Deblur paired-end sequences empty output

Jaroslaw_Grzadziel · December 1, 2017, 8:13pm

After migration to the 2017.11 version I tried to deblur my paired-end illumina files (V3-V4).
I went through community tutorial: analyzing paired-end reads in qiime 2 and after:

qiime deblur denoise-16S \
  --i-demultiplexed-seqs demux-joined-filtered.qza \
  --p-trim-length 250 \
  --o-representative-sequences rep-seqs.qza \
  --o-table table.qza \
  --p-sample-stats \
  --o-stats deblur-stats.qza

I realized that output artifacts: rep-seqs.qza, table.qza are empty.

The very same files were successfully analyzed through DADA2 in 2017.10 qiime2.

Here's deblur log:

INFO(140236079888128)2017-12-01 14:09:28,274:*************************
INFO(140236079888128)2017-12-01 14:09:28,275:deblurring started
WARNING(140236079888128)2017-12-01 14:09:28,275:deblur version 1.0.3 workflow started on /tmp/qiime2-archive-3llb9qks/b055dc96-e416-488b-a725-91ab141898dc/data
WARNING(140236079888128)2017-12-01 14:09:28,275:parameters: {'pos_ref_fp': (), 'log_level': 2, 'overwrite': True, 'output_dir': '/tmp/tmpu_e8m2e5', 'min_reads': 10, 'neg_ref_fp': (), 'seqs_fp': '/tmp/qiime2-archive-3llb9qks/b055dc96-e416-488b-a725-91ab141898dc/data', 'keep_tmp_files': True, 'pos_ref_db_fp': (), 'trim_length': 250, 'indel_prob': 0.01, 'indel_max': 3, 'jobs_to_start': 1, 'mean_error': 0.005, 'threads_per_sample': 1, 'neg_ref_db_fp': (), 'logger': <logging.Logger object at 0x7f8b1cd351d0>, 'is_worker_thread': None, 'error_dist': [1, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'log_file': '/home/qiime2/mojetesty/deblur.log', 'left_trim_length': 0, 'min_size': 2}
INFO(140236079888128)2017-12-01 14:09:28,275:error_dist is : [1, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005]
INFO(140236079888128)2017-12-01 14:09:28,275:deblur main program started
INFO(140236079888128)2017-12-01 14:09:28,275:processing directory /tmp/qiime2-archive-3llb9qks/b055dc96-e416-488b-a725-91ab141898dc/data
INFO(140236079888128)2017-12-01 14:09:28,279:building negative db sortmerna index files
INFO(140236079888128)2017-12-01 14:09:28,279:build_index_sortmerna files ['/home/qiime2/miniconda/envs/qiime2-2017.11/lib/python3.5/site-packages/deblur/support_files/artifacts.fa'] to dir /tmp/tmpu_e8m2e5/deblur_working_dir
INFO(140236079888128)2017-12-01 14:09:28,369:building positive db sortmerna index files
INFO(140236079888128)2017-12-01 14:09:28,370:build_index_sortmerna files ['/home/qiime2/miniconda/envs/qiime2-2017.11/lib/python3.5/site-packages/deblur/support_files/88_otus.fasta'] to dir /tmp/tmpu_e8m2e5/deblur_working_dir
INFO(140236079888128)2017-12-01 14:10:41,315:processing per sample fasta files
INFO(140236079888128)2017-12-01 14:10:41,316:--------------------------------------------------------
INFO(140236079888128)2017-12-01 14:10:41,319:launch_workflow for file /tmp/qiime2-archive-3llb9qks/b055dc96-e416-488b-a725-91ab141898dc/data/MZ2_1_L001_R1_001.fastq.gz
INFO(140236079888128)2017-12-01 14:12:44,451:dereplicate seqs file /tmp/tmpu_e8m2e5/deblur_working_dir/MZ2_1_L001_R1_001.fastq.gz.trim
INFO(140236079888128)2017-12-01 14:12:44,748:remove_artifacts_seqs file /tmp/tmpu_e8m2e5/deblur_working_dir/MZ2_1_L001_R1_001.fastq.gz.trim.derep
INFO(140236079888128)2017-12-01 14:12:46,587:total sequences 9283, passing sequences 9283, failing sequences 0
INFO(140236079888128)2017-12-01 14:12:46,587:multiple_sequence_alignment seqs file /tmp/tmpu_e8m2e5/deblur_working_dir/MZ2_1_L001_R1_001.fastq.gz.trim.derep.no_artifacts
INFO(140236079888128)2017-12-01 14:18:45,360:deblurring 9283 sequences
INFO(140236079888128)2017-12-01 14:25:18,625:6720 unique sequences left following deblurring
INFO(140236079888128)2017-12-01 14:25:19,109:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpu_e8m2e5/deblur_working_dir/MZ2_1_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpu_e8m2e5/deblur_working_dir
