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biocore / deblur

Deblur is a greedy deconvolution algorithm based on known read error profiles.
BSD 3-Clause "New" or "Revised" License
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Crash after saving biom table and attempting to remove artifacts #201

Open nameerbaker opened 5 years ago

nameerbaker commented 5 years ago

Hello,

I was attempting to deblur a significant number of samples and had an error that resulted in a crash out after the samples have all been deblurred and had their chimeras removed, when it had saved the biom file and I believe when it was attempting to remove temp files that were no longer needed. I found a previous reference to a similar error here: https://github.com/biocore/deblur/issues/150 but since the error appears to have been resolved by ensuring that the version of sortmerna was correct, and mine is, I figured that I should create a new thread. Please just let me know if I'm not on the right track, I would really love to be able to denoise these samples in some fashion at some point.

The command I ran is as follows:

qiime deblur denoise-16S --i-demultiplexed-seqs demux-join-filter.qza --p-trim-length 290 --p-sample-stats --o-representative-sequences deblur-rep-seqs.qza --o-table deblur-table.qza --o-stats deblur-stats.qza --verbose

And here is the relevant portion of the log file:

INFO(4518299072)2019-10-04 09:46:42,624:total sequences 32108, passing sequences 29127, failing sequences 2981 INFO(4518299072)2019-10-04 09:46:42,625:multiple_sequence_alignment seqs file /private/var/folders/67/f0_gybpd5gs2cddcyjgv86_r0000gn/T/tmphg2322rm/deblur_working_dir/13Bin3_16_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(4518299072)2019-10-05 08:47:19,224:deblurring 29127 sequences INFO(4518299072)2019-10-05 09:00:01,768:9083 unique sequences left following deblurring INFO(4518299072)2019-10-05 09:00:01,896:remove_chimeras_denovo_from_seqs seqs file /private/var/folders/67/f0_gybpd5gs2cddcyjgv86_r0000gn/T/tmphg2322rm/deblur_working_dir/13Bin3_16_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /private/var/folders/67/f0_gybpd5gs2cddcyjgv86_r0000gn/T/tmphg2322rm/deblur_working_dir INFO(4518299072)2019-10-05 09:00:12,162:finished processing file INFO(4518299072)2019-10-05 09:00:12,196:finished processing per sample fasta files INFO(4518299072)2019-10-05 09:00:12,203:create_otu_table for 127 samples, into output table /private/var/folders/67/f0_gybpd5gs2cddcyjgv86_r0000gn/T/tmphg2322rm/all.biom INFO(4518299072)2019-10-05 09:00:18,362:for output biom table loaded 127 samples, 91592 unique sequences INFO(4518299072)2019-10-05 09:00:18,444:keeping 6688 (out of 91592 sequences) with >=10 reads WARNING(4518299072)2019-10-05 09:00:18,861:removed 1 samples with reads per sample<1 INFO(4518299072)2019-10-05 09:00:19,003:saved to biom file /private/var/folders/67/f0_gybpd5gs2cddcyjgv86_r0000gn/T/tmphg2322rm/all.biom INFO(4518299072)2019-10-05 09:00:19,026:saved sequence fasta file to /private/var/folders/67/f0_gybpd5gs2cddcyjgv86_r0000gn/T/tmphg2322rm/all.seqs.fa INFO(4518299072)2019-10-05 09:00:19,068:getting 16s sequences from the biom table INFO(4518299072)2019-10-05 09:00:19,068:remove_artifacts_seqs file /private/var/folders/67/f0_gybpd5gs2cddcyjgv86_r0000gn/T/tmphg2322rm/all.seqs.fa ERROR(4518299072)2019-10-05 09:00:19,260:sortmerna error on file /private/var/folders/67/f0_gybpd5gs2cddcyjgv86_r0000gn/T/tmphg2322rm/all.seqs.fa ERROR(4518299072)2019-10-05 09:00:19,260:stdout : Program: SortMeRNA version 2.0, 29/11/2014 Copyright: 2012-2015 Bonsai Bioinformatics Research Group: LIFL, University Lille 1, CNRS UMR 8022, INRIA Nord-Europe OTU-picking extensions and continuing support developed in the Knight Lab, BioFrontiers Institute, University of Colorado at Boulder Disclaimer: SortMeRNA comes with ABSOLUTELY NO WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. Contact: Evguenia Kopylova, jenya.kopylov@gmail.com Laurent Noé, laurent.noe@lifl.fr Hélène Touzet, helene.touzet@lifl.fr

Computing read file statistics ... done [0.18 sec] size of reads file: 3899104 bytes partial section(s) to be executed: 1 of size 3899104 bytes

ERROR(4518299072)2019-10-05 09:00:19,261:stderr : ERROR: The index '/private/var/folders/67/f0_gybpd5gs2cddcyjgv86_r0000gn/T/tmphg2322rm/deblur_working_dir/88_otus.stats' does not exist. Make sure you have constructed your index using the command indexdb'. Seeindexdb -h' for help.