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broadinstitute / infercnv

Inferring CNV from Single-Cell RNA-Seq
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I have something wrong in running infercnv #532

Closed antho199 closed 1 year ago

antho199 commented 1 year ago

INFO [2023-04-26 09:32:05] ::process_data:Start INFO [2023-04-26 09:32:05] Creating output path cnv1/ INFO [2023-04-26 09:32:05] Checking for saved results. INFO [2023-04-26 09:32:05] 

STEP 1: incoming data

INFO [2023-04-26 10:13:55] 

STEP 02: Removing lowly expressed genes

INFO [2023-04-26 10:13:55] ::above_min_mean_expr_cutoff:Start INFO [2023-04-26 10:14:39] Removing 11432 genes from matrix as below mean expr threshold: 0.1 INFO [2023-04-26 10:16:04] validating infercnv_obj INFO [2023-04-26 10:16:04] There are 8490 genes and 232361 cells remaining in the expr matrix. INFO [2023-04-26 10:26:47] no genes removed due to min cells/gene filter INFO [2023-04-26 10:55:57] 

STEP 03: normalization by sequencing depth

INFO [2023-04-26 10:55:57] normalizing counts matrix by depth INFO [2023-04-26 11:06:16] Computed total sum normalization factor as median libsize: 4650.000000 INFO [2023-04-26 11:32:16] 

STEP 04: log transformation of data

INFO [2023-04-26 11:32:16] transforming log2xplus1() INFO [2023-04-26 11:55:57] 

STEP 08: removing average of reference data (before smoothing)

INFO [2023-04-26 11:55:57] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE INFO [2023-04-26 11:55:58] -no reference cells specified... using mean of all cells as proxy INFO [2023-04-26 12:10:05] -subtracting expr per gene, use_bounds=TRUE INFO [2023-04-26 13:08:57] 

STEP 09: apply max centered expression threshold: 3

INFO [2023-04-26 13:08:57] ::process_data:setting max centered expr, threshold set to: +/-: 3 INFO [2023-04-26 13:58:33] 

STEP 10: Smoothing data per cell by chromosome

INFO [2023-04-26 13:58:33] smooth_by_chromosome: chr: chr1 INFO [2023-04-26 14:18:16] smooth_by_chromosome: chr: chr2 INFO [2023-04-26 14:37:27] smooth_by_chromosome: chr: chr3 INFO [2023-04-26 14:52:42] smooth_by_chromosome: chr: chr4 INFO [2023-04-26 15:06:00] smooth_by_chromosome: chr: chr5 INFO [2023-04-26 15:19:29] smooth_by_chromosome: chr: chr6 INFO [2023-04-26 15:32:22] smooth_by_chromosome: chr: chr7 INFO [2023-04-26 15:47:08] smooth_by_chromosome: chr: chr8 INFO [2023-04-26 15:59:47] smooth_by_chromosome: chr: chr9 INFO [2023-04-26 16:13:31] smooth_by_chromosome: chr: chr10 INFO [2023-04-26 16:29:36] smooth_by_chromosome: chr: chr11 INFO [2023-04-26 16:45:46] smooth_by_chromosome: chr: chr12 INFO [2023-04-26 16:58:51] smooth_by_chromosome: chr: chr13 INFO [2023-04-26 17:08:50] smooth_by_chromosome: chr: chr14 INFO [2023-04-26 17:20:21] smooth_by_chromosome: chr: chr15 INFO [2023-04-26 17:32:36] smooth_by_chromosome: chr: chr16 INFO [2023-04-26 17:45:38] smooth_by_chromosome: chr: chr17 INFO [2023-04-26 17:55:07] smooth_by_chromosome: chr: chr18 INFO [2023-04-26 18:06:22] smooth_by_chromosome: chr: chr19 INFO [2023-04-26 18:16:31] smooth_by_chromosome: chr: chr20 INFO [2023-04-26 18:25:48] smooth_by_chromosome: chr: chr21 INFO [2023-04-26 18:33:52] smooth_by_chromosome: chr: chr22 INFO [2023-04-26 19:11:12] 

STEP 11: re-centering data across chromosome after smoothing

INFO [2023-04-26 19:11:12] ::center_smooth across chromosomes per cell INFO [2023-04-26 19:51:26] 

STEP 12: removing average of reference data (after smoothing)

INFO [2023-04-26 19:51:26] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE INFO [2023-04-26 19:51:26] -no reference cells specified... using mean of all cells as proxy INFO [2023-04-26 19:55:43] -subtracting expr per gene, use_bounds=TRUE INFO [2023-04-26 20:29:29] 

STEP 14: invert log2(FC) to FC

INFO [2023-04-26 20:29:29] invert_log2(), computing 2^x INFO [2023-04-26 21:06:27] 

