Missing samples when visualizing all samples

[drtamermansour]

I can't find a reason for filtering out these samples

• Missing samples in PRJEB31756: ERX3253126
• Missing samples in PRJNA338327: SRX2010868
• Missing samples in PRJNA407973: It should have 50 samples, only 40 displayed
• Missing whole project (PRJNA882864)

[drtamermansour]

We have SAMN11079552_SRX5487588.sig among the sketches but searching by the experiment accession gives No matching data points found.

[mr-eyes]

We have SAMN11079552_SRX5487588.sig among the sketches but searching by the experiment accession gives No matching data points found.

The sigs I sent you are the downloaded sigs from sra, not the final sigs included in the snipe explore and manuscript. Check the sample filtration report.

[drtamermansour]

Where is this report?

[drtamermansour]

I can't find a reason for filtering out these samples

• Missing samples in PRJEB31756: ERX3253126
• Missing samples in PRJNA338327: SRX2010868
• Missing samples in PRJNA407973: It should have 50 samples, only 40 displayed
• Missing whole project (PRJNA882864)

The first 3 are found the sample filtration report.
The 4th one is published July 2024 and thus missing from our current dataset

[drtamermansour]

All the experiments in the sample filtration report have signatures in our dataset (expect the 54 RNA samples) which means that these samples are just filtered from the visualization which is GREAT!

However, based on the targeted search phrase, the run selector has 19860 runs. The current signatures are missing 208 runs for no obvious reasons (not reported in the sample filtration report). I think thay may failed the sketching step/
(txid9615[organism]) AND "illumina"[Platform] AND ("wgs"[Strategy] OR "wxs"[Strategy]) AND ("genomic"[Source] OR "metagenomic"[Source]) AND ("2000/01/01"[PDAT]: "2023/12/25"[PDAT])

Here they are:

