Hello All,
I tried to run the denoising step with dada2 on my imported data, but I keep having this error according to the attached file. I ran a debug on the imported qza file using script provided by @thermokarst and I realised most of my samples are not arranged in pairs even though the read count is the same. I have looked at my manifest to see if the problem is due to typos in the manifest and also validated the manifest using keemei but I couldn't find any suspicious error. Could it be that my denoising steps failed due to forward and reverse reads of some of my samples not being in their respective pairs? Thank you.
for f in *.fastq.gz; do r=(( (gunzip -c $f | wc -l | tr -d '[:space:]') / 4 )); echo $r $f; done.
qiime dada2 denoise-paired
--i-demultiplexed-seqs 02_analyses/seqs/paired.qza
--p-trim-left-f 13
--p-trim-left-r 13
--p-trunc-len-f 220
--p-trunc-len-r 160
--o-table 02_analyses/dada2/table.qza
--verbose
--o-representative-sequences 02_analyses/dada2/rep-seqs.qza
--o-denoising-stats 02_analyses/dada2/denoising-stats.qza
113108 Blank_0_L001_R1_001.fastq.gz
113108 Blank_150_L001_R2_001.fastq.gz
124677 MBAS10_155_L001_R2_001.fastq.gz
124677 MBAS10_5_L001_R1_001.fastq.gz
165085 MBAS11_156_L001_R2_001.fastq.gz
138830 MBAS1_151_L001_R2_001.fastq.gz
165085 MBAS11_6_L001_R1_001.fastq.gz
138830 MBAS1_1_L001_R1_001.fastq.gz
138087 MBAS12_157_L001_R2_001.fastq.gz
138087 MBAS12_7_L001_R1_001.fastq.gz
124779 MBAS14_158_L001_R2_001.fastq.gz
124779 MBAS14_8_L001_R1_001.fastq.gz
148487 MBAS15_159_L001_R2_001.fastq.gz
148487 MBAS15_9_L001_R1_001.fastq.gz
82346 MBAS16_10_L001_R1_001.fastq.gz
82346 MBAS16_160_L001_R2_001.fastq.gz
124536 MBAS17_11_L001_R1_001.fastq.gz
124536 MBAS17_161_L001_R2_001.fastq.gz
113775 MBAS18_12_L001_R1_001.fastq.gz
113775 MBAS18_162_L001_R2_001.fastq.gz
144459 MBAS19_13_L001_R1_001.fastq.gz
144459 MBAS19_163_L001_R2_001.fastq.gz
110644 MBAS20_14_L001_R1_001.fastq.gz
110644 MBAS20_164_L001_R2_001.fastq.gz
105435 MBAS22_15_L001_R1_001.fastq.gz
105435 MBAS22_165_L001_R2_001.fastq.gz
132804 MBAS25_166_L001_R2_001.fastq.gz
132804 MBAS25_16_L001_R1_001.fastq.gz
83925 MBAS29_167_L001_R2_001.fastq.gz
83925 MBAS29_17_L001_R1_001.fastq.gz
91493 MBAS30_168_L001_R2_001.fastq.gz
91493 MBAS30_18_L001_R1_001.fastq.gz
94563 MBAS31_169_L001_R2_001.fastq.gz
94563 MBAS31_19_L001_R1_001.fastq.gz
96928 MBAS3_152_L001_R2_001.fastq.gz
93234 MBAS32_170_L001_R2_001.fastq.gz
93234 MBAS32_20_L001_R1_001.fastq.gz
96928 MBAS3_2_L001_R1_001.fastq.gz
92151 MBAS34_171_L001_R2_001.fastq.gz
92151 MBAS34_21_L001_R1_001.fastq.gz
89514 MBAS4_153_L001_R2_001.fastq.gz
89514 MBAS4_3_L001_R1_001.fastq.gz
