Issues running metaWRAP quant_bins #531
Comments
I think you used the ressembly bins produced by the 'reassembly' modulem, right? I'm not the developer, but I have also encountered this problem before. Metawrap need the contig id to split the entire abundance result to each bins, but ressembly module will change the contig id of some bins. Therefore, these id-changed bins will not appear in the final result. You can use non-ressembly bins to perform 'quant_bins' again. By the way, I don't recommend you to use this module, because there is a serious bug that the calculation method in the metawrap script is totally different to what the developer said on the github website. Please see the question which I submit recentlly: You can use this module after modifying the script. However, I don't think the CPM in metawrap or TPM in coverM is a good way to calculate the abundance of a set of bins when these bins do not reperesent the entire community in the sample. You can also see above link. |
|
Hi friends!
I runned metaWRAP quant_bins without any errors, but I entered 808 bins and ended up with only 7 bins in bin_abundance_table.tab, I don't know why, and hope you can answer, thank you very much!
----- 9 forward and 9 reverse read files detected -----
########################################################################################################################
SETTING UP OUTPUT AND INDEXING ASSEMBLY
########################################################################################################################
----- Indexing assembly file with salmon. Ignore any warnings -----
Version Info: ### PLEASE UPGRADE SALMON ###
A newer version of salmon with important bug fixes and improvements is available.
The newest version, available at https://github.com/COMBINE-lab/salmon/releases
contains new features, improvements, and bug fixes; please upgrade at your
earliest convenience.
Sign up for the salmon mailing list to hear about new versions, features and updates at:
https://oceangenomics.com/subscribe
index ["matewrap_quant_bins_Water//assembly_index"] did not previously exist . . . creating it
[2024-01-02 09:57:13.141] [jLog] [info] building index
[2024-01-02 09:57:13.142] [jointLog] [info] [Step 1 of 4] : counting k-mers
[2024-01-02 09:57:13.742] [jointLog] [warning] Entry with header [NODE_1_length_1062125_cov_349.064552] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:13.804] [jointLog] [warning] Entry with header [NODE_2_length_872461_cov_152.511836] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:13.864] [jointLog] [warning] Entry with header [NODE_3_length_854593_cov_27.051776] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:13.906] [jointLog] [warning] Entry with header [NODE_4_length_584794_cov_58.452294] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:13.938] [jointLog] [warning] Entry with header [NODE_5_length_474077_cov_26.957405] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:13.960] [jointLog] [warning] Entry with header [NODE_6_length_459765_cov_7.702253] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:13.971] [jointLog] [warning] Entry with header [NODE_7_length_431186_cov_16.919051] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:13.983] [jointLog] [warning] Entry with header [NODE_8_length_422748_cov_5.010015] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:13.993] [jointLog] [warning] Entry with header [NODE_9_length_420739_cov_218.686471] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.005] [jointLog] [warning] Entry with header [NODE_10_length_415964_cov_4.231099] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.015] [jointLog] [warning] Entry with header [NODE_11_length_408504_cov_27.169650] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.024] [jointLog] [warning] Entry with header [NODE_12_length_403857_cov_969.221249] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.032] [jointLog] [warning] Entry with header [NODE_13_length_396776_cov_28.542840] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.040] [jointLog] [warning] Entry with header [NODE_14_length_388008_cov_56.017324] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.049] [jointLog] [warning] Entry with header [NODE_15_length_384623_cov_25.936459] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.057] [jointLog] [warning] Entry with header [NODE_16_length_374634_cov_92.828924] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.070] [jointLog] [warning] Entry with header [NODE_17_length_372089_cov_201.556832] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.078] [jointLog] [warning] Entry with header [NODE_18_length_363691_cov_17.119032] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.085] [jointLog] [warning] Entry with header [NODE_19_length_357408_cov_12.906932] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.093] [jointLog] [warning] Entry with header [NODE_20_length_355835_cov_12.758211] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.101] [jointLog] [warning] Entry with header [NODE_21_length_343039_cov_356.091267] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.108] [jointLog] [warning] Entry with header [NODE_22_length_337456_cov_9.350388] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.115] [jointLog] [warning] Entry with header [NODE_23_length_336446_cov_144.943225] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.122] [jointLog] [warning] Entry with header [NODE_24_length_333157_cov_155.144638] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.129] [jointLog] [warning] Entry with header [NODE_25_length_331809_cov_24.057234] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.135] [jointLog] [warning] Entry with header [NODE_26_length_320745_cov_8.624520] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.142] [jointLog] [warning] Entry with header [NODE_27_length_311327_cov_34.004906] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.158] [jointLog] [warning] Entry with header [NODE_28_length_308837_cov_24.431596] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.167] [jointLog] [warning] Entry with header [NODE_29_length_306406_cov_20.230752] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.176] [jointLog] [warning] Entry with header [NODE_30_length_305538_cov_36.190526] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.184] [jointLog] [warning] Entry with header [NODE_31_length_290629_cov_22.446037] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.193] [jointLog] [warning] Entry with header [NODE_32_length_289969_cov_159.631431] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.201] [jointLog] [warning] Entry with header [NODE_33_length_289514_cov_27.553171] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.209] [jointLog] [warning] Entry with header [NODE_34_length_289026_cov_160.592188] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.218] [jointLog] [warning] Entry with header [NODE_35_length_288641_cov_9.780067] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.226] [jointLog] [warning] Entry with header [NODE_36_length_282296_cov_9.288515] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.234] [jointLog] [warning] Entry with header [NODE_37_length_273060_cov_27.473185] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.242] [jointLog] [warning] Entry with header [NODE_38_length_269433_cov_57.173621] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.250] [jointLog] [warning] Entry with header [NODE_39_length_269027_cov_23.817732] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.258] [jointLog] [warning] Entry with header [NODE_40_length_267917_cov_56.104362] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.265] [jointLog] [warning] Entry with header [NODE_41_length_266309_cov_152.617073] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.273] [jointLog] [warning] Entry with header [NODE_42_length_265067_cov_156.490882] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.278] [jointLog] [warning] Entry with header [NODE_43_length_258004_cov_7.590210] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.284] [jointLog] [warning] Entry with header [NODE_44_length_255886_cov_18.073014] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.289] [jointLog] [warning] Entry with header [NODE_45_length_255305_cov_155.468614] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.294] [jointLog] [warning] Entry with header [NODE_46_length_254866_cov_494.283408] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.300] [jointLog] [warning] Entry with header [NODE_47_length_254622_cov_36.198513] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.305] [jointLog] [warning] Entry with header [NODE_48_length_253348_cov_35.346742] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.310] [jointLog] [warning] Entry with header [NODE_49_length_252131_cov_7.230868] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.329] [jointLog] [warning] Entry with header [NODE_50_length_251480_cov_531.114344] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.335] [jointLog] [warning] Entry with header [NODE_51_length_250749_cov_18.613656] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.342] [jointLog] [warning] Entry with header [NODE_52_length_250595_cov_148.045849] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.348] [jointLog] [warning] Entry with header [NODE_53_length_249839_cov_56.391411] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.354] [jointLog] [warning] Entry with header [NODE_54_length_248901_cov_11.676900] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.360] [jointLog] [warning] Entry with header [NODE_55_length_246502_cov_16.757921] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.366] [jointLog] [warning] Entry with header [NODE_56_length_245506_cov_7.344790] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.372] [jointLog] [warning] Entry with header [NODE_57_length_243889_cov_57.070220] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.378] [jointLog] [warning] Entry with header [NODE_58_length_241659_cov_36.242474] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.384] [jointLog] [warning] Entry with header [NODE_59_length_239651_cov_963.259706] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.390] [jointLog] [warning] Entry with header [NODE_60_length_238725_cov_261.595413] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.398] [jointLog] [warning] Entry with header [NODE_61_length_237358_cov_33.908724] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.414] [jointLog] [warning] Entry with header [NODE_62_length_237192_cov_182.209365] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.429] [jointLog] [warning] Entry with header [NODE_63_length_236631_cov_24.111676] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.439] [jointLog] [warning] Entry with header [NODE_64_length_235845_cov_211.772399] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.444] [jointLog] [warning] Entry with header [NODE_65_length_235775_cov_33.075065] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.450] [jointLog] [warning] Entry with header [NODE_66_length_234975_cov_25.576117] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.455] [jointLog] [warning] Entry with header [NODE_67_length_229485_cov_23.778143] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.460] [jointLog] [warning] Entry with header [NODE_68_length_227926_cov_980.735268] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.465] [jointLog] [warning] Entry with header [NODE_69_length_225042_cov_652.491720] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.470] [jointLog] [warning] Entry with header [NODE_70_length_224476_cov_698.977190] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.474] [jointLog] [warning] Entry