Run,Assay Type,BioProject,BioSample,Experiment,LibrarySource,sample_type
DRR001566,WGS,PRJDB2266,SAMD00009664,DRX001090,GENOMIC,
ERR019093,WGS,PRJEB2162,SAMEA676114,ERX007596,GENOMIC,
ERR10879384,WGS,PRJEB16012,SAMEA112638849,ERX10324146,GENOMIC,
ERR10879385,WGS,PRJEB16012,SAMEA112638850,ERX10324147,GENOMIC,
ERR10879386,WGS,PRJEB16012,SAMEA112638851,ERX10324148,GENOMIC,
ERR10879387,WGS,PRJEB16012,SAMEA112638852,ERX10324149,GENOMIC,
ERR10879388,WGS,PRJEB16012,SAMEA112638853,ERX10324150,GENOMIC,
ERR10879389,WGS,PRJEB16012,SAMEA112638854,ERX10324151,GENOMIC,
ERR10879390,WGS,PRJEB16012,SAMEA112638855,ERX10324152,GENOMIC,
ERR10879391,WGS,PRJEB16012,SAMEA112638856,ERX10324153,GENOMIC,
ERR10879392,WGS,PRJEB16012,SAMEA112638857,ERX10324154,GENOMIC,
ERR10879393,WGS,PRJEB16012,SAMEA112638858,ERX10324155,GENOMIC,
ERR10879394,WGS,PRJEB16012,SAMEA112638859,ERX10324156,GENOMIC,
ERR10879395,WGS,PRJEB16012,SAMEA112638860,ERX10324157,GENOMIC,
ERR10879396,WGS,PRJEB16012,SAMEA112638861,ERX10324158,GENOMIC,
ERR10879398,WGS,PRJEB16012,SAMEA112638862,ERX10324159,GENOMIC,
ERR10879399,WGS,PRJEB16012,SAMEA112638863,ERX10324160,GENOMIC,
ERR10879400,WGS,PRJEB16012,SAMEA112638864,ERX10324161,GENOMIC,
ERR10879401,WGS,PRJEB16012,SAMEA112638865,ERX10324162,GENOMIC,
ERR10879402,WGS,PRJEB16012,SAMEA112638866,ERX10324163,GENOMIC,
ERR10879403,WGS,PRJEB16012,SAMEA112638867,ERX10324164,GENOMIC,
ERR10879404,WGS,PRJEB16012,SAMEA112638868,ERX10324165,GENOMIC,
ERR10879405,WGS,PRJEB16012,SAMEA112638869,ERX10324166,GENOMIC,
ERR10879406,WGS,PRJEB16012,SAMEA112638870,ERX10324167,GENOMIC,
ERR10879407,WGS,PRJEB16012,SAMEA112638871,ERX10324168,GENOMIC,
ERR10879408,WGS,PRJEB16012,SAMEA112638872,ERX10324169,GENOMIC,
ERR10879409,WGS,PRJEB16012,SAMEA112638873,ERX10324170,GENOMIC,
ERR10879410,WGS,PRJEB16012,SAMEA112638874,ERX10324171,GENOMIC,
ERR10879411,WGS,PRJEB16012,SAMEA112638875,ERX10324172,GENOMIC,
ERR10879412,WGS,PRJEB16012,SAMEA112638876,ERX10324173,GENOMIC,
ERR10879413,WGS,PRJEB16012,SAMEA112638877,ERX10324174,GENOMIC,
ERR10879414,WGS,PRJEB16012,SAMEA112638878,ERX10324175,GENOMIC,
ERR10879415,WGS,PRJEB16012,SAMEA112638879,ERX10324176,GENOMIC,
ERR10879416,WGS,PRJEB16012,SAMEA112638880,ERX10324177,GENOMIC,
ERR10879417,WGS,PRJEB16012,SAMEA112638881,ERX10324178,GENOMIC,
ERR10879418,WGS,PRJEB16012,SAMEA112638882,ERX10324179,GENOMIC,
ERR11284568,WGS,PRJEB36029,SAMEA7190222,ERX10692177,GENOMIC,
ERR12042708,WGS,PRJEB16012,SAMEA114382012,ERX11425910,GENOMIC,
ERR12042722,WGS,PRJEB16012,SAMEA114382026,ERX11425924,GENOMIC,
ERR12042723,WGS,PRJEB16012,SAMEA114382027,ERX11425925,GENOMIC,