INFO(140236079888128)2017-12-01 14:25:26,861:finished processing file
INFO(140236079888128)2017-12-01 14:25:26,880:--------------------------------------------------------
INFO(140236079888128)2017-12-01 14:25:26,880:launch_workflow for file /tmp/qiime2-archive-3llb9qks/b055dc96-e416-488b-a725-91ab141898dc/data/MZ1_0_L001_R1_001.fastq.gz
INFO(140236079888128)2017-12-01 14:27:51,528:dereplicate seqs file /tmp/tmpu_e8m2e5/deblur_working_dir/MZ1_0_L001_R1_001.fastq.gz.trim
INFO(140236079888128)2017-12-01 14:27:51,871:remove_artifacts_seqs file /tmp/tmpu_e8m2e5/deblur_working_dir/MZ1_0_L001_R1_001.fastq.gz.trim.derep
INFO(140236079888128)2017-12-01 14:27:53,291:total sequences 6532, passing sequences 6532, failing sequences 0
INFO(140236079888128)2017-12-01 14:27:53,291:multiple_sequence_alignment seqs file /tmp/tmpu_e8m2e5/deblur_working_dir/MZ1_0_L001_R1_001.fastq.gz.trim.derep.no_artifacts
INFO(140236079888128)2017-12-01 14:30:47,598:deblurring 6532 sequences
INFO(140236079888128)2017-12-01 14:33:32,608:4039 unique sequences left following deblurring
INFO(140236079888128)2017-12-01 14:33:32,849:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpu_e8m2e5/deblur_working_dir/MZ1_0_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpu_e8m2e5/deblur_working_dir
INFO(140236079888128)2017-12-01 14:33:36,359:finished processing file
INFO(140236079888128)2017-12-01 14:33:36,370:--------------------------------------------------------
INFO(140236079888128)2017-12-01 14:33:36,370:launch_workflow for file /tmp/qiime2-archive-3llb9qks/b055dc96-e416-488b-a725-91ab141898dc/data/MZ4_3_L001_R1_001.fastq.gz
INFO(140236079888128)2017-12-01 14:36:18,796:dereplicate seqs file /tmp/tmpu_e8m2e5/deblur_working_dir/MZ4_3_L001_R1_001.fastq.gz.trim
INFO(140236079888128)2017-12-01 14:36:19,172:remove_artifacts_seqs file /tmp/tmpu_e8m2e5/deblur_working_dir/MZ4_3_L001_R1_001.fastq.gz.trim.derep
INFO(140236079888128)2017-12-01 14:36:20,794:total sequences 9593, passing sequences 9593, failing sequences 0
INFO(140236079888128)2017-12-01 14:36:20,794:multiple_sequence_alignment seqs file /tmp/tmpu_e8m2e5/deblur_working_dir/MZ4_3_L001_R1_001.fastq.gz.trim.derep.no_artifacts
INFO(140236079888128)2017-12-01 14:42:39,802:deblurring 9593 sequences
INFO(140236079888128)2017-12-01 14:49:07,302:6403 unique sequences left following deblurring
INFO(140236079888128)2017-12-01 14:49:07,710:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpu_e8m2e5/deblur_working_dir/MZ4_3_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpu_e8m2e5/deblur_working_dir
INFO(140236079888128)2017-12-01 14:49:12,998:finished processing file
INFO(140236079888128)2017-12-01 14:49:13,016:--------------------------------------------------------
INFO(140236079888128)2017-12-01 14:49:13,016:launch_workflow for file /tmp/qiime2-archive-3llb9qks/b055dc96-e416-488b-a725-91ab141898dc/data/MZ3_2_L001_R1_001.fastq.gz
INFO(140236079888128)2017-12-01 14:51:14,955:dereplicate seqs file /tmp/tmpu_e8m2e5/deblur_working_dir/MZ3_2_L001_R1_001.fastq.gz.trim
INFO(140236079888128)2017-12-01 14:51:15,269:remove_artifacts_seqs file /tmp/tmpu_e8m2e5/deblur_working_dir/MZ3_2_L001_R1_001.fastq.gz.trim.derep
INFO(140236079888128)2017-12-01 14:51:16,784:total sequences 8654, passing sequences 8654, failing sequences 0
INFO(140236079888128)2017-12-01 14:51:16,784:multiple_sequence_alignment seqs file /tmp/tmpu_e8m2e5/deblur_working_dir/MZ3_2_L001_R1_001.fastq.gz.trim.derep.no_artifacts
INFO(140236079888128)2017-12-01 14:56:16,058:deblurring 8654 sequences
INFO(140236079888128)2017-12-01 15:01:25,263:5814 unique sequences left following deblurring
INFO(140236079888128)2017-12-01 15:01:25,626:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpu_e8m2e5/deblur_working_dir/MZ3_2_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpu_e8m2e5/deblur_working_dir
INFO(140236079888128)2017-12-01 15:01:30,389:finished processing file
INFO(140236079888128)2017-12-01 15:01:30,404:--------------------------------------------------------
