Zero-count samples being imported with counts #7
Description
Hello,
I have observed unexpected behavior when importing biom files from QIIME2 when there are samples that have zero counts. Two behaviors can occur:
1- The table is not imported with the error message :
Error in read_biom("33752d9e0-3f1c-43d8-838b-35c7ad6dac89/data/feature-table.biom") :
Both attempts to read input file:
33752d9e0-3f1c-43d8-838b-35c7ad6dac89/data/feature-table.biom
either as JSON (BIOM-v1) or HDF5 (BIOM-v2).
Check file path, file name, file itself, then try again.
2- And the more problematic issue: counts get assigned to 0-count samples into 2 features (NTC4 should be 0 count):
library(tidyverse)
library(biomformat)
unzip("SV_minsamp.qza")
read_biom("3372d9e0-3f1c-43d8-838b-35c7ad6dac89/data/feature-table.biom") %>%
biom_data() %>%
as.matrix()
KM_A8 NTC4 NTC5
377f74e2ecbc10a3aae743befaa94b42 10 8 8
c4a7d3b208ece70a26268344fbb93c52 3987 0 7
db35c906865fb1665ab2ed219d1e567e 461 0 42
c924dab705d2e28608e074f1268fae86 3024 0 13
438fb020cf251f2c2f4e89552e4a78ff 8200 0 42
db66ab43add889efc6f36d999d74bd9f 20587 0 0
d8f099d313df42c4bd55367dfcba5b1e 1677 0 37
36cea88ef583f67d3a52984894f65715 248 0 9
de17fa4e217c05126bad3d8e4a5ed1ae 56 0 24
2ca55cb0488522690d66eafbffd6fcd1 0 0 21
311489528f0a97315baae027ec1de217 1343 0 0
456995cfe33fb271939359fb93d62adc 617 0 6
d5b22a367668019c66d346e758f7a1ee 10 0 34
caa314c8bbe94ec49c4b5e7ac761c89c 255 0 6
5a1b49ed2eeb1f595a07330646fa90d6 2255 0 2
a04152eb23b2b714891a76b94fc50d13 0 0 27
b5fd958c94be2774cec38e5b7dd9d7a0 1280 0 0
768377abe500ad4d09c43a4532e533b1 273 0 18
a009250174a6396c22cbd6d4883ace66 102 0 0
ab4f6ce559f19ba6367b9585e0c52d1d 530 0 0
a6c8365b5ed70eb46c4b19bc65769ffe 3159 0 0
00d4ba73bac9f0ef8dc55c4f6fa7a31d 602 0 0
f399e9e512f1901cfbb178f25b35c429 358 0 0
f27c18211f38a2b8824f2a0ffa75d352 3402 0 0
1cdedc5e590c48596c5815727eeabbfd 359 0 0
24d5e2004c0981906654773dba703657 793 0 0
654b48c81387ba95154eec6fef598518 18 0 0
cd1032dccdcdadb3b177b8bfd184fe52 2241 0 2
9e1e6091fc8df34c70d2758663e82568 122 0 9
4ac00a18a91a648a417a7244c93be36e 624 0 0
7196309e808ea0a0343569ba13b6475a 33 0 0
2d8190871d82fb3c2841f72e3cf0724b 0 0 7
f00c8887a5932c68f3407f53990f7d7f 417 0 0
9ca9e80bb08ba22912ea23d7c2ba17fd 0 0 20
4322f71ec394024540834021c505ed8c 883 0 0