ERR12042726,WGS,PRJEB16012,SAMEA114382030,ERX11425928,GENOMIC,
ERR12042727,WGS,PRJEB16012,SAMEA114382031,ERX11425929,GENOMIC,
ERR12042728,WGS,PRJEB16012,SAMEA114382032,ERX11425930,GENOMIC,
ERR12042729,WGS,PRJEB16012,SAMEA114382033,ERX11425931,GENOMIC,
ERR12042730,WGS,PRJEB16012,SAMEA114382034,ERX11425932,GENOMIC,
ERR12042733,WGS,PRJEB16012,SAMEA114382037,ERX11425935,GENOMIC,
ERR12042734,WGS,PRJEB16012,SAMEA114382038,ERX11425936,GENOMIC,
ERR12042735,WGS,PRJEB16012,SAMEA114382039,ERX11425937,GENOMIC,
ERR12042737,WGS,PRJEB16012,SAMEA114382041,ERX11425939,GENOMIC,
ERR12042739,WGS,PRJEB16012,SAMEA114382043,ERX11425941,GENOMIC,
ERR12042742,WGS,PRJEB16012,SAMEA114382046,ERX11425944,GENOMIC,
ERR12042744,WGS,PRJEB16012,SAMEA114382048,ERX11425946,GENOMIC,
ERR12042745,WGS,PRJEB16012,SAMEA114382049,ERX11425947,GENOMIC,
ERR12042746,WGS,PRJEB16012,SAMEA114382050,ERX11425948,GENOMIC,
ERR12042748,WGS,PRJEB16012,SAMEA114382052,ERX11425950,GENOMIC,
ERR12042749,WGS,PRJEB16012,SAMEA114382053,ERX11425951,GENOMIC,
ERR12128356,WXS,PRJEB55864,SAMEA111341937,ERX11504274,GENOMIC,
ERR12128395,WXS,PRJEB55864,SAMEA111341914,ERX11504313,GENOMIC,
ERR12128453,WXS,PRJEB55865,SAMEA111342006,ERX11504371,GENOMIC,
ERR12128549,WXS,PRJEB55865,SAMEA111342023,ERX11504467,GENOMIC,
ERR12128558,WXS,PRJEB55865,SAMEA111342038,ERX11504476,GENOMIC,
ERR12128579,WXS,PRJEB55865,SAMEA111341978,ERX11504497,GENOMIC,
ERR12128582,WXS,PRJEB55865,SAMEA111341981,ERX11504500,GENOMIC,
ERR12128588,WXS,PRJEB55865,SAMEA111341990,ERX11504506,GENOMIC,
ERR12128594,WXS,PRJEB55865,SAMEA111341994,ERX11504512,GENOMIC,
ERR12389295,WGS,PRJEB71384,SAMEA115059303,ERX11765419,GENOMIC,
ERR12389296,WGS,PRJEB71384,SAMEA115059304,ERX11765420,GENOMIC,
ERR12389297,WGS,PRJEB71384,SAMEA115059305,ERX11765421,GENOMIC,
ERR1672230,WXS,PRJEB12081,SAMEA3955983,ERX1742282,GENOMIC,
ERR1688115,WGS,PRJEB16012,SAMEA4506890,ERX1757732,GENOMIC,
ERR1994752,WGS,PRJEB21089,SAMEA104106509,ERX2054621,GENOMIC,
ERR1994753,WGS,PRJEB21089,SAMEA104106510,ERX2054622,GENOMIC,
ERR2008787,WGS,PRJEB16012,SAMEA104125122,ERX2068550,GENOMIC,
ERR2061041,WGS,PRJEB22026,SAMEA104190270,ERX2120098,GENOMIC,
ERR2061048,WGS,PRJEB22026,SAMEA104190272,ERX2120105,GENOMIC,
ERR206211,WGS,PRJEB2311,SAMEA1561463,ERX180896,GENOMIC,
ERR2196282,WGS,PRJEB17926,SAMEA104389243,ERX2252492,GENOMIC,
ERR2516739,WGS,PRJEB16012,SAMEA3444493,ERX2536341,GENOMIC,
ERR3153863,WGS,PRJEB28163,SAMEA4825472,ERX3182940,GENOMIC,
ERR3687187,WGS,PRJEB16012,SAMEA6249486,ERX3676792,GENOMIC,
ERR3687194,WGS,PRJEB16012,SAMEA6249493,ERX3676799,GENOMIC,