INFO(140236079888128)2017-12-01 15:01:30,404:launch_workflow for file /tmp/qiime2-archive-3llb9qks/b055dc96-e416-488b-a725-91ab141898dc/data/MZ7_6_L001_R1_001.fastq.gz
INFO(140236079888128)2017-12-01 15:03:26,741:dereplicate seqs file /tmp/tmpu_e8m2e5/deblur_working_dir/MZ7_6_L001_R1_001.fastq.gz.trim
INFO(140236079888128)2017-12-01 15:03:27,046:remove_artifacts_seqs file /tmp/tmpu_e8m2e5/deblur_working_dir/MZ7_6_L001_R1_001.fastq.gz.trim.derep
INFO(140236079888128)2017-12-01 15:03:28,621:total sequences 9616, passing sequences 9616, failing sequences 0
INFO(140236079888128)2017-12-01 15:03:28,621:multiple_sequence_alignment seqs file /tmp/tmpu_e8m2e5/deblur_working_dir/MZ7_6_L001_R1_001.fastq.gz.trim.derep.no_artifacts
INFO(140236079888128)2017-12-01 15:09:50,986:deblurring 9616 sequences
INFO(140236079888128)2017-12-01 15:16:51,757:7245 unique sequences left following deblurring
INFO(140236079888128)2017-12-01 15:16:52,233:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpu_e8m2e5/deblur_working_dir/MZ7_6_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpu_e8m2e5/deblur_working_dir
INFO(140236079888128)2017-12-01 15:16:58,114:finished processing file
INFO(140236079888128)2017-12-01 15:16:58,131:--------------------------------------------------------
INFO(140236079888128)2017-12-01 15:16:58,131:launch_workflow for file /tmp/qiime2-archive-3llb9qks/b055dc96-e416-488b-a725-91ab141898dc/data/MZ8_7_L001_R1_001.fastq.gz
INFO(140236079888128)2017-12-01 15:19:48,979:dereplicate seqs file /tmp/tmpu_e8m2e5/deblur_working_dir/MZ8_7_L001_R1_001.fastq.gz.trim
INFO(140236079888128)2017-12-01 15:19:49,318:remove_artifacts_seqs file /tmp/tmpu_e8m2e5/deblur_working_dir/MZ8_7_L001_R1_001.fastq.gz.trim.derep
INFO(140236079888128)2017-12-01 15:19:50,694:total sequences 7038, passing sequences 7038, failing sequences 0
INFO(140236079888128)2017-12-01 15:19:50,694:multiple_sequence_alignment seqs file /tmp/tmpu_e8m2e5/deblur_working_dir/MZ8_7_L001_R1_001.fastq.gz.trim.derep.no_artifacts
INFO(140236079888128)2017-12-01 15:22:57,395:deblurring 7038 sequences
INFO(140236079888128)2017-12-01 15:25:34,167:3732 unique sequences left following deblurring
INFO(140236079888128)2017-12-01 15:25:34,368:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpu_e8m2e5/deblur_working_dir/MZ8_7_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpu_e8m2e5/deblur_working_dir
INFO(140236079888128)2017-12-01 15:25:37,330:finished processing file
INFO(140236079888128)2017-12-01 15:25:37,339:--------------------------------------------------------
INFO(140236079888128)2017-12-01 15:25:37,339:launch_workflow for file /tmp/qiime2-archive-3llb9qks/b055dc96-e416-488b-a725-91ab141898dc/data/MZ5_4_L001_R1_001.fastq.gz
INFO(140236079888128)2017-12-01 15:27:46,895:dereplicate seqs file /tmp/tmpu_e8m2e5/deblur_working_dir/MZ5_4_L001_R1_001.fastq.gz.trim
INFO(140236079888128)2017-12-01 15:27:47,328:remove_artifacts_seqs file /tmp/tmpu_e8m2e5/deblur_working_dir/MZ5_4_L001_R1_001.fastq.gz.trim.derep
INFO(140236079888128)2017-12-01 15:27:48,837:total sequences 9020, passing sequences 9020, failing sequences 0
INFO(140236079888128)2017-12-01 15:27:48,837:multiple_sequence_alignment seqs file /tmp/tmpu_e8m2e5/deblur_working_dir/MZ5_4_L001_R1_001.fastq.gz.trim.derep.no_artifacts
INFO(140236079888128)2017-12-01 15:32:49,259:deblurring 9020 sequences
INFO(140236079888128)2017-12-01 15:36:55,357:4605 unique sequences left following deblurring
INFO(140236079888128)2017-12-01 15:36:55,627:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpu_e8m2e5/deblur_working_dir/MZ5_4_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpu_e8m2e5/deblur_working_dir
INFO(140236079888128)2017-12-01 15:36:59,269:finished processing file
INFO(140236079888128)2017-12-01 15:36:59,282:--------------------------------------------------------