134219 MBAS7_154_L001_R2_001.fastq.gz
134219 MBAS7_4_L001_R1_001.fastq.gz
104656 MBC10AS_183_L001_R2_001.fastq.gz
104656 MBC10AS_33_L001_R1_001.fastq.gz
105148 MBC10S_184_L001_R2_001.fastq.gz
105148 MBC10S_34_L001_R1_001.fastq.gz
216931 MBC11AS_185_L001_R2_001.fastq.gz
216931 MBC11AS_35_L001_R1_001.fastq.gz
172369 MBC11S_186_L001_R2_001.fastq.gz
172369 MBC11S_36_L001_R1_001.fastq.gz
128024 MBC13AS_187_L001_R2_001.fastq.gz
128024 MBC13AS_37_L001_R1_001.fastq.gz
108644 MBC13S_188_L001_R2_001.fastq.gz
108644 MBC13S_38_L001_R1_001.fastq.gz
544697 MBC14AS_189_L001_R2_001.fastq.gz
544697 MBC14AS_39_L001_R1_001.fastq.gz
128278 MBC14S_190_L001_R2_001.fastq.gz
128278 MBC14S_40_L001_R1_001.fastq.gz
124844 MBC15AS_191_L001_R2_001.fastq.gz
124844 MBC15AS_41_L001_R1_001.fastq.gz
164337 MBC15SF_192_L001_R2_001.fastq.gz
164337 MBC15SF_42_L001_R1_001.fastq.gz
110661 MBC16AS_193_L001_R2_001.fastq.gz
110661 MBC16AS_43_L001_R1_001.fastq.gz
82054 MBC16S_194_L001_R2_001.fastq.gz
82054 MBC16S_44_L001_R1_001.fastq.gz
109245 MBC17AS_195_L001_R2_001.fastq.gz
109245 MBC17AS_45_L001_R1_001.fastq.gz
91635 MBC17S_196_L001_R2_001.fastq.gz
91635 MBC17S_46_L001_R1_001.fastq.gz
132022 MBC18AS_197_L001_R2_001.fastq.gz
132022 MBC18AS_47_L001_R1_001.fastq.gz
118392 MBC19AS_198_L001_R2_001.fastq.gz
118392 MBC19AS_48_L001_R1_001.fastq.gz
82830 MBC19S_199_L001_R2_001.fastq.gz
82830 MBC19S_49_L001_R1_001.fastq.gz
114641 MBC1AS_172_L001_R2_001.fastq.gz
114641 MBC1AS_22_L001_R1_001.fastq.gz
105485 MBC1S_173_L001_R2_001.fastq.gz
105485 MBC1S_23_L001_R1_001.fastq.gz
162384 MBC20AS_200_L001_R2_001.fastq.gz
162384 MBC20AS_50_L001_R1_001.fastq.gz
102903 MBC20S_201_L001_R2_001.fastq.gz
102903 MBC20S_51_L001_R1_001.fastq.gz
97728 MBC21S_202_L001_R2_001.fastq.gz
97728 MBC21S_52_L001_R1_001.fastq.gz
105313 MBC22AS_203_L001_R2_001.fastq.gz
105313 MBC22AS_53_L001_R1_001.fastq.gz
95015 MBC22S_204_L001_R2_001.fastq.gz
95015 MBC22S_54_L001_R1_001.fastq.gz
137894 MBC23AS_205_L001_R2_001.fastq.gz
137894 MBC23AS_55_L001_R1_001.fastq.gz
79734 MBC23S_206_L001_R2_001.fastq.gz
79734 MBC23S_56_L001_R1_001.fastq.gz
86377 MBC24S_207_L001_R2_001.fastq.gz
86377 MBC24S_57_L001_R1_001.fastq.gz
81072 MBC26S_208_L001_R2_001.fastq.gz
81072 MBC26S_58_L001_R1_001.fastq.gz
215190 MBC27AS_209_L001_R2_001.fastq.gz
215190 MBC27AS_59_L001_R1_001.fastq.gz
92015 MBC27S_210_L001_R2_001.fastq.gz
92015 MBC27S_60_L001_R1_001.fastq.gz
85003 MBC28AS_211_L001_R2_001.fastq.gz
85003 MBC28AS_61_L001_R1_001.fastq.gz
142054 MBC28S_212_L001_R2_001.fastq.gz
142054 MBC28S_62_L001_R1_001.fastq.gz
95525 MBC29AS_213_L001_R2_001.fastq.gz
95525 MBC29AS_63_L001_R1_001.fastq.gz