ERR3687198,WGS,PRJEB16012,SAMEA6249497,ERX3676803,GENOMIC,
ERR3687200,WGS,PRJEB16012,SAMEA6249499,ERX3676805,GENOMIC,
ERR410265,WGS,PRJEB2162,SAMEA1706024,ERX376626,GENOMIC,
ERR7251998,WGS,PRJEB16012,SAMEA10644715,ERX6821454,GENOMIC,
ERR7251999,WGS,PRJEB16012,SAMEA10644716,ERX6821455,GENOMIC,
ERR7252000,WGS,PRJEB16012,SAMEA10644717,ERX6821456,GENOMIC,
ERR7252001,WGS,PRJEB16012,SAMEA10644718,ERX6821457,GENOMIC,
ERR7252002,WGS,PRJEB16012,SAMEA10644719,ERX6821458,GENOMIC,
ERR7252003,WGS,PRJEB16012,SAMEA10644720,ERX6821459,GENOMIC,
ERR7252004,WGS,PRJEB16012,SAMEA10644721,ERX6821460,GENOMIC,
ERR7252005,WGS,PRJEB16012,SAMEA10644722,ERX6821461,GENOMIC,
ERR7252006,WGS,PRJEB16012,SAMEA10644723,ERX6821462,GENOMIC,
ERR7252007,WGS,PRJEB16012,SAMEA10644724,ERX6821463,GENOMIC,
ERR7252008,WGS,PRJEB16012,SAMEA10644725,ERX6821464,GENOMIC,
ERR7252009,WGS,PRJEB16012,SAMEA10644726,ERX6821465,GENOMIC,
ERR7252010,WGS,PRJEB16012,SAMEA10644727,ERX6821466,GENOMIC,
ERR7252011,WGS,PRJEB16012,SAMEA10644728,ERX6821467,GENOMIC,
ERR7252012,WGS,PRJEB16012,SAMEA10644729,ERX6821468,GENOMIC,
ERR7252013,WGS,PRJEB16012,SAMEA10644730,ERX6821469,GENOMIC,
ERR7252014,WGS,PRJEB16012,SAMEA10644731,ERX6821470,GENOMIC,
ERR7252015,WGS,PRJEB16012,SAMEA10644732,ERX6821471,GENOMIC,
ERR7252016,WGS,PRJEB16012,SAMEA10644733,ERX6821472,GENOMIC,
ERR7252017,WGS,PRJEB16012,SAMEA10644734,ERX6821473,GENOMIC,
ERR7252018,WGS,PRJEB16012,SAMEA10644736,ERX6821474,GENOMIC,
ERR7252019,WGS,PRJEB16012,SAMEA10644737,ERX6821475,GENOMIC,
ERR7252020,WGS,PRJEB16012,SAMEA10644738,ERX6821476,GENOMIC,
ERR7252021,WGS,PRJEB16012,SAMEA10644739,ERX6821477,GENOMIC,
ERR7252022,WGS,PRJEB16012,SAMEA10644740,ERX6821478,GENOMIC,
ERR7252023,WGS,PRJEB16012,SAMEA10644741,ERX6821479,GENOMIC,
ERR7252024,WGS,PRJEB16012,SAMEA10644742,ERX6821480,GENOMIC,
ERR7252025,WGS,PRJEB16012,SAMEA10644743,ERX6821481,GENOMIC,
ERR7252026,WGS,PRJEB16012,SAMEA10644744,ERX6821482,GENOMIC,
ERR7252027,WGS,PRJEB16012,SAMEA10644745,ERX6821483,GENOMIC,
ERR7252028,WGS,PRJEB16012,SAMEA10644746,ERX6821484,GENOMIC,
ERR7252029,WGS,PRJEB16012,SAMEA10644747,ERX6821485,GENOMIC,
ERR7252030,WGS,PRJEB16012,SAMEA10644748,ERX6821486,GENOMIC,
ERR7252031,WGS,PRJEB16012,SAMEA10644749,ERX6821487,GENOMIC,
ERR7252032,WGS,PRJEB16012,SAMEA10644750,ERX6821488,GENOMIC,
ERR7530913,WGS,PRJEB16012,SAMEA10833662,ERX7101609,GENOMIC,
ERR7530914,WGS,PRJEB16012,SAMEA10833663,ERX7101610,GENOMIC,
ERR7530915,WGS,PRJEB16012,SAMEA10833664,ERX7101611,GENOMIC,
ERR870949,WXS,PRJEB7540,SAMEA2706839,ERX950550,GENOMIC,