with header [NODE_71_length_223166_cov_160.622992] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.479] [jointLog] [warning] Entry with header [NODE_72_length_221952_cov_9.253001] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.484] [jointLog] [warning] Entry with header [NODE_73_length_221671_cov_383.384241] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.488] [jointLog] [warning] Entry with header [NODE_74_length_221568_cov_984.963322] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.493] [jointLog] [warning] Entry with header [NODE_75_length_220022_cov_9.654143] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.498] [jointLog] [warning] Entry with header [NODE_76_length_219963_cov_9.768602] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.502] [jointLog] [warning] Entry with header [NODE_77_length_217847_cov_1011.158086] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.507] [jointLog] [warning] Entry with header [NODE_78_length_217653_cov_58.388281] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.511] [jointLog] [warning] Entry with header [NODE_79_length_216129_cov_9.684414] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.516] [jointLog] [warning] Entry with header [NODE_80_length_216014_cov_25.430276] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.520] [jointLog] [warning] Entry with header [NODE_81_length_215824_cov_4.814922] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.525] [jointLog] [warning] Entry with header [NODE_82_length_214919_cov_8.938009] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.529] [jointLog] [warning] Entry with header [NODE_83_length_214362_cov_166.485501] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.534] [jointLog] [warning] Entry with header [NODE_84_length_214259_cov_31.122549] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.538] [jointLog] [warning] Entry with header [NODE_85_length_213306_cov_27.802483] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.543] [jointLog] [warning] Entry with header [NODE_86_length_212704_cov_17.917199] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.547] [jointLog] [warning] Entry with header [NODE_87_length_212632_cov_30.298217] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.552] [jointLog] [warning] Entry with header [NODE_88_length_211622_cov_9.172185] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.556] [jointLog] [warning] Entry with header [NODE_89_length_209874_cov_28.877507] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.580] [jointLog] [warning] Entry with header [NODE_90_length_208954_cov_27.109325] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.585] [jointLog] [warning] Entry with header [NODE_91_length_206996_cov_24.164526] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.589] [jointLog] [warning] Entry with header [NODE_92_length_205465_cov_11.805820] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.593] [jointLog] [warning] Entry with header [NODE_93_length_204815_cov_175.477842] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.598] [jointLog] [warning] Entry with header [NODE_94_length_203981_cov_31.451482] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.602] [jointLog] [warning] Entry with header [NODE_95_length_203051_cov_27.370694] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
[2024-01-02 09:57:14.606] [jointLog] [warning] Entry with header [NODE_96_length_200710_cov_155.256746] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
counted k-mers for 1,940,000 transcriptsElapsed time: 69.5113s
[2024-01-02 09:58:22.653] [jointLog] [info] Replaced 0 non-ATCG nucleotides
[2024-01-02 09:58:22.653] [jointLog] [info] Clipped poly-A tails from 37 transcripts
[2024-01-02 09:58:22.751] [jointLog] [info] Building rank-select dictionary and saving to disk
[2024-01-02 09:58:22.941] [jointLog] [info] done
Elapsed time: 0.189185s
[2024-01-02 09:58:22.941] [jointLog] [info] Writing sequence data to file . . .
[2024-01-02 09:58:25.313] [jointLog] [info] done
Elapsed time: 2.37214s
[2024-01-02 09:58:25.356] [jointLog] [info] Building 32-bit suffix array (length of generalized text is 1,614,670,661)
[2024-01-02 09:58:31.051] [jointLog] [info] Building suffix array . . .
success
saving to disk . . . done
Elapsed time: 10.5754s
done
Elapsed time: 396.433s
processed 1,614,000,000 positions[2024-01-02 10:47:18.884] [jointLog] [info] khash had 1,499,478,720 keys
[2024-01-02 10:47:18.884] [jointLog] [info] saving hash to disk . . .
[2024-01-02 10:52:01.270] [jointLog] [info] done
Elapsed time: 282.386s
[2024-01-02 10:53:19.677] [jLog] [info] done building index
########################################################################################################################
EXTRACTING AVERAGE ABUNDANCE OF EACH BIN
########################################################################################################################
----- There were 9 samples detected. Making abundance table! -----
----- Average bin abundance table stored in matewrap_quant_bins_Water//abundance_table.tab -----
########################################################################################################################
MAKING GENOME ABUNDANCE HEATMAP WITH SEABORN
########################################################################################################################
----- making heatmap with Seaborn -----
loading libs...
loading abundance data...
drawing clustermap...
----- cleaning up... -----
########################################################################################################################
QUANT_BINS PIPELINE SUCCESSFULLY FINISHED!!!
########################################################################################################################
The text was updated successfully, but these errors were encountered: