Hello! I meet the same question, I had run qiime demux summarize, and use QIIME 2, but I can only find how many reads are in each sample, total, not perdirection. I can't figure it out. Could you help me! Thanks very much!
!
Greetings to all,
I am trying to analyze with Qiime2 a set of 148 samples (paired-ended) and I obtain an error when I try to execute Dada2. I have searched about this issue in the forum and I have already applied the recomendations described. Below I explain the steps that I followed and the error that I get, which is like LuciaGG.
1\ read
qiime tools import --type 'SampleData[PairedEndSequencesWithQuality]' --input-path Samples_list.csv --output-path paired-end-demux.qza --input-format PairedEndFastqManifestPhred33
2\ qzv
qiime demux summarize --i-data paired-end-demux.qza --o-visualization demux.qzv
demux.qzv (291.1 KB)
3\ DADA2 then error
Plugin error from dada2:
An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.
Debug info has been saved to /tmp/qiime2-q2cli-err-zwc75agn.log
Running external command line application(s). This may print messages to stdout and/or stderr.
The command(s) being run are below. These commands cannot be manually re-run as they will depend on temporary files that no longer exist.
Command: run_dada_paired.R /home/stu_4/jzt/qiime2-tmp/tmpwhk168no/forward /home/stu_4/jzt/qiime2-tmp/tmpwhk168no/reverse /home/stu_4/jzt/qiime2-tmp/tmpwhk168no/output.tsv.biom /home/stu_4/jzt/qiime2-tmp/tmpwhk168no/track.tsv /home/stu_4/jzt/qiime2-tmp/tmpwhk168no/filt_f /home/stu_4/jzt/qiime2-tmp/tmpwhk168no/filt_r 260 250 24 17 2.0 2.0 2 consensus 1.0 20 1000000
R version 3.5.1 (2018-07-02)
Loading required package: Rcpp
DADA2: 1.10.0 / Rcpp: 1.0.2 / RcppParallel: 4.4.3
1) Filtering Error in filterAndTrim(unfiltsF, filtsF, unfiltsR, filtsR, truncLen = c(truncLenF, :
These are the errors (up to 5) encountered in individual cores...
Error in (function (fn, fout, maxN = c(0, 0), truncQ = c(2, 2), truncLen = c(0, :
Mismatched forward and reverse sequence files: 42160, 54490.
Error in (function (fn, fout, maxN = c(0, 0), truncQ = c(2, 2), truncLen = c(0, :
Mismatched forward and reverse sequence files: 47016, 26949.
Error in (function (fn, fout, maxN = c(0, 0), truncQ = c(2, 2), truncLen = c(0, :
Mismatched forward and reverse sequence files: 42160, 54490.
Error in (function (fn, fout, maxN = c(0, 0), truncQ = c(2, 2), truncLen = c(0, :
Mismatched forward and reverse sequence files: 47016, 26949.
Error in (function (fn, fout, maxN = c(0, 0), truncQ = c(2, 2), truncLen = c(0, :
Mismatched forward and reverse sequence files: 42160, 54490.
Execution halted
Traceback (most recent call last):
File "/home/foodbio/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 234, in denoise_paired
run_commands([cmd])
File "/home/foodbio/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/home/foodbio/miniconda3/envs/qiime2-2019.7/lib/python3.6/subprocess.py", line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_dada_paired.R', '/home/stu_4/jzt/qiime2-tmp/tmpwhk168no/forward', '/home/stu_4/jzt/qiime2-tmp/tmpwhk168no/reverse', '/home/stu_4/jzt/qiime2-tmp/tmpwhk168no/output.tsv.biom', '/home/stu_4/jzt/qiime2-tmp/tmpwhk168no/track.tsv', '/home/stu_4/jzt/qiime2-tmp/tmpwhk168no/filt_f', '/home/stu_4/jzt/qiime2-tmp/tmpwhk168no/filt_r', '260', '250', '24', '17', '2.0', '2.0', '2', 'consensus', '1.0', '20', '1000000']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/foodbio/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/commands.py", line 327, in __call__
results = action(**arguments)
File "</home/foodbio/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/decorator.py:decorator-gen-459>", line 2, in denoise_paired
File "/home/foodbio/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py", line 240, in bound_callable
output_types, provenance)
File "/home/foodbio/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py", line 383, in _callable_executor_
output_views = self._callable(**view_args)
File "/home/foodbio/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 249, in denoise_paired
" and stderr to learn more." % e.returncode)
Exception: An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.
4\Then check
50751 10B_0_L001_R1_001.fastq.gz
50751 10B_1_L001_R2_001.fastq.gz
43124 10t_2_L001_R1_001.fastq.gz
43124 10t_3_L001_R2_001.fastq.gz
11060 10y_4_L001_R1_001.fastq.gz
11060 10y_5_L001_R2_001.fastq.gz
44703 11B_6_L001_R1_001.fastq.gz
44703 11B_7_L001_R2_001.fastq.gz
44624 11t_8_L001_R1_001.fastq.gz
44624 11t_9_L001_R2_001.fastq.gz
48598 11y_10_L001_R1_001.fastq.gz
48598 11y_11_L001_R2_001.fastq.gz
40332 12B_12_L001_R1_001.fastq.gz
40332 12B_13_L001_R2_001.fastq.gz
53491 12H_14_L001_R1_001.fastq.gz
53491 12H_15_L001_R2_001.fastq.gz
61316 12t_16_L001_R1_001.fastq.gz
61316 12t_17_L001_R2_001.fastq.gz
29091 12y_18_L001_R1_001.fastq.gz
29091 12y_19_L001_R2_001.fastq.gz
18198 13B_20_L001_R1_001.fastq.gz
18198 13B_21_L001_R2_001.fastq.gz
82925 13t_22_L001_R1_001.fastq.gz
82925 13t_23_L001_R2_001.fastq.gz
61360 14B_24_L001_R1_001.fastq.gz
61360 14B_25_L001_R2_001.fastq.gz
64500 14H_26_L001_R1_001.fastq.gz
64500 14H_27_L001_R2_001.fastq.gz
53708 14t_28_L001_R1_001.fastq.gz
53708 14t_29_L001_R2_001.fastq.gz
68718 14y_30_L001_R1_001.fastq.gz
68718 14y_31_L001_R2_001.fastq.gz
47319 15B_32_L001_R1_001.fastq.gz
47319 15B_33_L001_R2_001.fastq.gz
56031 15t_34_L001_R1_001.fastq.gz
56031 15t_35_L001_R2_001.fastq.gz
1071 15y_36_L001_R1_001.fastq.gz
1071 15y_37_L001_R2_001.fastq.gz
49819 16B_38_L001_R1_001.fastq.gz
49819 16B_39_L001_R2_001.fastq.gz
50357 16t_40_L001_R1_001.fastq.gz
50357 16t_41_L001_R2_001.fastq.gz
48913 16y_42_L001_R1_001.fastq.gz
48913 16y_43_L001_R2_001.fastq.gz
8547 17B_44_L001_R1_001.fastq.gz
8547 17B_45_L001_R2_001.fastq.gz
62787 17t_46_L001_R1_001.fastq.gz
62787 17t_47_L001_R2_001.fastq.gz
60213 17y_48_L001_R1_001.fastq.gz
60213 17y_49_L001_R2_001.fastq.gz
16322 19B_50_L001_R1_001.fastq.gz
16322 19B_51_L001_R2_001.fastq.gz
2185 19t_52_L001_R1_001.fastq.gz
2185 19t_53_L001_R2_001.fastq.gz
23606 19y_54_L001_R1_001.fastq.gz
23606 19y_55_L001_R2_001.fastq.gz
10373 1B_56_L001_R1_001.fastq.gz
10373 1B_57_L001_R2_001.fastq.gz
16431 1t_58_L001_R1_001.fastq.gz
16431 1t_59_L001_R2_001.fastq.gz
53030 1y_60_L001_R1_001.fastq.gz
53030 1y_61_L001_R2_001.fastq.gz
27254 20B_62_L001_R1_001.fastq.gz
27254 20B_63_L001_R2_001.fastq.gz
47641 20t_64_L001_R1_001.fastq.gz
47641 20t_65_L001_R2_001.fastq.gz
60108 21B_66_L001_R1_001.fastq.gz
60108 21B_67_L001_R2_001.fastq.gz
42778 21t_68_L001_R1_001.fastq.gz
42778 21t_69_L001_R2_001.fastq.gz
33477 21y_70_L001_R1_001.fastq.gz
33477 21y_71_L001_R2_001.fastq.gz
83386 22B_72_L001_R1_001.fastq.gz
83386 22B_73_L001_R2_001.fastq.gz
49490 22t_74_L001_R1_001.fastq.gz
49490 22t_75_L001_R2_001.fastq.gz
61830 22y_76_L001_R1_001.fastq.gz
61830 22y_77_L001_R2_001.fastq.gz
48416 23B_78_L001_R1_001.fastq.gz
48416 23B_79_L001_R2_001.fastq.gz
44488 23t_80_L001_R1_001.fastq.gz
44488 23t_81_L001_R2_001.fastq.gz
42180 23y_82_L001_R1_001.fastq.gz
42180 23y_83_L001_R2_001.fastq.gz
55070 24B_84_L001_R1_001.fastq.gz
55070 24B_85_L001_R2_001.fastq.gz
37126 24t_86_L001_R1_001.fastq.gz
37126 24t_87_L001_R2_001.fastq.gz
16107 24y_88_L001_R1_001.fastq.gz
16107 24y_89_L001_R2_001.fastq.gz
31684 25B_90_L001_R1_001.fastq.gz
31684 25B_91_L001_R2_001.fastq.gz
17688 25t_92_L001_R1_001.fastq.gz
17688 25t_93_L001_R2_001.fastq.gz
18637 25y_94_L001_R1_001.fastq.gz
18637 25y_95_L001_R2_001.fastq.gz
30806 26B_96_L001_R1_001.fastq.gz
30806 26B_97_L001_R2_001.fastq.gz
19450 26t_98_L001_R1_001.fastq.gz
19450 26t_99_L001_R2_001.fastq.gz
32390 26y_100_L001_R1_001.fastq.gz
32390 26y_101_L001_R2_001.fastq.gz
40187 27B_102_L001_R1_001.fastq.gz
40187 27B_103_L001_R2_001.fastq.gz
19757 27t_104_L001_R1_001.fastq.gz
19757 27t_105_L001_R2_001.fastq.gz
24684 27y_106_L001_R1_001.fastq.gz
24684 27y_107_L001_R2_001.fastq.gz
31438 29y_108_L001_R1_001.fastq.gz
31438 29y_109_L001_R2_001.fastq.gz
25720 2B_110_L001_R1_001.fastq.gz
25720 2B_111_L001_R2_001.fastq.gz
39380 2t_112_L001_R1_001.fastq.gz
39380 2t_113_L001_R2_001.fastq.gz
22750 2y_114_L001_R1_001.fastq.gz
22750 2y_115_L001_R2_001.fastq.gz
19519 30B_116_L001_R1_001.fastq.gz
19519 30B_117_L001_R2_001.fastq.gz
19992 30H_118_L001_R1_001.fastq.gz
19992 30H_119_L001_R2_001.fastq.gz
13389 30t_120_L001_R1_001.fastq.gz
13389 30t_121_L001_R2_001.fastq.gz
8945 31B_122_L001_R1_001.fastq.gz
8945 31B_123_L001_R2_001.fastq.gz
14063 31H_124_L001_R1_001.fastq.gz
14063 31H_125_L001_R2_001.fastq.gz
12436 31t_126_L001_R1_001.fastq.gz
12436 31t_127_L001_R2_001.fastq.gz
22577 31y_128_L001_R1_001.fastq.gz
22577 31y_129_L001_R2_001.fastq.gz
48859 32B_130_L001_R1_001.fastq.gz
48859 32B_131_L001_R2_001.fastq.gz
761 32t_132_L001_R1_001.fastq.gz
761 32t_133_L001_R2_001.fastq.gz
426 32y_134_L001_R1_001.fastq.gz
426 32y_135_L001_R2_001.fastq.gz
41283 33H_136_L001_R1_001.fastq.gz
41283 33H_137_L001_R2_001.fastq.gz
81365 33t_138_L001_R1_001.fastq.gz
81365 33t_139_L001_R2_001.fastq.gz
59018 33y_140_L001_R1_001.fastq.gz
59018 33y_141_L001_R2_001.fastq.gz
42551 34H_142_L001_R1_001.fastq.gz
42551 34H_143_L001_R2_001.fastq.gz
38332 34t_144_L001_R1_001.fastq.gz
38332 34t_145_L001_R2_001.fastq.gz
32301 34y_146_L001_R1_001.fastq.gz
32301 34y_147_L001_R2_001.fastq.gz
61677 35B_148_L001_R1_001.fastq.gz
61677 35B_149_L001_R2_001.fastq.gz
37243 35t_150_L001_R1_001.fastq.gz
37243 35t_151_L001_R2_001.fastq.gz
2864 35y_152_L001_R1_001.fastq.gz
2864 35y_153_L001_R2_001.fastq.gz
69673 36B_154_L001_R1_001.fastq.gz
69673 36B_155_L001_R2_001.fastq.gz
59734 36t_156_L001_R1_001.fastq.gz
59734 36t_157_L001_R2_001.fastq.gz
73337 36y_158_L001_R1_001.fastq.gz
73337 36y_159_L001_R2_001.fastq.gz
53236 37B_160_L001_R1_001.fastq.gz
53236 37B_161_L001_R2_001.fastq.gz
41758 37t_162_L001_R1_001.fastq.gz
41758 37t_163_L001_R2_001.fastq.gz
43496 37y_164_L001_R1_001.fastq.gz
43496 37y_165_L001_R2_001.fastq.gz
18404 38B_166_L001_R1_001.fastq.gz
18404 38B_167_L001_R2_001.fastq.gz
2815 38H_168_L001_R1_001.fastq.gz
2815 38H_169_L001_R2_001.fastq.gz
42019 38t_170_L001_R1_001.fastq.gz
42019 38t_171_L001_R2_001.fastq.gz
48376 38y_172_L001_R1_001.fastq.gz
48376 38y_173_L001_R2_001.fastq.gz
6547 39B_174_L001_R1_001.fastq.gz
6547 39B_175_L001_R2_001.fastq.gz
42757 39t_176_L001_R1_001.fastq.gz
42757 39t_177_L001_R2_001.fastq.gz
24974 39y_178_L001_R1_001.fastq.gz
24974 39y_179_L001_R2_001.fastq.gz
14792 3B_180_L001_R1_001.fastq.gz
14792 3B_181_L001_R2_001.fastq.gz
14418 3t_182_L001_R1_001.fastq.gz
14418 3t_183_L001_R2_001.fastq.gz
14527 3y_184_L001_R1_001.fastq.gz
14527 3y_185_L001_R2_001.fastq.gz
41603 40B_186_L001_R1_001.fastq.gz
41603 40B_187_L001_R2_001.fastq.gz
22026 40t_188_L001_R1_001.fastq.gz
22026 40t_189_L001_R2_001.fastq.gz
72263 40y_190_L001_R1_001.fastq.gz
72263 40y_191_L001_R2_001.fastq.gz
393 4B_192_L001_R1_001.fastq.gz
393 4B_193_L001_R2_001.fastq.gz
16180 4t_194_L001_R1_001.fastq.gz
16180 4t_195_L001_R2_001.fastq.gz
24301 4y_196_L001_R1_001.fastq.gz
24301 4y_197_L001_R2_001.fastq.gz
34418 51H_198_L001_R1_001.fastq.gz
34418 51H_199_L001_R2_001.fastq.gz
60104 51t_200_L001_R1_001.fastq.gz
60104 51t_201_L001_R2_001.fastq.gz
35695 51y_202_L001_R1_001.fastq.gz
35695 51y_203_L001_R2_001.fastq.gz
60488 52B_204_L001_R1_001.fastq.gz
60488 52B_205_L001_R2_001.fastq.gz
51171 52t_206_L001_R1_001.fastq.gz
51171 52t_207_L001_R2_001.fastq.gz
15956 52y_208_L001_R1_001.fastq.gz
15956 52y_209_L001_R2_001.fastq.gz
28199 53B_210_L001_R1_001.fastq.gz
28199 53B_211_L001_R2_001.fastq.gz
48083 53t_212_L001_R1_001.fastq.gz
48083 53t_213_L001_R2_001.fastq.gz
24749 53y_214_L001_R1_001.fastq.gz
24749 53y_215_L001_R2_001.fastq.gz
64329 57H_216_L001_R1_001.fastq.gz
64329 57H_217_L001_R2_001.fastq.gz
51445 57t_218_L001_R1_001.fastq.gz
51445 57t_219_L001_R2_001.fastq.gz
47016 57y_220_L001_R1_001.fastq.gz
26949 57y_221_L001_R2_001.fastq.gz
40997 58B_222_L001_R1_001.fastq.gz
40997 58B_223_L001_R2_001.fastq.gz
54490 58H_224_L001_R1_001.fastq.gz
54490 58H_225_L001_R2_001.fastq.gz
36725 58t_226_L001_R1_001.fastq.gz
36725 58t_227_L001_R2_001.fastq.gz
42160 59H_228_L001_R1_001.fastq.gz
54490 59H_229_L001_R2_001.fastq.gz
29242 59t_230_L001_R1_001.fastq.gz
29242 59t_231_L001_R2_001.fastq.gz
34590 59y_232_L001_R1_001.fastq.gz
34590 59y_233_L001_R2_001.fastq.gz
86005 5H_234_L001_R1_001.fastq.gz
86005 5H_235_L001_R2_001.fastq.gz
29536 5t_236_L001_R1_001.fastq.gz
29536 5t_237_L001_R2_001.fastq.gz
26949 5y_238_L001_R1_001.fastq.gz
26949 5y_239_L001_R2_001.fastq.gz
10865 60B_240_L001_R1_001.fastq.gz
10865 60B_241_L001_R2_001.fastq.gz
25371 60t_242_L001_R1_001.fastq.gz
25371 60t_243_L001_R2_001.fastq.gz
