 1.040073 1.927764 4.917901 1.778033 3.905965 1.638823 2.629665 0.133212 1.400547 1.647038 0.138576 0.715257 0.762835 0.861437 0.474078 0.267721 0.152837 0.424976 0.655706 0.276536 0 0.451414 0 0.342016 0.979082 0.685206 0.18318 1.041492 0.204209 0.308678 0.171538 0.037843 0.456383 0 0.666393 0.094747 1.02581 0 0 4.226226 1.265938 0.093635 0.546776 0 0 0 0.527646 0 0 0 0 0.275725 0 0 0 0 0 0 0 0 0 0.803752 0 1.478849 0.267149 0 0 0 0 0 0 0 0 0 0 0 0 0.261909 0 0 0 0 0 0 0 0 0.392536 0 1.27389 0 0 0 ENSMUST00000000049.11 0 0 0 0 0 0 0 0 0 0.094161 0.066553 0 0 1.844433 0 0 0 0.48678 2.113169 0 0 0.159442 0 0 0.172137 2.781913 0.551429 0 0 0 1.014575 1.197547 0 0 0 0 0 0 0 0 0 0 0 0 0.082429 1.097804 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.9848 1.326141 2.386995 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.707816 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0.349952 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2.099105 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 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 0 ENSMUST00000000056.7 17.187512 13.058084 4.291559 9.11523 12.196756 1.371174 14.519641 15.961982 14.54995 11.364278 17.237419 7.636103 11.429688 15.962366 13.482118 4.494861 7.4047 7.379121 11.494511 2.948095 2.235935 4.784682 5.03162 4.629424 6.436491 3.622792 11.237226 6.645275 7.27671 3.333031 2.396052 2.599962 1.742445 2.714846 2.604052 6.996126 6.041317 1.889107 2.109791 0.726275 1.344082 0.391768 0.586408 1.391763 0.561092 1.243266 0.552313 2.33301 1.268324 1.466415 0.86832 5.033286 1.131888 0.768047 5.106209 0.552444 2.122361 1.072117 6.82694 2.97854 0.422183 1.153859 1.883945 3.626643 1.612209 2.596037 2.797803 9.007971 1.000934 0.408824 1.968968 2.240878 1.230686 0.204509 2.032762 0.719276 0.866593 0.593356 0.981222 1.333139 2.721297 3.00614 0.626275 2.649634 0.803929 0.806335 1.39015 6.603095 0.306491 1.528758 2.024114 1.681923 0.2311 0.180091 4.319847 7.957845 0.624883 3.973218 2.438944 2.157658 3.29869 5.317567 0.77714 1.165276 1.484474 6.390725 2.468354 3.261578 0.47389 3.457451 0.170976 0 0.025804 0.347547 0.182796 0 3.069161 0.542874 0.76409 0.830152 3.006962 0.787631 0.921914 0.656929 0.696819 5.955753 2.748242 0.800274 1.69992 0.055446 0.912617 0.246044 0.07241 0 0.523698 0.040831 0.921923 5.309277 2.11425 1.780577 1.341101 1.006866 0.297962 0.211149 0.826585 2.897688 0.115359 2.689669 0.625922 1.37512 0.566299 0.450046 0.471763 0.047284 1.030074 0.736055 1.25303 0.083059 0.61076 1.863088 0.209617 1.685458 0 1.905557 0.241697 0.205425 2.560553 0 1.60621 0.044555 0.192723 0 0.150728 0.06862 0.109628 0 0 0.174565 0.029669 0 1.685689 0.160053 0 1.192529 0 0 0 0.287531 0.521546 0.625429 0.427445 0 0 1.341059 1.01833 0.067062 0.432336 0.335277 0.351064 0.446807 0 0 0.386405 0.157184 0.097316 0 3.299547 0.307102 0 0.105779 0 8.253722 0.292858 0 0 0.191984 0.080827 0 0.751888 0 0.342276 ENSMUST00000000058.6 0.334586 0.581514 0.118006 0.965179 0.423004 0 0.474112 0.959381 0.524554 0.179814 0.594764 0.282361 0.916395 0.140514 0.136942 0.31012 0 0 0 0.537502 0 0 0 0 0.704925 0 0.061858 0 0.744494 0.090307 0.249218 0 0.036042 0.14437 0.079107 0 1.073943 0 0 0 0 0 0 0 0 0 0.049282 0.158349 0 0 0 0.173292 0.038168 0.905395 0 0 0.034135 0 0 0 0 0 1.215849 0 0 0 0 0 0 0 0 0 0 0 0.05925 0.050995 0 0 0 0 0 0.310825 0.284575 0 0.209418 0.138712 0 0 0.031908 0 0 0.208439 0.628426 0 0 0 2.753125 0 0 0 0 0.800573 0.374292 0 0 0 0 0 0.655527 0 2.692298 0.157516 0.085326 0.656848 0.17322 0.191096 0.876312 2.741018 0.299748 2.295354 0.072269 1.450715 0.096213 2.17961 0 0.940804 