Hi,
I attempted to run deblur on my joined-read data (“Result vsjoin.qza appears to be valid at level=max.”)
I was given the next error message:
Városi Vadvizek Vizsgálata
Plugin error from deblur:
*** Deblur cannot operate on sample IDs that contain underscores. The following ID(s) contain one or more underscores: DB-05-S81_L001, DB-06-S25_L001, DB-07-S2_L001, DB-08-S34_L001, DB-09-S23_L001, DBA-05-S78_L001, DBA-06-S11_L001, DBA-07-S38_L001, DBA-08-S24_L001, DBA-09-…***
I am now stuck., pls give me a hint!
First I believed that it is like that dada2 does not accept my sample with 46 character long read names that come from the MySeq machine so 1st I must always rename all reads to less than 40 characters. So, I almost started renaming my sample files and updating the metadata file, to start up the whole pipeline again, when it came to my mind that I already used deblur a month ago on underscore-containing filenames. So this Error Message may not even be true. I have even found the deblur log from that time, which says:
"
more deblur.log
INFO(140639269128000)2019-10-11 16:18:50,532:*************************
INFO(140639269128000)2019-10-11 16:18:50,532:deblurring started
WARNING(140639269128000)2019-10-11 16:18:50,532:deblur version 1.1.0 workflow started on /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-dpwmebh7
WARNING(140639269128000)2019-10-11 16:18:50,532:parameters: {‘logger’: <Logger main (INFO)>, ‘is_worker_thread’: None, ‘jobs_to_start’: 1, ‘log_file’: ‘/mnt/sda1/home/kp/old.duna/deblur.log’, ‘log_level’
: 2, ‘keep_tmp_files’: None, ‘threads_per_sample’: 1, ‘min_size’: 2, ‘min_reads’: 10, ‘left_trim_length’: 0, ‘trim_length’: 249, ‘indel_max’: 3, ‘indel_prob’: 0.01, ‘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, ‘overwrite’: True, ‘neg_ref_db_fp’: (), ‘neg_ref_fp’: (), ‘pos_ref_db_fp’: (), ‘pos_ref_fp’: (), ‘output_dir’: ‘/tmp/tmpk1t0rc4u’, ‘seq
s_fp’: ‘/tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-dpwmebh7’}
INFO(140639269128000)2019-10-11 16:18:50,532: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(140639269128000)2019-10-11 16:18:50,532:deblur main program started
INFO(140639269128000)2019-10-11 16:18:50,532:processing directory /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-dpwmebh7
INFO(140639269128000)2019-10-11 16:18:50,534:building negative db sortmerna index files
INFO(140639269128000)2019-10-11 16:18:50,534:build_index_sortmerna files [’/home/kp/.conda/envs/qiime2-2019.7/lib/python3.6/site-packages/deblur/support_files/artifacts.fa’] to dir /tmp/tmpk1t0rc4u/deblur_wo
rking_dir
INFO(140639269128000)2019-10-11 16:18:50,584:building positive db sortmerna index files
INFO(140639269128000)2019-10-11 16:18:50,584:build_index_sortmerna files [’/home/kp/.conda/envs/qiime2-2019.7/lib/python3.6/site-packages/deblur/support_files/88_otus.fasta’] to dir /tmp/tmpk1t0rc4u/deblur_w
orking_dir
INFO(140639269128000)2019-10-11 16:19:27,202:processing per sample fasta files
INFO(140639269128000)2019-10-11 16:19:27,203:--------------------------------------------------------
INFO(140639269128000)2019-10-11 16:19:27,203:launch_workflow for file /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-dpwmebh7/RR15_S86_L001_R1_001.fastq.gz
INFO(140639269128000)2019-10-11 16:19:51,510:dereplicate seqs file /tmp/tmpk1t0rc4u/deblur_working_dir/RR15_S86_L001_R1_001.fastq.gz.trim
INFO(140639269128000)2019-10-11 16:19:51,682:remove_artifacts_seqs file /tmp/tmpk1t0rc4u/deblur_working_dir/RR15_S86_L001_R1_001.fastq.gz.trim.derep
INFO(140639269128000)2019-10-11 16:19:52,548:total sequences 11084, passing sequences 11084, failing sequences 0
INFO(140639269128000)2019-10-11 16:19:52,549:multiple_sequence_alignment seqs file /tmp/tmpk1t0rc4u/deblur_working_dir/RR15_S86_L001_R1_001.fastq.gz.trim.derep.no_artifacts
INFO(140639269128000)2019-10-11 16:22:01,894:deblurring 11084 sequences
INFO(140639269128000)2019-10-11 16:23:58,183:6116 unique sequences left following deblurring
INFO(140639269128000)2019-10-11 16:23:58,220:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpk1t0rc4u/deblur_working_dir/RR15_S86_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp
/tmpk1t0rc4u/deblur_working_dir
INFO(140639269128000)2019-10-11 16:24:03,286:finished processing file
INFO(140639269128000)2019-10-11 16:24:03,298:-------------------------
…
…
"