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_single.R /tmp/qiime2-archive-t9e3qsd0/dd839035-be1a-49d9-b53b-2b3b581ffad4/data /tmp/tmpnv22zkiq/ output.tsv.biom /tmp/tmpnv22zkiq 120 0 2.0 2 consensus 1.0 0 1000000 R version 3.4.1 (2017-06-30) Loading required package: Rcpp DADA2 R package version: 1.6.0 1) Filtering The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2000.052.EMP1_2047_L001_R1_001.fastq.gz not writt en. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2000.060.EMP1_2055_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2003.182.EMP1_2369_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2005.024.EMP1_2619_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2004.008.EMP1_2425_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2004.045.EMP1_2456_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2005.096.EMP1_2678_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2005.017.EMP1_2612_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2005.077.EMP1_2659_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2004.048.EMP1_2459_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2006.129.EMP1_2843_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2007.044.EMP1_3011_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2006.106.EMP1_2820_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2007.046.EMP1_3013_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2007.095.EMP1_3062_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2007.053.EMP1_3020_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2007.039.EMP1_3006_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2007.068.EMP1_3035_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2007.238.EMP2_3205_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2007.267.EMP2_3234_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2007.258.EMP2_3225_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2007.314.EMP2_3281_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2007.041.EMP1_3008_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2008.357.EMP2_3812_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2008.069.EMP2_3550_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2008.131.EMP2_3612_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2008.251.EMP2_3707_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2008.278.EMP2_3733_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2008.432.EMP2_3887_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2008.369.EMP2_3824_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.078.EMP3_4503_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2008.450.EMP2_3905_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2008.411.EMP2_3866_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.025.EMP3_4450_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.005.EMP3_4430_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.036.EMP3_4461_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.120.EMP3_4545_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.132.EMP3_4557_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.064.EMP3_4489_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.071.EMP3_4496_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.124.EMP3_4549_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.220.EMP3_4644_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.057.EMP3_4482_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.117.EMP3_4542_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.206.EMP3_4630_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.166.EMP3_4591_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.074.EMP3_4499_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2011.103.EMP3_4914_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.018.EMP3_4443_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.065.EMP3_4490_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.040.EMP3_4465_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.086.EMP3_4511_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.048.EMP3_4473_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.272.EMP3_4695_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.094.EMP3_4519_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.029.EMP3_4454_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.023.EMP3_4448_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.087.EMP3_4512_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.050.EMP3_4475_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.237.EMP3_4660_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.081.EMP3_4506_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2011.332.EMP4_5110_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.024.EMP3_4449_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.088.EMP3_4513_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.265.EMP3_4688_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.039.EMP3_4464_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.046.EMP3_4471_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.033.EMP3_4458_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.288.EMP3_4711_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.067.EMP3_4492_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.122.EMP3_4547_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.028.EMP3_4453_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.059.EMP3_4484_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.118.EMP3_4543_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.061.EMP3_4486_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.038.EMP3_4463_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.194.EMP3_4619_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.262.EMP3_4685_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.185.EMP3_4610_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.247.EMP3_4670_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.091.EMP3_4516_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.175.EMP3_4600_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.082.EMP3_4507_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.031.EMP3_4456_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.095.EMP3_4520_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.053.EMP3_4478_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.284.EMP3_4707_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2011.390.EMP4_5147_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2011.516.EMP4_5255_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.279.EMP3_4702_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.049.EMP3_4474_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2011.510.EMP4_5249_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.280.EMP3_4703_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.199.EMP3_4624_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2011.392.EMP4_5148_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.045.EMP3_4470_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2011.396.EMP4_5150_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2011.508.EMP4_5247_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2011.400.EMP4_5152_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2011.517.EMP4_5256_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2010.047.EMP3_4472_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2011.514.EMP4_5253_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2011.511.EMP4_5250_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2011.520.EMP4_5259_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2011.342.EMP4_5115_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2011.504.EMP4_5243_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2011.340.EMP4_5114_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2011.548.EMP4_5287_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2011.503.EMP4_5242_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2011.512.EMP4_5251_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2011.513.EMP4_5252_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2011.515.EMP4_5254_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2011.518.EMP4_5257_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2011.555.EMP4_5294_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2011.371.EMP4_5132_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2011.521.EMP4_5260_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2013.337.89_695_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.2011.556.EMP4_5295_L001_R1_001.fastq.gz not written. The filter removed all reads: /tmp/tmpnv22zkiq/ltreb.blankplate1.89_1986_L001_R1_001.fastq.gz not written. Some input samples had no reads pass the filter. ...............................................x.......x........................................................... ................................................................................................................... ................................................................................................................... ............................x.......................................................x.............................. x..x............................................................................................................... ..........................................x......x.......................................x..................x...... ................................................................................................................... ..................................x...................................x............................................ 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xx..x..xx.........................x.x...x...x...x.............x.................................................... .x...............x.........x........x....x.....x.............x...............x.............x....................... ......x.....x..........x.........xx...x....x....................................................................... ................................................................................................................... ...................................x............................................................................... ................................................................................................................... ................x...xx................x..............xx.x.x........................................................ .................................xx...x.xxxxxxxxx.xx..........................x......xx............................ 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................................................................................................................... ................................................................................................................... ................................................................................................................... ................................................................................................................... ................................................................................................................... ..................................................................................................................x ................. 2) Learning Error Rates Error in dada(drps[1:i], err = NULL, selfConsist = TRUE, multithread = multithread, : Invalid derep$quals matrix. Quality values must be positive integers. Execution halted Traceback (most recent call last): File "/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 126, in denoise_sing le run_commands([cmd]) File "/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 35, in run_commands subprocess.run(cmd, check=True) File "/miniconda/envs/qiime2-2017.12/lib/python3.5/subprocess.py", line 398, in run output=stdout, stderr=stderr) subprocess.CalledProcessError: Command '['run_dada_single.R', '/tmp/qiime2-archive-t9e3qsd0/dd839035-be1a-49d9-b53b -2b3b581ffad4/data', '/tmp/tmpnv22zkiq/output.tsv.biom', '/tmp/tmpnv22zkiq', '120', '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 "/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/q2cli/commands.py", line 224, in __call__ results = action(**arguments) File "", line 2, in denoise_single File "/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/action.py", line 228, in bound_callab le output_types, provenance) File "/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/action.py", line 363, in _callable_ex ecutor_ output_views = self._callable(**view_args) File "/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 137, in denoise_sing le " 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 l earn more.