Hello,
I am currently using qiime2-2019.10. While running DADA2 I ran into a mismatched forward and reverse sequence file error. I found similar issues in other threads in the forum and attempted to repeat the steps but the mismatched files don’t seem to exist.
My input and the qiime2 output is below:
qiime dada2 denoise-paired \
> --i-demultiplexed-seqs demux-paired-end.qza \
> --p-trim-left-f 13 \
> --p-trim-left-r 13 \
> --p-trunc-len-f 247 \
> --p-trunc-len-r 247 \
> --o-table table.qza \
> --o-representative-sequences rep-seqs.qza \
> --o-denoising-stats denoising-stats.qza \
> --p-n-threads 0 \
> --verbose
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 /tmp/tmpivordppa/forward /tmp/tmpivordppa/reverse /tmp/tmpivordppa/output.tsv.biom /tmp/tmpivordppa/track.tsv /tmp/tmpivordppa/filt_f /tmp/tmpivordppa/filt_r 247 247 13 13 2.0 2.0 2 consensus 1.0 0 1000000
R version 3.5.1 (2018-07-02)
Loading required package: Rcpp
DADA2: 1.10.0 / Rcpp: 1.0.2 / RcppParallel: 4.4.4
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: 38678, 100000.
Error in (function (fn, fout, maxN = c(0, 0), truncQ = c(2, 2), truncLen = c(0, :
Mismatched forward and reverse sequence files: 38678, 100000.
Error in (function (fn, fout, maxN = c(0, 0), truncQ = c(2, 2), truncLen = c(0, :
Mismatched forward and reverse sequence files: 38678, 100000.
Error in (function (fn, fout, maxN = c(0, 0), truncQ = c(2, 2), truncLen = c(0, :
Mismatched forward and reverse sequence files: 38678, 100000.
Error in (function (fn, fout, maxN = c(0, 0), truncQ = c(2, 2), truncLen = c(0, :
Mismatched forward and reverse sequence files: 38678, 100000.
Execution halted
Traceback (most recent call last):
File "/home/sceb/anaconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 257, in denoise_paired
run_commands([cmd])
File "/home/sceb/anaconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/home/sceb/anaconda3/envs/qiime2-2019.10/lib/python3.6/subprocess.py", line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_dada_paired.R', '/tmp/tmpivordppa/forward', '/tmp/tmpivordppa/reverse', '/tmp/tmpivordppa/output.tsv.biom', '/tmp/tmpivordppa/track.tsv', '/tmp/tmpivordppa/filt_f', '/tmp/tmpivordppa/filt_r', '247', '247', '13', '13', '2.0', '2.0', '2', 'consensus', '1.0', '0', '1000000']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/sceb/anaconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2cli/commands.py", line 328, in __call__
results = action(**arguments)
File "</home/sceb/anaconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/decorator.py:decorator-gen-459>", line 2, in denoise_paired
File "/home/sceb/anaconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py", line 240, in bound_callable
output_types, provenance)
File "/home/sceb/anaconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py", line 383, in _callable_executor_
output_views = self._callable(**view_args)
File "/home/sceb/anaconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 272, 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.
Plugin error from dada2:
An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.
See above for debug info.
I searched the forum and found threads about similar errors and repeated the troubleshooting steps.
Specifically I did the following:
qiime tools export --output-path import-check --input-path demux-paired-end.qza
cd import-check
for f in *.fastq.gz; do r=(( (wc -l < $f | tr -d ‘[:space:]’) / 4 )); echo $r $f; done
But when I search the results for the mismatched files (38678, 100000), they don’t exist.
Here is the output I get:
24219 10-1_74_L001_R1_001.fastq.gz
29585 10-1_74_L001_R2_001.fastq.gz
1928 10-2_75_L001_R1_001.fastq.gz
2580 10-2_75_L001_R2_001.fastq.gz
6245 10-4_77_L001_R1_001.fastq.gz
7938 10-4_77_L001_R2_001.fastq.gz
2284 10-5_78_L001_R1_001.fastq.gz
2965 10-5_78_L001_R2_001.fastq.gz
2199 10-6_79_L001_R1_001.fastq.gz
2902 10-6_79_L001_R2_001.fastq.gz
10545 10-7_80_L001_R1_001.fastq.gz
12285 10-7_80_L001_R2_001.fastq.gz
3418 10-B_73_L001_R1_001.fastq.gz
4326 10-B_73_L001_R2_001.fastq.gz
1880 11-1_82_L001_R1_001.fastq.gz
2591 11-1_82_L001_R2_001.fastq.gz
3338 11-2_144_L001_R1_001.fastq.gz
3603 11-2_144_L001_R2_001.fastq.gz
2395 1-1_2_L001_R1_001.fastq.gz
2940 1-1_2_L001_R2_001.fastq.gz
9361 11-3_84_L001_R1_001.fastq.gz
11353 11-3_84_L001_R2_001.fastq.gz
2412 11-4_85_L001_R1_001.fastq.gz
2828 11-4_85_L001_R2_001.fastq.gz
2194 11-5_86_L001_R1_001.fastq.gz
2848 11-5_86_L001_R2_001.fastq.gz
9162 11-6_87_L001_R1_001.fastq.gz
11243 11-6_87_L001_R2_001.fastq.gz
11795 11-7_88_L001_R1_001.fastq.gz
14777 11-7_88_L001_R2_001.fastq.gz
8287 11-B_81_L001_R1_001.fastq.gz
9744 11-B_81_L001_R2_001.fastq.gz
2569 12-1_90_L001_R1_001.fastq.gz
3282 12-1_90_L001_R2_001.fastq.gz
15869 12-2_91_L001_R1_001.fastq.gz
20015 12-2_91_L001_R2_001.fastq.gz
2775 12-3_92_L001_R1_001.fastq.gz
3496 12-3_92_L001_R2_001.fastq.gz
2710 1-2_3_L001_R1_001.fastq.gz
3150 1-2_3_L001_R2_001.fastq.gz
3094 12-4_94_L001_R1_001.fastq.gz
3679 12-4_94_L001_R2_001.fastq.gz
2071 12-5_93_L001_R1_001.fastq.gz
2571 12-5_93_L001_R2_001.fastq.gz
2491 12-6_95_L001_R1_001.fastq.gz
3007 12-6_95_L001_R2_001.fastq.gz
3736 12-7_96_L001_R1_001.fastq.gz
4305 12-7_96_L001_R2_001.fastq.gz
2490 12-B_145_L001_R1_001.fastq.gz
2912 12-B_145_L001_R2_001.fastq.gz
18913 13-1_98_L001_R1_001.fastq.gz
24139 13-1_98_L001_R2_001.fastq.gz
5168 13-2_99_L001_R1_001.fastq.gz
6472 13-2_99_L001_R2_001.fastq.gz
4851 13-3_100_L001_R1_001.fastq.gz
6381 13-3_100_L001_R2_001.fastq.gz
2615 1-3_4_L001_R1_001.fastq.gz
3657 1-3_4_L001_R2_001.fastq.gz
8752 13-5_102_L001_R1_001.fastq.gz
11042 13-5_102_L001_R2_001.fastq.gz
2867 13-6_103_L001_R1_001.fastq.gz
3751 13-6_103_L001_R2_001.fastq.gz
2335 13-7_104_L001_R1_001.fastq.gz
2641 13-7_104_L001_R2_001.fastq.gz
11288 13-B_97_L001_R1_001.fastq.gz