INFO(140236079888128)2017-12-01 15:36:59,282:launch_workflow for file /tmp/qiime2-archive-3llb9qks/b055dc96-e416-488b-a725-91ab141898dc/data/MZ6_5_L001_R1_001.fastq.gz
INFO(140236079888128)2017-12-01 15:39:08,787:dereplicate seqs file /tmp/tmpu_e8m2e5/deblur_working_dir/MZ6_5_L001_R1_001.fastq.gz.trim
INFO(140236079888128)2017-12-01 15:39:09,124:remove_artifacts_seqs file /tmp/tmpu_e8m2e5/deblur_working_dir/MZ6_5_L001_R1_001.fastq.gz.trim.derep
INFO(140236079888128)2017-12-01 15:39:10,440:total sequences 7188, passing sequences 7188, failing sequences 0
INFO(140236079888128)2017-12-01 15:39:10,440:multiple_sequence_alignment seqs file /tmp/tmpu_e8m2e5/deblur_working_dir/MZ6_5_L001_R1_001.fastq.gz.trim.derep.no_artifacts
INFO(140236079888128)2017-12-01 15:42:23,348:deblurring 7188 sequences
INFO(140236079888128)2017-12-01 15:45:19,407:4186 unique sequences left following deblurring
INFO(140236079888128)2017-12-01 15:45:19,642:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpu_e8m2e5/deblur_working_dir/MZ6_5_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpu_e8m2e5/deblur_working_dir
INFO(140236079888128)2017-12-01 15:45:22,888:finished processing file
INFO(140236079888128)2017-12-01 15:45:22,898:finished processing per sample fasta files
INFO(140236079888128)2017-12-01 15:45:22,899:create_otu_table for 8 samples, into output table /tmp/tmpu_e8m2e5/all.biom
INFO(140236079888128)2017-12-01 15:45:25,150:for output biom table loaded 8 samples, 29097 unique sequences
INFO(140236079888128)2017-12-01 15:45:25,177:keeping 3916 (out of 29097 sequences) with >=10 reads
INFO(140236079888128)2017-12-01 15:45:25,485:saved to biom file /tmp/tmpu_e8m2e5/all.biom
INFO(140236079888128)2017-12-01 15:45:25,500:saved sequence fasta file to /tmp/tmpu_e8m2e5/all.seqs.fa
INFO(140236079888128)2017-12-01 15:45:25,514:getting 16s sequences from the biom table
INFO(140236079888128)2017-12-01 15:45:25,515:remove_artifacts_seqs file /tmp/tmpu_e8m2e5/all.seqs.fa
INFO(140236079888128)2017-12-01 15:45:29,263:total sequences 3916, passing sequences 0, failing sequences 3916
WARNING(140236079888128)2017-12-01 15:45:29,264:input file /tmp/tmpu_e8m2e5/all.seqs.fa.no_artifacts does not appear to be FASTA or FASTQ
INFO(140236079888128)2017-12-01 15:45:29,357:wrote artifact only filtered biom table to /tmp/tmpu_e8m2e5/reference-non-hit.biom
INFO(140236079888128)2017-12-01 15:45:29,366:saved biom table sequences to fasta file /tmp/tmpu_e8m2e5/reference-non-hit.seqs.fa
WARNING(140236079888128)2017-12-01 15:45:29,367:removed 8 samples with reads per sample<1
INFO(140236079888128)2017-12-01 15:45:29,373:wrote 16s filtered biom table to /tmp/tmpu_e8m2e5/reference-hit.biom
INFO(140236079888128)2017-12-01 15:45:29,373:saved biom table sequences to fasta file /tmp/tmpu_e8m2e5/reference-hit.seqs.fa
INFO(140236079888128)2017-12-01 15:45:29,373:Keeping temp files
INFO(140236079888128)2017-12-01 15:45:29,373:deblur workflow finished
INFO(140236079888128)2017-12-01 15:45:29,373:output saved to /tmp/tmpu_e8m2e5/all.biom
INFO(140236079888128)2017-12-01 15:45:29,373:------------------
INFO(139821597878016)2017-12-01 17:28:33,907:*************************
INFO(139821597878016)2017-12-01 17:28:33,907:deblurring started
WARNING(139821597878016)2017-12-01 17:28:33,907:deblur version 1.0.3 workflow started on /tmp/qiime2-archive-frx43cf2/b055dc96-e416-488b-a725-91ab141898dc/data
WARNING(139821597878016)2017-12-01 17:28:33,907:parameters: {'log_file': '/home/qiime2/mojetesty/deblur.log', 'min_reads': 10, 'is_worker_thread': None, 'log_level': 2, 'logger': <logging.Logger object at 0x7f2a9bc3c588>, 'pos_ref_fp': (), 'pos_ref_db_fp': (), 'output_dir': '/tmp/tmp0_2z1sef', 'overwrite': True, 'trim_length': 250, 'jobs_to_start': 1, 'keep_tmp_files': True, 'indel_prob': 0.01, 'min_size': 2, 'error_dist': [1, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'mean_error': 0.005, 'indel_max': 3, 'threads_per_sample': 1, 'left_trim_length': 0, 'seqs_fp': '/tmp/qiime2-archive-frx43cf2/b055dc96-e416-488b-a725-91ab141898dc/data', 'neg_ref_db_fp': (), 'neg_ref_fp': ()}