ERR871051,WXS,PRJEB7540,SAMEA2706845,ERX950652,GENOMIC,
ERR871110,WXS,PRJEB7540,SAMEA2706904,ERX950711,GENOMIC,
ERR871145,WXS,PRJEB7540,SAMEA2706843,ERX950746,GENOMIC,
ERR871206,WXS,PRJEB7540,SAMEA2706904,ERX950807,GENOMIC,
ERR9872050,WGS,PRJEB16012,SAMEA110175941,ERX9417282,GENOMIC,
ERR9872051,WGS,PRJEB16012,SAMEA110175942,ERX9417283,GENOMIC,
ERR9872052,WGS,PRJEB16012,SAMEA110175943,ERX9417284,GENOMIC,
ERR9872053,WGS,PRJEB16012,SAMEA110175944,ERX9417285,GENOMIC,
ERR9872054,WGS,PRJEB16012,SAMEA110175945,ERX9417286,GENOMIC,
ERR9872055,WGS,PRJEB16012,SAMEA110175946,ERX9417287,GENOMIC,
ERR9872056,WGS,PRJEB16012,SAMEA110175947,ERX9417288,GENOMIC,
ERR9872057,WGS,PRJEB16012,SAMEA110175948,ERX9417289,GENOMIC,
ERR9872058,WGS,PRJEB16012,SAMEA110175949,ERX9417290,GENOMIC,
ERR9872059,WGS,PRJEB16012,SAMEA110175950,ERX9417291,GENOMIC,
ERR9872060,WGS,PRJEB16012,SAMEA110175951,ERX9417292,GENOMIC,
ERR9872061,WGS,PRJEB16012,SAMEA110175952,ERX9417293,GENOMIC,
ERR9872062,WGS,PRJEB16012,SAMEA110175953,ERX9417294,GENOMIC,
ERR9872063,WGS,PRJEB16012,SAMEA110175954,ERX9417295,GENOMIC,
ERR9872064,WGS,PRJEB16012,SAMEA110175955,ERX9417296,GENOMIC,
ERR9872065,WGS,PRJEB16012,SAMEA110175956,ERX9417297,GENOMIC,
ERR9872066,WGS,PRJEB16012,SAMEA110175523,ERX9417298,GENOMIC,
ERR9872067,WGS,PRJEB16012,SAMEA110175524,ERX9417299,GENOMIC,
ERR9872068,WGS,PRJEB16012,SAMEA110175525,ERX9417300,GENOMIC,
ERR9872069,WGS,PRJEB16012,SAMEA110175526,ERX9417301,GENOMIC,
ERR9872070,WGS,PRJEB16012,SAMEA110175527,ERX9417302,GENOMIC,
ERR9872071,WGS,PRJEB16012,SAMEA110175528,ERX9417303,GENOMIC,
ERR9872072,WGS,PRJEB16012,SAMEA110175529,ERX9417304,GENOMIC,
ERR9872073,WGS,PRJEB16012,SAMEA110175530,ERX9417305,GENOMIC,
ERR9872074,WGS,PRJEB16012,SAMEA110175531,ERX9417306,GENOMIC,
ERR9872075,WGS,PRJEB16012,SAMEA110175532,ERX9417307,GENOMIC,
ERR9872076,WGS,PRJEB16012,SAMEA110175533,ERX9417308,GENOMIC,
ERR9872077,WGS,PRJEB16012,SAMEA110175534,ERX9417309,GENOMIC,
ERR9872078,WGS,PRJEB16012,SAMEA110175535,ERX9417310,GENOMIC,
ERR9872079,WGS,PRJEB16012,SAMEA110175536,ERX9417311,GENOMIC,
ERR9872080,WGS,PRJEB16012,SAMEA110175537,ERX9417312,GENOMIC,
ERR9872081,WGS,PRJEB16012,SAMEA110175538,ERX9417313,GENOMIC,
ERR9872082,WGS,PRJEB16012,SAMEA110175539,ERX9417314,GENOMIC,
ERR9872083,WGS,PRJEB16012,SAMEA110175540,ERX9417315,GENOMIC,
ERR9872084,WGS,PRJEB16012,SAMEA110175541,ERX9417316,GENOMIC,
ERR9872085,WGS,PRJEB16012,SAMEA110175542,ERX9417317,GENOMIC,
ERR9872086,WGS,PRJEB16012,SAMEA110175543,ERX9417318,GENOMIC,
SRR18398330,WGS,PRJNA816174,SAMN26850680,SRX14532237,GENOMIC,