0.841649 5.71168 0.71971 0 0.445418 0 0 0 0.608075 0.110151 0 0.099234 0.615226 0.844793 1.705237 2.597712 0.659162 2.345665 2.671118 0.098912 0.383492 0.131244 0 0 0.068193 0.033774 0.150698 0.1955 0 0 0.528241 0.192666 0.089953 0 0 0.111242 0 0.816722 0 0 0 0 0 0.961579 0 0 3.459506 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ENSMUST00000000078.7 2.789082 0.786019 1.648873 1.111271 3.958626 0.354417 0.533204 0.300765 1.594925 1.227791 0.574214 1.947925 3.196918 2.944017 1.886042 3.194435 0 4.12517 6.041348 0.017456 0.598237 1.112595 1.308569 1.478161 1.613228 2.326362 5.199598 1.755094 2.234203 8.351876 0.849126 5.149227 2.945548 1.791296 2.48624 0.158894 0.182872 0.019692 0.466196 0.141908 0.028705 0 0 0 0.020658 0 0 0 0 0.130467 0.05028 0.027241 0.21176 0.100056 0.027034 0.387896 0.72836 0.048589 0.020815 0.020665 0.052796 0.156881 0.014015 0.053435 0 0.23365 0 0.081903 0.122692 0.091284 0 0.143668 0.017102 0.009687 0.46148 0.207347 0 1.153838 0.025565 0.631703 0 0.084775 0.008477 0 0.026195 0.02894 0 0.373962 0.019972 0.054953 0.020099 0.071668 0 0 0.04495 0 1.228921 0.643451 0.020847 0.14465 0 0 0.022512 0.137435 0 0 0.077661 0 0 0 0 0 0 0 0 0 0 0.018858 0 0.017683 0.014266 0 0 0.035102 0.023424 0.078234 0.025291 0 0 0.346685 0 0.028489 0 0 0 0 0.126013 0 0 0 0.085844 0 0 0 2.716993 2.493614 0.529129 0.049219 7.295619 0.074536 0.119142 0.046107 0.211403 0.156354 1.958608 0.12835 0.112606 0 0.504242 0.159039 0.496361 0.069955 0 7.050469 46.318801 130.820329 76.055336 47.966273 16.220072 9.868566 20.004074 52.562058 36.918618 22.374552 35.859731 28.579825 64.036908 5.631939 50.881748 14.294865 8.591746 41.908902 10.926839 29.729299 12.170858 43.043501 6.126444 181.340477 66.653972 19.120437 34.679719 4.17127 18.037819 0.793591 6.361748 5.397245 5.578454 11.482219 17.836691 12.588418 16.400497 7.213011 13.435379 53.396345 27.518517 32.820368 15.170734 7.772046 74.804985 35.200485 67.525806 24.005462 46.15853 13.196706 16.424238 18.41913 21.684488 16.84778 10.805869 27.133212 25.6408
Please let me know if I can provide anything else. Many thanks for your help in advance!
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Hello , it seems like I get this error for all of my transcripts. Actually, I have a .psi output but I only have NA for all the lines of the file :/
Other possibilities are:
- file formats are not correct (e.g. no tab present, wrong number of labels, hidden characters... )
- transcripts have zero expression (or no entry) in the expression file. This will create undefined values and NA's in the output.
- input files are not correctly defined in the command line, so the input is not read correctly
Please let me know if you checked these things
Best
E.
I had the same problem. I think the trancriptID in the expression file was not found in the ioe file causing the error. as mentioned in The readme file, "The IDs must be the same as those provided in the expression (TPM) files".
I had the same problem. I think the trancriptID in the expression file was not found in the ioe file causing the error. as mentioned in The readme file, "The IDs must be the same as those provided in the expression (TPM) files".
Hey I encountered the same issue. It seems like you fixed the problem. Would you mind sharing your solution? My .ioe contains the gene_id (thats also included it in expression file e.g. STRG.1009) , but additionally the alternative transcripts with the .X suffix (e.g. STRG.1009.3,STRG.1009.4,STRG.1009.2,STRG.1009.1) the psicalculator seems to only consider the alternative transcripts..
Thanks in advance.
