[2023-03-18 23:11:06,946] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:11:06,946] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:11:06,946] [INFO] DQC Reference Directory: /var/lib/cwl/stga6d41612-24cc-476d-92f0-8c4c839fe1a7/dqc_reference
[2023-03-18 23:11:08,131] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:11:08,132] [INFO] Task started: Prodigal
[2023-03-18 23:11:08,132] [INFO] Running command: cat /var/lib/cwl/stgdd9ffb19-2bff-48dd-88df-07a9bc13b6da/OceanDNA-b35128.fa | prodigal -d OceanDNA-b35128/cds.fna -a OceanDNA-b35128/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:11:28,108] [INFO] Task succeeded: Prodigal
[2023-03-18 23:11:28,108] [INFO] Task started: HMMsearch
[2023-03-18 23:11:28,108] [INFO] Running command: hmmsearch --tblout OceanDNA-b35128/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga6d41612-24cc-476d-92f0-8c4c839fe1a7/dqc_reference/reference_markers.hmm OceanDNA-b35128/protein.faa > /dev/null
[2023-03-18 23:11:28,402] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:11:28,402] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgdd9ffb19-2bff-48dd-88df-07a9bc13b6da/OceanDNA-b35128.fa]
[2023-03-18 23:11:28,428] [INFO] Query marker FASTA was written to OceanDNA-b35128/markers.fasta
[2023-03-18 23:11:28,428] [INFO] Task started: Blastn
[2023-03-18 23:11:28,428] [INFO] Running command: blastn -query OceanDNA-b35128/markers.fasta -db /var/lib/cwl/stga6d41612-24cc-476d-92f0-8c4c839fe1a7/dqc_reference/reference_markers.fasta -out OceanDNA-b35128/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:11:29,065] [INFO] Task succeeded: Blastn
[2023-03-18 23:11:29,066] [INFO] Selected 12 target genomes.
[2023-03-18 23:11:29,066] [INFO] Target genome list was writen to OceanDNA-b35128/target_genomes.txt
[2023-03-18 23:11:29,072] [INFO] Task started: fastANI
[2023-03-18 23:11:29,072] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd9ffb19-2bff-48dd-88df-07a9bc13b6da/OceanDNA-b35128.fa --refList OceanDNA-b35128/target_genomes.txt --output OceanDNA-b35128/fastani_result.tsv --threads 1
[2023-03-18 23:11:38,442] [INFO] Task succeeded: fastANI
[2023-03-18 23:11:38,443] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga6d41612-24cc-476d-92f0-8c4c839fe1a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:11:38,443] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga6d41612-24cc-476d-92f0-8c4c839fe1a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:11:38,450] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:11:38,450] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 23:11:38,450] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Rheinheimera lutimaris	strain=YQF-2	GCA_013283795.1	2740584	2740584	type	True	83.1632	684	1157	95	below_threshold
Rheinheimera maricola	strain=MA-13	GCA_016918075.2	2793282	2793282	type	True	82.3907	656	1157	95	below_threshold
Rheinheimera maricola	strain=MA-13	GCA_017824735.1	2793282	2793282	type	True	82.3765	656	1157	95	below_threshold
Rheinheimera pleomorphica	strain=PKS7	GCA_011634895.1	2703963	2703963	type	True	81.4537	655	1157	95	below_threshold
Rheinheimera pacifica	strain=DSM 17616	GCA_900108485.1	173990	173990	type	True	80.8799	621	1157	95	below_threshold
Rheinheimera nanhaiensis	strain=E407-8	GCA_000296695.1	1163621	1163621	type	True	80.8314	632	1157	95	below_threshold
Rheinheimera hassiensis	strain=LMG 27268	GCA_022436675.1	1193627	1193627	type	True	80.8169	611	1157	95	below_threshold
Rheinheimera baltica	strain=DSM 14885	GCA_000425345.1	67576	67576	type	True	80.1373	493	1157	95	below_threshold
Rheinheimera aquimaris	strain=KCTC 12840	GCA_020531985.1	412437	412437	type	True	79.8537	491	1157	95	below_threshold
Rheinheimera salexigens	strain=KH87	GCA_001752395.1	1628148	1628148	type	True	77.7452	186	1157	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:11:38,450] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35128/tc_result.tsv
[2023-03-18 23:11:38,450] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:11:38,451] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:11:38,451] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga6d41612-24cc-476d-92f0-8c4c839fe1a7/dqc_reference/checkm_data
[2023-03-18 23:11:38,451] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:11:38,529] [INFO] Task started: CheckM
[2023-03-18 23:11:38,529] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35128/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35128/checkm_input OceanDNA-b35128/checkm_result
[2023-03-18 23:12:29,266] [INFO] Task succeeded: CheckM
[2023-03-18 23:12:29,266] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.21%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 23:12:29,269] [INFO] ===== Completeness check finished =====
[2023-03-18 23:12:29,269] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:12:29,270] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35128/markers.fasta)
[2023-03-18 23:12:29,270] [INFO] Task started: Blastn
[2023-03-18 23:12:29,270] [INFO] Running command: blastn -query OceanDNA-b35128/markers.fasta -db /var/lib/cwl/stga6d41612-24cc-476d-92f0-8c4c839fe1a7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35128/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:12:30,253] [INFO] Task succeeded: Blastn
[2023-03-18 23:12:30,253] [INFO] Selected 12 target genomes.
[2023-03-18 23:12:30,254] [INFO] Target genome list was writen to OceanDNA-b35128/target_genomes_gtdb.txt
[2023-03-18 23:12:30,269] [INFO] Task started: fastANI
[2023-03-18 23:12:30,269] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd9ffb19-2bff-48dd-88df-07a9bc13b6da/OceanDNA-b35128.fa --refList OceanDNA-b35128/target_genomes_gtdb.txt --output OceanDNA-b35128/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:12:39,593] [INFO] Task succeeded: fastANI
[2023-03-18 23:12:39,601] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 23:12:39,601] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_013283795.1	s__Rheinheimera sp013283795	83.1728	683	1157	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017824735.1	s__Rheinheimera sp017824735	82.3682	657	1157	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018826295.1	s__Rheinheimera sp018826295	82.1462	749	1157	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	99.95	99.91	0.97	0.92	5	-
GCA_002840125.1	s__Rheinheimera sp002840125	81.0283	634	1157	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108485.1	s__Rheinheimera pacifica	80.888	619	1157	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000296695.1	s__Rheinheimera nanhaiensis	80.8252	633	1157	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001513785.1	s__Rheinheimera sp001513785	80.7598	635	1157	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018831085.1	s__Rheinheimera sp018831085	80.6387	601	1157	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	100.00	100.00	1.00	1.00	3	-
GCF_004369005.1	s__Rheinheimera aquimaris	79.8404	505	1157	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	98.51	97.48	0.94	0.92	4	-
GCF_004345025.1	s__Rheinheimera sp004345025	78.8201	330	1157	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001752395.1	s__Rheinheimera salexigens	77.7307	186	1157	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004005375.1	s__Pararheinheimera sp004005375	77.0145	162	1157	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:12:39,601] [INFO] GTDB search result was written to OceanDNA-b35128/result_gtdb.tsv
[2023-03-18 23:12:39,602] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:12:39,603] [INFO] DFAST_QC result json was written to OceanDNA-b35128/dqc_result.json
[2023-03-18 23:12:39,603] [INFO] DFAST_QC completed!
[2023-03-18 23:12:39,603] [INFO] Total running time: 0h1m33s