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psiPerEvent - "transcript not found" #185

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bvien24 opened this issue Mar 11, 2024 · 6 comments
Open

psiPerEvent - "transcript not found" #185

bvien24 opened this issue Mar 11, 2024 · 6 comments

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@bvien24
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bvien24 commented Mar 11, 2024 •
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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
@InesLANDOLSI
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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 :)

@EduEyras
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EduEyras commented Mar 29, 2024 via email

@InesLANDOLSI
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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 :/

@EduEyras
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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.

@atongmuuu
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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".

@KeSchus
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KeSchus commented Jun 11, 2024

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.

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@EduEyras @atongmuuu @InesLANDOLSI @bvien24 @KeSchus