fa359e01cdc3abc65f7bc2bd1258c65b 0 0 4
49db3e027ba1c2052a3dea50efa3f85e 154 0 0
f8daf40b2587101f94d6d4bfeb1d11d5 552 0 0
41eb3683907ae630bf57caeb4108fee8 864 0 0
fa4b533d2a910c07092aab3362643b65 752 0 0
aecb167f1e300f126360c6623584d317 118 0 0
f7740fb251b4636f610015fdb43d2c80 419 0 0
3dfe193b1e846e30942fb86736b6b01d 3734 0 0
9ede21367fadb803e5210adf65fa6203 431 0 0
f50b35619ea5c65a041acf1dd0265d37 166 0 0
0d79a0dac9f32c534e53b4c7dedfbf39 101 0 0
a86625c0ccfc39fafc21cb9c7ba47373 1686 0 0
d319ec611d0eff414b496b2e46d5dd6f 0 0 9
9602f418feb9157c43ce22a801b86619 166 0 0
c0a64c29b86aa9015d95d6ac55f9ddaa 690 0 0
1f248fe7a1f3379cd0027df0bd6dda93 619 0 0
c440a62b6ccd1e12766c1adacf0e8ebe 392 0 0
c3f4d4259802b6cd0b22835226c1cbee 129 0 0
83bdb2d026a7c79f2f9b858f0c171c70 195 0 0
989fd0a6528155676a5d5d01e80b383f 1507 0 0
2355e96be7250ac06b2303b3dd1f94a8 299 0 0
6c64a41d73e00f788db4495301ad6479 90 0 0
492106d65d13feade3f768693872e83f 0 0 2
6ac825e56996acb620290f386f778abc 83 0 0
c3342d2a9a35fb23f494d299efedfcb9 0 0 9
1a5f2ceff57f382c9203d2bd6d313bd3 400 0 0
fe50c3928da7c378bb6dfe1ba82532a9 138 0 0
5951ab4fff00d969b3150b754ad4f286 0 0 2
a0800ab251ba81491f76bd9fe4302bf2 70 0 0
1e526d811df96209322de0a079db3012 212 0 0
46a9bce4deb54b24813583e0f9fb9cca 144 0 0
13c07d678a73558a30551df04730edb1 100 0 0
082c1b1aa45de90bca53ad835406e52c 71 0 9
263655a4b3918486546878267ff62a43 182 0 0
092d4585b8b75897b214ea1d45fe19f0 96 0 0
a4ab293fb73c2a48d7810ee5b47b637c 115 0 0
45aa1cb25b9e01293c2aef67e55877e3 146 0 0
c0a91f20b56212f02390bd7056dd0a55 24 0 0
7f8eddceb6bfcecfe8fd64f045ea382b 386 0 0
f773225220a5378c11e68e7e2d2febe2 375 0 0
1b4eb07d78bfeac60a6995109ec82487 160 0 0
37f5f8250851c65dd9d93ae7231129f5 531 0 0
b2df9d4c51c8ef09886ad11690f85b1e 464 0 0
09c41ba8cf43420d67d4909af0d2fc45 119 0 0
5a70c8e5e86d7559a18ac1665617c395 0 0 4
df61a14bd5475bb09a2a86ad75a4c200 49 0 0
c973282c675d1bd6d51aa1b8a3579c80 142 0 0
f52fcb1370d25721624041cefcc6794a 446 0 0
bee5a689430c7e5618820f3d2c601981 873 0 0
371e17aa1dd409acab1a21231405dd35 59 0 0
c6b5af7e07b9b826ae97b6c03156c6f7 50 0 0
2cabbe9e8a6f88d2831ac023efe4cc59 117 0 0
35d2f8b8ad9de9444aa1b7e640222502 16 0 0
8cd009f35d2afc61f00069615c164c30 142 0 0
f1c58819f13fb758dc63822d5ab3603f 165 0 0
2004f25a5f9682e988b7170924744c3b 103 0 0
534359e18c3d1be9ea9f4224d86fc878 27 0 0