INFO(139821597878016)2017-12-01 17:28:33,908:error_dist is : [1, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005]
INFO(139821597878016)2017-12-01 17:28:33,908:deblur main program started
INFO(139821597878016)2017-12-01 17:28:33,908:processing directory /tmp/qiime2-archive-frx43cf2/b055dc96-e416-488b-a725-91ab141898dc/data
INFO(139821597878016)2017-12-01 17:28:33,910:building negative db sortmerna index files
INFO(139821597878016)2017-12-01 17:28:33,910:build_index_sortmerna files ['/home/qiime2/miniconda/envs/qiime2-2017.11/lib/python3.5/site-packages/deblur/support_files/artifacts.fa'] to dir /tmp/tmp0_2z1sef/deblur_working_dir
INFO(139821597878016)2017-12-01 17:28:33,990:building positive db sortmerna index files
INFO(139821597878016)2017-12-01 17:28:33,991:build_index_sortmerna files ['/home/qiime2/miniconda/envs/qiime2-2017.11/lib/python3.5/site-packages/deblur/support_files/88_otus.fasta'] to dir /tmp/tmp0_2z1sef/deblur_working_dir
INFO(139970853230336)2017-12-01 17:29:44,164:*************************
INFO(139970853230336)2017-12-01 17:29:44,164:deblurring started
WARNING(139970853230336)2017-12-01 17:29:44,164:deblur version 1.0.3 workflow started on /tmp/qiime2-archive-l7b177tm/b055dc96-e416-488b-a725-91ab141898dc/data
WARNING(139970853230336)2017-12-01 17:29:44,164:parameters: {'logger': <logging.Logger object at 0x7f4d5c13e630>, 'min_reads': 10, 'keep_tmp_files': True, 'pos_ref_fp': (), 'seqs_fp': '/tmp/qiime2-archive-l7b177tm/b055dc96-e416-488b-a725-91ab141898dc/data', 'left_trim_length': 0, 'output_dir': '/tmp/tmpsr2gx2vo', 'neg_ref_db_fp': (), 'trim_length': 250, 'threads_per_sample': 1, 'indel_max': 3, 'is_worker_thread': None, 'log_level': 2, 'pos_ref_db_fp': (), 'mean_error': 0.005, 'jobs_to_start': 1, 'log_file': '/home/qiime2/mojetesty/deblur.log', 'indel_prob': 0.01, 'min_size': 2, 'neg_ref_fp': (), 'overwrite': True, 'error_dist': [1, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005]}
INFO(139970853230336)2017-12-01 17:29:44,164:error_dist is : [1, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005]
INFO(139970853230336)2017-12-01 17:29:44,164:deblur main program started
INFO(139970853230336)2017-12-01 17:29:44,164:processing directory /tmp/qiime2-archive-l7b177tm/b055dc96-e416-488b-a725-91ab141898dc/data
INFO(139970853230336)2017-12-01 17:29:44,166:building negative db sortmerna index files
INFO(139970853230336)2017-12-01 17:29:44,167:build_index_sortmerna files ['/home/qiime2/miniconda/envs/qiime2-2017.11/lib/python3.5/site-packages/deblur/support_files/artifacts.fa'] to dir /tmp/tmpsr2gx2vo/deblur_working_dir
INFO(139970853230336)2017-12-01 17:29:44,224:building positive db sortmerna index files
INFO(139970853230336)2017-12-01 17:29:44,224:build_index_sortmerna files ['/home/qiime2/miniconda/envs/qiime2-2017.11/lib/python3.5/site-packages/deblur/support_files/88_otus.fasta'] to dir /tmp/tmpsr2gx2vo/deblur_working_dir
INFO(139970853230336)2017-12-01 17:30:51,194:processing per sample fasta files
INFO(139970853230336)2017-12-01 17:30:51,194:--------------------------------------------------------
INFO(139970853230336)2017-12-01 17:30:51,194:launch_workflow for file /tmp/qiime2-archive-l7b177tm/b055dc96-e416-488b-a725-91ab141898dc/data/MZ2_1_L001_R1_001.fastq.gz
INFO(139970853230336)2017-12-01 17:32:47,292:dereplicate seqs file /tmp/tmpsr2gx2vo/deblur_working_dir/MZ2_1_L001_R1_001.fastq.gz.trim
INFO(139970853230336)2017-12-01 17:32:47,622:remove_artifacts_seqs file /tmp/tmpsr2gx2vo/deblur_working_dir/MZ2_1_L001_R1_001.fastq.gz.trim.derep
INFO(139970853230336)2017-12-01 17:32:49,255:total sequences 9283, passing sequences 9283, failing sequences 0
INFO(139970853230336)2017-12-01 17:32:49,255:multiple_sequence_alignment seqs file /tmp/tmpsr2gx2vo/deblur_working_dir/MZ2_1_L001_R1_001.fastq.gz.trim.derep.no_artifacts