13432 13-B_97_L001_R2_001.fastq.gz
2109 14-1_106_L001_R1_001.fastq.gz
2561 14-1_106_L001_R2_001.fastq.gz
9903 14-2_107_L001_R1_001.fastq.gz
12085 14-2_107_L001_R2_001.fastq.gz
4047 14_3_146_L001_R1_001.fastq.gz
4610 14_3_146_L001_R2_001.fastq.gz
9505 14-4_109_L001_R1_001.fastq.gz
12044 14-4_109_L001_R2_001.fastq.gz
2816 14-5_110_L001_R1_001.fastq.gz
3520 14-5_110_L001_R2_001.fastq.gz
2721 1-4_5_L001_R1_001.fastq.gz
3623 1-4_5_L001_R2_001.fastq.gz
8415 14-6_111_L001_R1_001.fastq.gz
9858 14-6_111_L001_R2_001.fastq.gz
1777 14-7_112_L001_R1_001.fastq.gz
2117 14-7_112_L001_R2_001.fastq.gz
6454 14-B_105_L001_R1_001.fastq.gz
7167 14-B_105_L001_R2_001.fastq.gz
8697 15-1_114_L001_R1_001.fastq.gz
10725 15-1_114_L001_R2_001.fastq.gz
7609 15-2_115_L001_R1_001.fastq.gz
9585 15-2_115_L001_R2_001.fastq.gz
9884 15-3_116_L001_R1_001.fastq.gz
12290 15-3_116_L001_R2_001.fastq.gz
9416 15-4_117_L001_R1_001.fastq.gz
12533 15-4_117_L001_R2_001.fastq.gz
11868 15-5_118_L001_R1_001.fastq.gz
14842 15-5_118_L001_R2_001.fastq.gz
10689 15-6_119_L001_R1_001.fastq.gz
12990 15-6_119_L001_R2_001.fastq.gz
3243 1-5_6_L001_R1_001.fastq.gz
4288 1-5_6_L001_R2_001.fastq.gz
2606 15-7_120_L001_R1_001.fastq.gz
3649 15-7_120_L001_R2_001.fastq.gz
2490 15-B_113_L001_R1_001.fastq.gz
3036 15-B_113_L001_R2_001.fastq.gz
1663 16-1_122_L001_R1_001.fastq.gz
1916 16-1_122_L001_R2_001.fastq.gz
4947 16_2_147_L001_R1_001.fastq.gz
5653 16_2_147_L001_R2_001.fastq.gz
10350 16-3_124_L001_R1_001.fastq.gz
13590 16-3_124_L001_R2_001.fastq.gz
1993 16-5_125_L001_R1_001.fastq.gz
2440 16-5_125_L001_R2_001.fastq.gz
2084 16-6_126_L001_R1_001.fastq.gz
2682 16-6_126_L001_R2_001.fastq.gz
7717 16-7_127_L001_R1_001.fastq.gz
9484 16-7_127_L001_R2_001.fastq.gz
3832 1-6_7_L001_R1_001.fastq.gz
4881 1-6_7_L001_R2_001.fastq.gz
2658 16-B_121_L001_R1_001.fastq.gz
3319 16-B_121_L001_R2_001.fastq.gz
7578 17-1_129_L001_R1_001.fastq.gz
8930 17-1_129_L001_R2_001.fastq.gz
12123 17-2_130_L001_R1_001.fastq.gz
14631 17-2_130_L001_R2_001.fastq.gz
11686 17-3_131_L001_R1_001.fastq.gz
14024 17-3_131_L001_R2_001.fastq.gz
1765 17-4_132_L001_R1_001.fastq.gz
2296 17-4_132_L001_R2_001.fastq.gz
8685 17-5_134_L001_R1_001.fastq.gz
10701 17-5_134_L001_R2_001.fastq.gz
2112 17-6_133_L001_R1_001.fastq.gz
2435 17-6_133_L001_R2_001.fastq.gz
7105 17-7_135_L001_R1_001.fastq.gz
8698 17-7_135_L001_R2_001.fastq.gz
3669 1-7_8_L001_R1_001.fastq.gz
4684 1-7_8_L001_R2_001.fastq.gz
7069 17-B_128_L001_R1_001.fastq.gz
8324 17-B_128_L001_R2_001.fastq.gz
1796 18-1_137_L001_R1_001.fastq.gz
2490 18-1_137_L001_R2_001.fastq.gz
2241 18-2_138_L001_R1_001.fastq.gz
3172 18-2_138_L001_R2_001.fastq.gz
14613 18-3_139_L001_R1_001.fastq.gz
18614 18-3_139_L001_R2_001.fastq.gz
11376 18-4_140_L001_R1_001.fastq.gz
14060 18-4_140_L001_R2_001.fastq.gz
10480 18-5_141_L001_R1_001.fastq.gz
13592 18-5_141_L001_R2_001.fastq.gz
2155 18-6_142_L001_R1_001.fastq.gz
2667 18-6_142_L001_R2_001.fastq.gz
2259 18-7_143_L001_R1_001.fastq.gz
2722 18-7_143_L001_R2_001.fastq.gz
15903 18-B_136_L001_R1_001.fastq.gz
20302 18-B_136_L001_R2_001.fastq.gz
3483 19-1_148_L001_R1_001.fastq.gz
4219 19-1_148_L001_R2_001.fastq.gz
7441 19-2_146_L001_R1_001.fastq.gz
9634 19-2_146_L001_R2_001.fastq.gz
2727 19-3_147_L001_R1_001.fastq.gz
3379 19-3_147_L001_R2_001.fastq.gz
3468 19-4_148_L001_R1_001.fastq.gz
4459 19-4_148_L001_R2_001.fastq.gz
12507 19-5_149_L001_R1_001.fastq.gz
15604 19-5_149_L001_R2_001.fastq.gz
4597 19-6_150_L001_R1_001.fastq.gz
5411 19-6_150_L001_R2_001.fastq.gz
3362 19-7_151_L001_R1_001.fastq.gz
4510 19-7_151_L001_R2_001.fastq.gz
3461 19-B_144_L001_R1_001.fastq.gz
4188 19-B_144_L001_R2_001.fastq.gz
3146 1-B_1_L001_R1_001.fastq.gz
4154 1-B_1_L001_R2_001.fastq.gz
8803 20-1_153_L001_R1_001.fastq.gz
10784 20-1_153_L001_R2_001.fastq.gz
7667 20-2_154_L001_R1_001.fastq.gz
9298 20-2_154_L001_R2_001.fastq.gz
12061 20-3_155_L001_R1_001.fastq.gz
14043 20-3_155_L001_R2_001.fastq.gz
2767 20-4_156_L001_R1_001.fastq.gz
3309 20-4_156_L001_R2_001.fastq.gz
2163 20-5_157_L001_R1_001.fastq.gz
3077 20-5_157_L001_R2_001.fastq.gz
7895 20-6_158_L001_R1_001.fastq.gz
8940 20-6_158_L001_R2_001.fastq.gz
12703 20-7_159_L001_R1_001.fastq.gz
15095 20-7_159_L001_R2_001.fastq.gz
16362 20-B_152_L001_R1_001.fastq.gz
18551 20-B_152_L001_R2_001.fastq.gz
2579 2-1_10_L001_R1_001.fastq.gz
3091 2-1_10_L001_R2_001.fastq.gz
7595 21-1_161_L001_R1_001.fastq.gz
9399 21-1_161_L001_R2_001.fastq.gz
1748 21-3_163_L001_R1_001.fastq.gz
2271 21-3_163_L001_R2_001.fastq.gz
13475 21-4_164_L001_R1_001.fastq.gz
16275 21-4_164_L001_R2_001.fastq.gz