47349 60y_244_L001_R1_001.fastq.gz
47349 60y_245_L001_R2_001.fastq.gz
30479 61B_246_L001_R1_001.fastq.gz
30479 61B_247_L001_R2_001.fastq.gz
24463 61H_248_L001_R1_001.fastq.gz
24463 61H_249_L001_R2_001.fastq.gz
23676 61t_250_L001_R1_001.fastq.gz
23676 61t_251_L001_R2_001.fastq.gz
28084 61y_252_L001_R1_001.fastq.gz
28084 61y_253_L001_R2_001.fastq.gz
41724 62B_254_L001_R1_001.fastq.gz
41724 62B_255_L001_R2_001.fastq.gz
41336 62t_256_L001_R1_001.fastq.gz
41336 62t_257_L001_R2_001.fastq.gz
44099 62y_258_L001_R1_001.fastq.gz
44099 62y_259_L001_R2_001.fastq.gz
51110 64B_260_L001_R1_001.fastq.gz
51110 64B_261_L001_R2_001.fastq.gz
54668 64t_262_L001_R1_001.fastq.gz
54668 64t_263_L001_R2_001.fastq.gz
64672 64y_264_L001_R1_001.fastq.gz
64672 64y_265_L001_R2_001.fastq.gz
50267 66B_266_L001_R1_001.fastq.gz
50267 66B_267_L001_R2_001.fastq.gz
77158 66t_268_L001_R1_001.fastq.gz
77158 66t_269_L001_R2_001.fastq.gz
29405 66y_270_L001_R1_001.fastq.gz
29405 66y_271_L001_R2_001.fastq.gz
59927 6B_272_L001_R1_001.fastq.gz
59927 6B_273_L001_R2_001.fastq.gz
27814 6H_274_L001_R1_001.fastq.gz
27814 6H_275_L001_R2_001.fastq.gz
54258 6t_276_L001_R1_001.fastq.gz
54258 6t_277_L001_R2_001.fastq.gz
42323 6y_278_L001_R1_001.fastq.gz
42323 6y_279_L001_R2_001.fastq.gz
15582 7B_280_L001_R1_001.fastq.gz
15582 7B_281_L001_R2_001.fastq.gz
19293 7H_282_L001_R1_001.fastq.gz
19293 7H_283_L001_R2_001.fastq.gz
38301 7t_284_L001_R1_001.fastq.gz
38301 7t_285_L001_R2_001.fastq.gz
33752 7y_286_L001_R1_001.fastq.gz
33752 7y_287_L001_R2_001.fastq.gz
36149 9B_288_L001_R1_001.fastq.gz
36149 9B_289_L001_R2_001.fastq.gz
57276 9t_290_L001_R1_001.fastq.gz
57276 9t_291_L001_R2_001.fastq.gz
51407 9y_292_L001_R1_001.fastq.gz
51407 9y_293_L001_R2_001.fastq.gz
All the paired samples had the same counts. But it lose a sample"13y".
Now I don't know how to figure it out!
Any help would be appreciated, thank you!
Hi @cherry!
Please take a few minutes to review our code of conduct, in particular, this section:
https://forum.qiime2.org/faq#patience
and this section
https://forum.qiime2.org/faq#cross-posting
Thanks!
Okay, on to your error...
This sample has mismatched sequences --- please double check the files prior to importing.
You appear to be running QIIME 2 2019.7 (I see this in the provenance for the file you shared) - the feature you're referring to wasn't added until 2020 - you can update to get that updated viz in the future.
I hope that helps - keep us posted!
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Firstly, I'm sorry that I didn't read the code of conduct. Then I check the sample_list again and again, as you mentioned, it is the error on the mismatched sample. Now I have run DADA2 successfully! Thank you for your time and suggestion!
Good luck!
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