8b2471c362e3095d9cbc85486a25605a 1070 0 0
9d07979519eb2f5d922d5d4ea75ed32c 32 0 0
8f20e8d05e62fad83c0accad82df42af 84 0 0
1c4847a64fdfa78a6094a2b60936d0b0 398 0 0
694dd510053de612f7339e2747acd98a 24 0 0
bc14c38f50bd718c07a6fad8d0b974f0 130 0 0
079d925c0948d498f5800e37f48a8edd 41 0 0
6f127432583b4c37762eb2d41ab779f2 884 0 0
4b5155655e9f0e466097c602043acbc7 21 0 0
4d7f9d157bedd5d6078d6465764a53c8 16 0 0
b00cbeb9749795e579bd50e157146f0d 86 0 0
592ffedf7f7221039afc844b2f4fdc66 72 0 4
18066d4ea972d9c36bc7b865466cd6eb 53 0 0
6d8d835cff05956f62c9bb99610206f6 1150 0 0
a6fb0cbabe0b67b00a8eb4a77fa000ae 199 0 0
8479c5090e759d6b0f74da1bd0933311 36 0 0
db7289690f70cc3fe5dd7f6a68dec65b 146 0 0
7770443d2c73db3247219f44c85330b6 35 0 0
8a88f51fbbd1cf4036edce693eabc86a 48 0 0
3de3bf92837333d25e078fb6947a574d 93 0 0
2f841fe83a4bada7a53eb4af827e9476 204 0 0
ca0d412ac4579bcdd14e08eb3f279978 528 0 0
5b858ca4949fd9cf5bba89756b01f26e 42 0 0
638ad3806ed5f0839bdcef6a6febd18d 520 0 0
a33fb9559e6006647c10f7a323dea54e 216 0 0
5eb00136b8c688e7c3dd88c3de9ef157 18 0 0
2613b4b2d006dd9bc1b9dc8904a3f766 25 0 0
11e18618bead81e79a362a5ef2ab38b8 43 0 0
6827eaf6fa512929f14eb3048bb78225 228 0 0
f5a06f8f56274c99cf775157e27645c3 48 0 0
43577e578520b2867697731105874b5d 6 0 0
ff408a41338d52c3115620bb5ef44b87 12 0 0
3f6c62a018f99ca18306bf8ba48abb2b 16 0 0
8e0a24cb4d7b3f57b9854b98bb776cbe 84 0 0
1edb26d65635049f8eaf8dad3b539238 1928 0 0
95707419a65692ab9a928ee6b941fbce 35 0 0
f5d873dbd84ce42d9e8f04c82b38ecfc 46 0 0
c186cfa9a4208738fc0f205ed23aeab7 44 0 0
3c039c131d1d5538b3699fd245f354dd 60 0 0
2be36e7c53a1ff9b53b596ce97533e58 18 0 0
2048d616d0369e6601a5a0f436dc5f4d 62 0 0
d254c6664252f2086b4f33679e0eaa52 16 0 0
b0dcf682d2bef5d4471797e8def4e1e0 51 0 0
327c2a9c912e7c1e9c4d1054767ee63b 73 0 0
9d894957ef6568842f0882cf6b36595c 8 0 0
67dabcca2b2e37bedc0505eb9112c387 105 0 0
28961c0aa4493196a8acf5e6ce52d994 13 0 0
d8cf0ec201f75ea7eef1d6508f4492a5 10 0 0
6db1ecacf0a9069bdc3769d566e6bc14 14 0 0
4ffc59a4f2fc9339077a288b0ae1e3a5 24 0 0
9db5b52f5a3f11a02e193ee93e4f81ce 75 0 0
b124cc19f9c82428804b0d52b3b05d6c 20 0 0
e3b211d560b5b2aff7de2d585dcea6b8 24 0 0
2266592eee2c0c8697e69e52a56c34bc 28 0 0
fb88635cbdce1e6dad7559366d648d8d 40 0 0
4080fc5501b77fa7027f0f557efe0fab 27 0 0
ad22d170d549ba4db81211353bc8568e 115 0 0
82d35bf6c80d4316579bdbd8f8384ec8 28 0 0
c6052f784c9c2675923c25f8f3587e7c 14 0 0
89c959a463cd1d79fc961dd82e9bf646 33 0 0
e330ffb86c570ac1873a9c636063ec2f 286 0 0
b3f5da2aa9fef278cfd6ec1fb552d13c 100 0 0
abf7d8f150084733736307be0ce95c30 5 0 0
4afcf81be0dd3de6b438c502f475e6f0 37 0 0
821f41a7282e6bb21a9a11e3eb1c351b 41 0 0
759128bbc80be1287e3c60023d11d097 13 0 0
2cc1afe613079292ccf3c45fd65ace47 49 0 0
23e36755aad7ff73733fed7c3db1dbc7 20 0 0
a79e7d52e7d021dc9b9e84c6e129aa90 53 0 0
5dcdcf41c20b1e88525cad8c41ba223c 70 0 0
37f237e4f643e74f18c07cade4c44034 17 0 0
8749a8f7c8be7c7ee3da7885a2b28b62 19 0 0
40959ad7a3eb84ce2491fa3117a1a4e0 34 0 0
1074f9ed7b28b8b17fc96f9714173a9c 19 0 0
634260cc29df8c70fdde3bbac5121d66 13 0 0
4dc17c8f0721eed9f53e16754e99f303 86 0 0
2e2272c7c1bb95fdfdb3a6cc8bb0898e 26 0 0
d43a73cf4b9c4fe2d4adb2ecb85fbda2 35 0 0
977934f6974142575e69930151c3cd25 18 0 0
4134ad8a7c05e84b58fc232fd4f325d3 18 0 0
e0f4395f69583f9d831c3f59a3139e78 21 0 0
2fd1d1213a4ed89ce119a041622b39b0 15 0 0
d10251383348c3df362779b518475eb8 9 0 0
958bb295ee69573d646af899c35a4728 22 0 0
61f50ba1b6017e968d69db3062972957 8 0 0
ebdb83c3ce6ffb9baa5d797041283e86 51 0 0
280a5152b14cfc86c66c4523aa6381a6 0 0 2
df1dd41fc64eb33cb587bb0215ee4aaf 37 0 0
9c114900e644efc08049ae7c7b848ec2 15 0 0
02c4cbcd5faaa21bc593ec031a78b167 5 0 0
814a6491e4f2e054f75ffb9fa643f91f 16 0 0
3c21a25545f66a1d1d582e5326eaca89 7 0 0
37c46c1b2d2807faf85453f6de29c42a 283 0 0
058109e0b5a4f748549464e140bc7b16 11 0 0
baf4416c38587d0c5222895b3d08f5f9 6 0 0
1f4c18f16f14415fe4c92bf28156b4e6 59 0 0
7dd93ae46821038682c068ced4636077 21 0 0
480cae699e90709442240687d533215d 9 0 0
3e638635a21addac92a53c13e6719299 20 0 0
f047a452cbefe36e5387436bbaefe060 44 0 0
04e5e80d3d51a845be3c3ece55ac3600 24 0 0
00eeeb8f0a446ea17d25b9ca1d467847 17 0 0
cb0debf5790a77b8bdd43c334af7c703 30 0 0
86f95e75f420d2c03895ca7c0b078d33 23 0 0
817d85b29971b63620ae27927a4592af 15 0 0
1d1c3bda5a5975bbe843f55fe862109b 48 0 0
22b16034d603a8d284a7b4096be1700c 29 0 0
9ab7a59e0c96d954b23e5cade160dcfc 337 0 0
f9e750ee58a7bc17b87edc80dd07f456 7 0 0
313c7de8878991e40a03523fe7e7ceab 14 0 0
cab121e47adc32b3ef4672f97f5ae0cc 15 0 0
6d0ad859321f6a50ca50d0c2eb60f44e 19 0 0
759c1757dc5fe5472de7baa7e1b4ade5 135 0 0
564d0bbc7b4b94c54ea240f27dbe8703 12 0 0
915b33f239b22bcde31aac43ba205959 36 0 0
c165f4d27ae206eb68c2fc89c1516649 11 0 0
6db3617f51d8650ffe5278591c86f0f4 38 0 0
b054aca2fa49ab0f8e9328b3462b740f 8 0 0
407bcce1cc008cc04f24e9bc112f5d36 10 0 0
b982b4c7e70504c463c264a5f00634cb 27 0 0
05c4884ce3fb795cac6607c3d1b7f678 12 0 0
7953e08ae1700754e8a79dd3a8a729c3 20 0 0
86e4f6fdc3bf7fbc6ea4336fdeedd97b 6 0 0
980be93d59e7147c584cbcb8a00ca56d 26 0 0
748e1354db01c1523859b6c4b1ba59d0 0 0 3
3c7bf5eff89c2c8a1d9509c3665c2e64 15 0 0
c8185b43be60c0306d0963c0883256b5 2 0 0
a556442b113d4769fcd3ef7d67a6fd77 27 0 0
684ec7bae4bb914632362dd52a015b02 23 0 0
055fb55d49e5b5fcad4153d7bca16da6 8 0 0
912eb9e0ec32a4843286b9fe2e6e7e51 14 0 0
1cd554cc78d730e45081889c4e58bad6 18 0 0
629af7dca148961cfd7477b2fc123902 23 0 0
b47eba1cd6a35c81f60d7d2bb97e6013 16 0 0
e776abb839c8e7bc4f58a5687e6a9957 12 0 0
88af29c3793e963589a64dde0544cc29 2 0 0
a503010c9fc4c4d70f27613e921a60d5 11 0 0
eab1128d4aafc16bd8599231ce4d7e25 12 0 0
ca5ffdd321647c68d6fd00214667476c 4 0 0
657c89fe0e618d21a1daed79cff8a6d1 9 0 0
b40e3c4f7f6460eef3da6862f00403a8 9 0 0
6607de21ec1969c619ba25378913ebbf 35 0 0
8cb1a447f8faacc6f1f1f5c5eea8692e 7 0 0
0425d580a9521c4e1a833b43bf4171e6 13 0 0
48bd6d53d89110cdf7750bf54f96206e 11 0 0
570ab9a74b810cb4627106c308d8b27e 24 0 0
c22ff4ffe10a315708619e87a9d53ea1 9 0 0
1c4c2e4933f24c62106229503280247b 14 0 0
d7d3c03925c0a513f846679b2983e900 5 0 0
41abb39d67341400bd33d737f094f5e1 6 0 0
aa8e385f09626f099e5fd2e3ecfe2a28 6 0 0
ed2a98e1d8ff278e4bc8ce7d15ccb736 7 0 0
6ea93dbef3a649eea231f45bb8aaaa6f 19 0 0
863d2d7d828cc6bbe58869a85df1f148 15 0 0
62de98a89839395d0d8ae327c2c0017d 10 0 0
2c796538ebe5bdf80383a492e53c2719 3 0 0
f4af63e11c49c5cea2e0a95c62586060 15 0 0
2652111df3332028c194ac30a845cced 13 0 0
e1efde95432a538374b3300892f743be 5 5 0
Here is the result from biom:
biom summarize-table -i feature-table.biom
Num samples: 3
Num observations: 251
Total count: 89,855
Table density (fraction of non-zero values): 0.356
Counts/sample summary:
Min: 0.000
Max: 89,473.000
Median: 382.000
Mean: 29,951.667
Std. dev.: 42,088.227
Sample Metadata Categories: None provided
Observation Metadata Categories: None provided
Counts/sample detail:
NTC4: 0.000
NTC5: 382.000
KM_A8: 89,473.000
SV_minsamp.zip
^^^ changed from qza to zip to upload to github ^^^
Thanks again for making this package!
Jordan