Thanks

colinbrislawn · December 1, 2017, 8:37pm

Good afternoon,

This line caught my eye.

I wonder if your 'deblured' features are less then 250 bp long. That might conflict with --p-trim-length 250 setting.

Jaroslaw_Grzadziel · December 1, 2017, 9:26pm

I will try to set --p-trim-length 250 different values and check if this was an issue. I will post a result tomorrow.
Thank you for advise

Jaroslaw_Grzadziel · December 4, 2017, 3:52pm

Hello,
Suprisingly the fastq files were corrupted after migration from 2017.10 to 2017.11 version, I don’t know why, but now I restored original ones, and everything is working .

To sum up: It was my mistake, not qiime2 error
Thanks everyone

thermokarst · December 4, 2017, 3:56pm

Hi @Jaroslaw_Grzadziel - thanks for the update! Can I ask though, what do you mean here:

How were your files "corrupted"? Something doesn't sound quite right here - QIIME 2 Artifacts have some pretty excellent backwards-compatible guarantees, and once an Artifact is created, it is immutable, and is never modified or edited (by QIIME 2, at least). This is part of how we make things like provenance happen! Anyway, if you have any additional info here about what happened, that would be really helpful!

Jaroslaw_Grzadziel · December 5, 2017, 1:29pm

Actually my fastq.gz files were corrupted, not artifacts. I don't know which step exactly caused this situation, but I realized that my fastq.gz files had a different size after copying them from previous to a new virtual machine. I removed them and copied again directly from the primary disk, run analysis from the scratch, and everytching was fine.

system · January 5, 2018, 7:30pm

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