Crash after saving biom table and attempting to remove artifacts #201
Description
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: #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, [email protected]
Laurent Noé, [email protected]
Hélène Touzet, [email protected]
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 :
�[0;31mERROR�[0m: 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'. See indexdb -h' for help.