STEP 15: computing tumor subclusters via leiden

INFO [2023-04-26 21:06:27] define_signif_tumor_subclusters(p_val=0.1 INFO [2023-04-26 21:06:27] define_signif_tumor_subclusters(), tumor: allobservations Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **| Centering and scaling data matrix |======================================================================================================| 100% PC 1 Positive: NOTCH4, HLA-DRA, HLA-DRB5, HLA-DRB1, HLA-DQA1, HLA-DQB1, HLA-DQA2, TAP2, MTF2, TMED5 CCDC18-AS1, DR1, ABL2, FNBP1L, DNTTIP2, ARHGAP29, GCLM, NR4A2, RPRM, ARL6IP6 GPD2, PRPF40A, CYTIP, TOR3A, PKP4, DAPL1, TANC1, FAM20B, BAZ2B, MARCH7 Negative: C11orf24, KMT5B, LRP5, CHKA, PPP6R3, TCIRG1, GAL, SCAND1, NDUFS8, ROMO1 NFS1, PHF20, CNBD2, NORAD, RBM39, RBM12, EPB41L1, CPNE1, ALDH3B1, SPAG4 CPT1A, DLGAP4, ERGIC3, UQCC1, EIF6, EDEM2, MYL9, TRPC4AP, UNC93B1, GSS PC 2 Positive: SMYD2, PROX1, CENPF, KCTD3, ANGEL2, GPATCH2, RRP15, FLVCR1, LYPLAL1, EPRS TATDN3, IARS2, NSL1, ATF3, RAB3GAP2, NENF, PPP2R5A, C1orf115, LPGAT1, DUSP10 SLC30A1, SIPA1L2, TSNAX, NTPCR, MIA3, EGLN1, KCNK1, SPRTN, COA6, TARBP1 Negative: KMT2B, EIF1AD, BANF1, SART1, CST6, SF3B2, PACS1, RAB1B, YIF1A, BRMS1 COX6B1, B4GAT1, MRPL11, DPP3, ZDHHC24, RBM42, CTSF, CCS, RBM14, RBM4 RCE1, TMEM147, RHOD, KDM2A, GRK2, ANKRD13D, DMKN, SSH3, USF2, RAD9A PC 3 Positive: POLG, FANCI, ABHD2, ANPEP, MFGE8, AP3S2, ISG20, MRPS11, MRPL46, AKAP13 ARPIN, PDE8A, ZNF592, IDH2, SEC11A, SEMA4B, NMB, WDR73, TM6SF1, CIB1 BTBD1, NGRN, C15orf40, IQGAP1, WHAMM, CRTC3, RPS17, IL16, ABHD17C, FURIN Negative: NPW, SLC9A3R2, ZNF598, NTHL1, GFER, TSC2, TBL3, PKD1, SNHG9, TRAF7 RPS2, MLST8, PGP, NDUFB10, ECI1, RNPS1, MSRB1, ATP6V0C, AMDHD2, PDPK1 FAHD1, KCTD5, SRRM2, HAGH, ZG16B, PRSS22, NUBP2, FLYWCH2, SPSB3, TNFRSF12A PC 4 Positive: MDFIC, TMEM168, IFRD1, TFEC, ZNF277, TES, IMMP2L, DOCK4, DNAJB9, CAV2 THAP5, PNPLA8, CAV1, LAMB1, MET, LSM8, CAPZA2, TSPAN12, DLD, ING3 CPED1, CBLL1, FAM3C, AASS, CADPS2, NDUFA5, BCAP29, WASL, ZNF800, COG5 Negative: MT1M, MT1A, MT1E, MT1F, MT2A, MRPL48, COA4, MT1G, OGFOD1, PAAF1 RAB6A, NUDT21, UCP2, PLEKHB1, AMFR, PPME1, FAM168A, MT1H, CES1, PGM2L1 RELT, KCNE3, LPCAT2, FCHSD2, MT1X, POLD3, ATG16L2, MMP2, RNF169, NUP93 PC 5 Positive: POLB, IKBKB, PLAT, AP3M2, KAT6A, GPAT4, SEC62, MYNN, GPR160, PHC3 MECOM, GOLGA7, PRKCI, SKIL, GOLIM4, CLDN11, SERPINI1, PDCD10, SLC7A14, BCHE SFRP1, RPL22L1, NMD3, KPNA4, IDO1, EIF5A2, TRIM59, SMC4, ADAM9, SLC2A2 Negative: IGLC2, IGLC3, IGLC1, IGLC7, IGLV2-11, IGLV2-14, BCR, GRK3, PRAME, SNRPD3 PPM1F, GUCD1, MAPK1, HPS4, PPIL2, SPECC1L, SDF2L1, CHCHD10, YDJC, CABIN1 SRRD, MMP11, DDT, SMARCB1, TFIP11, UBE2L3, DERL3, MIF, TPST2, PITPNB Computing nearest neighbor graph Computing SNN INFO [2023-04-27 12:30:00] ::plot_cnv:Start INFO [2023-04-27 12:30:00] ::plot_cnv:Current data dimensions (r,c)=8490,232361 Total=1975382217.61418 Min=0.648741183664771 Max=2.54576230571394. INFO [2023-04-27 12:30:14] ::plot_cnv:Depending on the size of the matrix this may take a moment. INFO [2023-04-27 12:33:11] plot_cnv(): auto thresholding at: (0.847739 , 1.154935) INFO [2023-04-27 12:36:03] plot_cnv_observation:Start INFO [2023-04-27 12:36:03] Observation data size: Cells= 232361 Genes= 8490 INFO [2023-04-27 12:36:03] clustering observations via method: ward.D Error in seq_len(max(obs_annotations_groups)) : argument must be coercible to non-negative integer In addition: Warning message: In max(nchar(obs_annotations_names)) : no non-missing arguments to max; returning -Inf

dipingxian431 commented 1 month ago

Hello, I also have the same question. Did you resolve it? Thank you!