5683 21-6_166_L001_R1_001.fastq.gz
8187 21-6_166_L001_R2_001.fastq.gz
2423 21-7_167_L001_R1_001.fastq.gz
2995 21-7_167_L001_R2_001.fastq.gz
4268 21-B_160_L001_R1_001.fastq.gz
5031 21-B_160_L001_R2_001.fastq.gz
10116 22-1_169_L001_R1_001.fastq.gz
12296 22-1_169_L001_R2_001.fastq.gz
10097 2-2_11_L001_R1_001.fastq.gz
12615 2-2_11_L001_R2_001.fastq.gz
5332 22-2_170_L001_R1_001.fastq.gz
6534 22-2_170_L001_R2_001.fastq.gz
4103 22-3_150_L001_R1_001.fastq.gz
4370 22-3_150_L001_R2_001.fastq.gz
4774 22-6_151_L001_R1_001.fastq.gz
5693 22-6_151_L001_R2_001.fastq.gz
5162 22-7_152_L001_R1_001.fastq.gz
5748 22-7_152_L001_R2_001.fastq.gz
4179 22-B_149_L001_R1_001.fastq.gz
4479 22-B_149_L001_R2_001.fastq.gz
2114 2-3_12_L001_R1_001.fastq.gz
2653 2-3_12_L001_R2_001.fastq.gz
9229 2-4_13_L001_R1_001.fastq.gz
10527 2-4_13_L001_R2_001.fastq.gz
4371 2-5_140_L001_R1_001.fastq.gz
5645 2-5_140_L001_R2_001.fastq.gz
3128 2-6_15_L001_R1_001.fastq.gz
3648 2-6_15_L001_R2_001.fastq.gz
10314 2-7_16_L001_R1_001.fastq.gz
13030 2-7_16_L001_R2_001.fastq.gz
4075 2-B_9_L001_R1_001.fastq.gz
4837 2-B_9_L001_R2_001.fastq.gz
2149 3-1_18_L001_R1_001.fastq.gz
2717 3-1_18_L001_R2_001.fastq.gz
1977 3-2_19_L001_R1_001.fastq.gz
2412 3-2_19_L001_R2_001.fastq.gz
3563 3-3_20_L001_R1_001.fastq.gz
4225 3-3_20_L001_R2_001.fastq.gz
3193 3-4_21_L001_R1_001.fastq.gz
3657 3-4_21_L001_R2_001.fastq.gz
2050 3-5_22_L001_R1_001.fastq.gz
2542 3-5_22_L001_R2_001.fastq.gz
3131 3-6_23_L001_R1_001.fastq.gz
3588 3-6_23_L001_R2_001.fastq.gz
4042 3-7_24_L001_R1_001.fastq.gz
4582 3-7_24_L001_R2_001.fastq.gz
3865 3-B_17_L001_R1_001.fastq.gz
4483 3-B_17_L001_R2_001.fastq.gz
7002 4-1_26_L001_R1_001.fastq.gz
8839 4-1_26_L001_R2_001.fastq.gz
6476 4-2_27_L001_R1_001.fastq.gz
7696 4-2_27_L001_R2_001.fastq.gz
2488 4-3_28_L001_R1_001.fastq.gz
3337 4-3_28_L001_R2_001.fastq.gz
2041 4-4_29_L001_R1_001.fastq.gz
2597 4-4_29_L001_R2_001.fastq.gz
2381 4-5_30_L001_R1_001.fastq.gz
2791 4-5_30_L001_R2_001.fastq.gz
7901 4-6_31_L001_R1_001.fastq.gz
9075 4-6_31_L001_R2_001.fastq.gz
7547 4-7_32_L001_R1_001.fastq.gz
9261 4-7_32_L001_R2_001.fastq.gz
7450 4-B_25_L001_R1_001.fastq.gz
9207 4-B_25_L001_R2_001.fastq.gz
2302 5-1_34_L001_R1_001.fastq.gz
2853 5-1_34_L001_R2_001.fastq.gz