SRR18398332,WGS,PRJNA816174,SAMN26850678,SRX14532235,GENOMIC,
SRR18398343,WGS,PRJNA816174,SAMN26850691,SRX14532224,GENOMIC,
SRR18398351,WGS,PRJNA816174,SAMN26850675,SRX14532216,GENOMIC,
SRR18637676,WGS,PRJNA823593,SAMN27307438,SRX14744599,GENOMIC,
SRR2016114,WGS,PRJNA263947,SAMN03580379,SRX1022220,GENOMIC,
SRR2016116,WGS,PRJNA263947,SAMN03580379,SRX1022222,GENOMIC,
SRR2016118,WGS,PRJNA263947,SAMN03580380,SRX1022224,GENOMIC,
SRR2016120,WGS,PRJNA263947,SAMN03580380,SRX1022226,GENOMIC,
SRR21770665,WGS,PRJNA800779,SAMN25330635,SRX17765696,GENOMIC,
SRR21770683,WGS,PRJNA800779,SAMN25331248,SRX17765678,GENOMIC,
SRR21770691,WGS,PRJNA800779,SAMN25332909,SRX17765670,GENOMIC,
SRR21770703,WGS,PRJNA800779,SAMN25333853,SRX17765658,GENOMIC,
SRR21770708,WGS,PRJNA800779,SAMN25330636,SRX17765653,GENOMIC,
SRR21770715,WGS,PRJNA800779,SAMN25331352,SRX17765646,GENOMIC,
SRR24220295,WGS,PRJNA957464,SAMN34254335,SRX20016709,GENOMIC,
SRR2756256,WGS,PRJNA299099,SAMN04195504,SRX1360965,GENOMIC,
SRR2827592,WGS,PRJNA266585,SAMN03168374,SRX1386894,GENOMIC,
SRR4302047,WGS,PRJNA344694,SAMN05831101,SRX2196351,GENOMIC,
SRR5798843,WGS,PRJNA384927,SAMN06893646,SRX2978277,GENOMIC,
SRR5798844,WGS,PRJNA384927,SAMN06893647,SRX2978276,GENOMIC,
SRR7107656,WXS,PRJNA448733,SAMN02144217,SRX4035893,GENOMIC,
SRR7120280,WGS,PRJNA448733,SAMN08873492,SRX4041907,GENOMIC,
SRR776307,WGS,PRJNA192935,SAMN01974489,SRX249948,GENOMIC,
SRR776429,WGS,PRJNA192935,SAMN01974489,SRX249987,GENOMIC,
SRR776430,WGS,PRJNA192935,SAMN01974489,SRX249988,GENOMIC,
SRR776431,WGS,PRJNA192935,SAMN01974489,SRX250030,GENOMIC,
SRR776435,WGS,PRJNA192935,SAMN01974489,SRX250034,GENOMIC,
SRR7780833,WXS,PRJNA489159,SAMN09948259,SRX4636055,GENOMIC,
SRR7780840,WXS,PRJNA489159,SAMN09949394,SRX4636048,GENOMIC,
SRR782083,WGS,PRJNA192935,SAMN01974494,SRX250954,GENOMIC,
SRR782085,WGS,PRJNA192935,SAMN01974495,SRX250956,GENOMIC,
SRR867444,WGS,PRJNA203084,SAMN02144217,SRX286473,GENOMIC,
SRR867445,WGS,PRJNA203084,SAMN02144217,SRX286473,GENOMIC,
SRR870510,WXS,PRJNA203084,SAMN02144215,SRX288295,GENOMIC,
SRR870511,WXS,PRJNA203084,SAMN02144215,SRX288295,GENOMIC,
SRR870512,WXS,PRJNA203084,SAMN02144219,SRX288297,GENOMIC,
SRR870513,WXS,PRJNA203084,SAMN02144219,SRX288297,GENOMIC,
SRR870514,WXS,PRJNA203084,SAMN02144217,SRX288296,GENOMIC,
SRR870515,WXS,PRJNA203084,SAMN02144217,SRX288296,GENOMIC,
SRR870517,WXS,PRJNA203084,SAMN02178578,SRX288298,GENOMIC,
SRR870519,WXS,PRJNA203084,SAMN02178578,SRX288298,GENOMIC,
SRR870520,WXS,PRJNA203085,SAMN02178576,SRX288294,GENOMIC,
SRR870521,WXS,PRJNA203085,SAMN02178576,SRX288294,GENOMIC,