10316 5-2_35_L001_R1_001.fastq.gz
12591 5-2_35_L001_R2_001.fastq.gz
1793 5-3_36_L001_R1_001.fastq.gz
2170 5-3_36_L001_R2_001.fastq.gz
1561 5-4_37_L001_R1_001.fastq.gz
1984 5-4_37_L001_R2_001.fastq.gz
9097 5-5_38_L001_R1_001.fastq.gz
12464 5-5_38_L001_R2_001.fastq.gz
1879 5-6_39_L001_R1_001.fastq.gz
2415 5-6_39_L001_R2_001.fastq.gz
2281 5-7_40_L001_R1_001.fastq.gz
3412 5-7_40_L001_R2_001.fastq.gz
3083 5-B_33_L001_R1_001.fastq.gz
3882 5-B_33_L001_R2_001.fastq.gz
1740 6-1_42_L001_R1_001.fastq.gz
2275 6-1_42_L001_R2_001.fastq.gz
1413 6-3_44_L001_R1_001.fastq.gz
1766 6-3_44_L001_R2_001.fastq.gz
8332 6-4_45_L001_R1_001.fastq.gz
10471 6-4_45_L001_R2_001.fastq.gz
4905 6-5_46_L001_R1_001.fastq.gz
6234 6-5_46_L001_R2_001.fastq.gz
2297 6-6_47_L001_R1_001.fastq.gz
2704 6-6_47_L001_R2_001.fastq.gz
1832 6-7_48_L001_R1_001.fastq.gz
2495 6-7_48_L001_R2_001.fastq.gz
1460 6-B_41_L001_R1_001.fastq.gz
1836 6-B_41_L001_R2_001.fastq.gz
4443 7-1_141_L001_R1_001.fastq.gz
10454 7-1_141_L001_R2_001.fastq.gz
11342 7-3_52_L001_R1_001.fastq.gz
14601 7-3_52_L001_R2_001.fastq.gz
11362 7-4_53_L001_R1_001.fastq.gz
14225 7-4_53_L001_R2_001.fastq.gz
1532 7-5_54_L001_R1_001.fastq.gz
2184 7-5_54_L001_R2_001.fastq.gz
7172 7-7_56_L001_R1_001.fastq.gz
8914 7-7_56_L001_R2_001.fastq.gz
7462 7-B_49_L001_R1_001.fastq.gz
9358 7-B_49_L001_R2_001.fastq.gz
12833 8-2_59_L001_R1_001.fastq.gz
15666 8-2_59_L001_R2_001.fastq.gz
12295 8-3_60_L001_R1_001.fastq.gz
14453 8-3_60_L001_R2_001.fastq.gz
32711 8-4_61_L001_R1_001.fastq.gz
40269 8-4_61_L001_R2_001.fastq.gz
3616 8-6_143_L001_R1_001.fastq.gz
4245 8-6_143_L001_R2_001.fastq.gz
8531 8-7_64_L001_R1_001.fastq.gz
10518 8-7_64_L001_R2_001.fastq.gz
2899 8-B_142_L001_R1_001.fastq.gz
3227 8-B_142_L001_R2_001.fastq.gz
8861 9-2_67_L001_R1_001.fastq.gz
10660 9-2_67_L001_R2_001.fastq.gz
4243 9-3_68_L001_R1_001.fastq.gz
5066 9-3_68_L001_R2_001.fastq.gz
10135 9-4_69_L001_R1_001.fastq.gz
12186 9-4_69_L001_R2_001.fastq.gz
8069 9-5_70_L001_R1_001.fastq.gz
10039 9-5_70_L001_R2_001.fastq.gz
11678 9-6_71_L001_R1_001.fastq.gz
13727 9-6_71_L001_R2_001.fastq.gz
14466 9-7_72_L001_R1_001.fastq.gz
17243 9-7_72_L001_R2_001.fastq.gz
3929 9-B_65_L001_R1_001.fastq.gz
4603 9-B_65_L001_R2_001.fastq.gz
Any ideas what the issue is and how to fix it?
Thanks!
