[2023-03-14 13:48:47,184] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:48:47,185] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:48:47,185] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd1e0569-f93e-4531-b056-e653823cc92a/dqc_reference
[2023-03-14 13:48:48,661] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:48:48,669] [INFO] Task started: Prodigal
[2023-03-14 13:48:48,669] [INFO] Running command: cat /var/lib/cwl/stg4c727c8e-373b-4619-9132-31f224fa55a6/OceanDNA-b6423.fa | prodigal -d OceanDNA-b6423/cds.fna -a OceanDNA-b6423/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:49:05,920] [INFO] Task succeeded: Prodigal
[2023-03-14 13:49:05,920] [INFO] Task started: HMMsearch
[2023-03-14 13:49:05,920] [INFO] Running command: hmmsearch --tblout OceanDNA-b6423/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd1e0569-f93e-4531-b056-e653823cc92a/dqc_reference/reference_markers.hmm OceanDNA-b6423/protein.faa > /dev/null
[2023-03-14 13:49:06,217] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:49:06,218] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg4c727c8e-373b-4619-9132-31f224fa55a6/OceanDNA-b6423.fa]
[2023-03-14 13:49:06,239] [INFO] Query marker FASTA was written to OceanDNA-b6423/markers.fasta
[2023-03-14 13:49:06,242] [INFO] Task started: Blastn
[2023-03-14 13:49:06,242] [INFO] Running command: blastn -query OceanDNA-b6423/markers.fasta -db /var/lib/cwl/stgdd1e0569-f93e-4531-b056-e653823cc92a/dqc_reference/reference_markers.fasta -out OceanDNA-b6423/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:49:07,612] [INFO] Task succeeded: Blastn
[2023-03-14 13:49:07,612] [INFO] Selected 12 target genomes.
[2023-03-14 13:49:07,612] [INFO] Target genome list was writen to OceanDNA-b6423/target_genomes.txt
[2023-03-14 13:49:07,621] [INFO] Task started: fastANI
[2023-03-14 13:49:07,621] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c727c8e-373b-4619-9132-31f224fa55a6/OceanDNA-b6423.fa --refList OceanDNA-b6423/target_genomes.txt --output OceanDNA-b6423/fastani_result.tsv --threads 1
[2023-03-14 13:49:15,773] [INFO] Task succeeded: fastANI
[2023-03-14 13:49:15,774] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd1e0569-f93e-4531-b056-e653823cc92a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:49:15,774] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd1e0569-f93e-4531-b056-e653823cc92a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:49:15,780] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 13:49:15,780] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 13:49:15,781] [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
Aequorivita lipolytica	strain=Y10-2	GCA_007997135.1	153267	153267	type	True	79.4058	336	543	95	below_threshold
Aequorivita aquimaris	strain=D-24	GCA_001573155.1	1548749	1548749	type	True	79.2582	331	543	95	below_threshold
Aequorivita vladivostokensis	strain=KMM 3516	GCA_000952855.1	171194	171194	type	True	79.2571	312	543	95	below_threshold
Aequorivita antarctica	strain=SW49	GCA_007997155.1	153266	153266	type	True	79.2145	334	543	95	below_threshold
Aequorivita iocasae	strain=KX20305	GCA_016757735.1	2803865	2803865	type	True	79.1465	309	543	95	below_threshold
Aequorivita soesokkakensis	strain=RSSK-12	GCA_001641085.1	1385699	1385699	type	True	79.1386	332	543	95	below_threshold
Aequorivita sublithincola	strain=DSM 14238	GCA_000265385.1	101385	101385	type	True	78.6712	296	543	95	below_threshold
Aequorivita echinoideorum	strain=JCM30378	GCA_018476645.1	1549647	1549647	type	True	77.5729	183	543	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 13:49:15,781] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6423/tc_result.tsv
[2023-03-14 13:49:15,781] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:49:15,781] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:49:15,781] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd1e0569-f93e-4531-b056-e653823cc92a/dqc_reference/checkm_data
[2023-03-14 13:49:15,782] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:49:16,008] [INFO] Task started: CheckM
[2023-03-14 13:49:16,008] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6423/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6423/checkm_input OceanDNA-b6423/checkm_result
[2023-03-14 13:49:52,875] [INFO] Task succeeded: CheckM
[2023-03-14 13:49:52,875] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 13:49:52,878] [INFO] ===== Completeness check finished =====
[2023-03-14 13:49:52,878] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:49:52,878] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6423/markers.fasta)
[2023-03-14 13:49:52,879] [INFO] Task started: Blastn
[2023-03-14 13:49:52,879] [INFO] Running command: blastn -query OceanDNA-b6423/markers.fasta -db /var/lib/cwl/stgdd1e0569-f93e-4531-b056-e653823cc92a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6423/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:49:53,666] [INFO] Task succeeded: Blastn
[2023-03-14 13:49:53,667] [INFO] Selected 13 target genomes.
[2023-03-14 13:49:53,667] [INFO] Target genome list was writen to OceanDNA-b6423/target_genomes_gtdb.txt
[2023-03-14 13:49:53,680] [INFO] Task started: fastANI
[2023-03-14 13:49:53,680] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c727c8e-373b-4619-9132-31f224fa55a6/OceanDNA-b6423.fa --refList OceanDNA-b6423/target_genomes_gtdb.txt --output OceanDNA-b6423/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:50:06,562] [INFO] Task succeeded: fastANI
[2023-03-14 13:50:06,570] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 13:50:06,571] [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_007997135.1	s__Aequorivita lipolytica	79.4058	336	543	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002733915.1	s__Aequorivita sp002733915	79.3869	296	543	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001573155.1	s__Aequorivita aquimaris	79.2582	331	543	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000952855.1	s__Aequorivita vladivostokensis	79.2571	312	543	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	98.24	98.00	0.93	0.90	7	-
GCF_007997155.1	s__Aequorivita antarctica	79.2126	333	543	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.98	99.98	0.99	0.99	2	-
GCF_900489465.1	s__Aequorivita sp900489465	79.1481	320	543	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016757735.1	s__Aequorivita sp016757735	79.1465	309	543	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001641085.1	s__Aequorivita soesokkakensis	79.1386	332	543	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	97.26	97.26	0.92	0.92	2	-
GCA_002364215.1	s__Aequorivita sp002364215	79.0979	336	543	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.66	98.55	0.97	0.89	12	-
GCA_002715485.1	s__Aequorivita sp002715485	78.7865	296	543	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.49	99.49	0.87	0.87	2	-
GCF_000265385.1	s__Aequorivita sublithincola	78.6712	296	543	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002375695.1	s__Aequorivita sp002375695	78.6286	263	543	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.99	99.99	0.99	0.99	2	-
GCA_016649715.1	s__Aequorivita sp016649715	78.6192	289	543	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 13:50:06,571] [INFO] GTDB search result was written to OceanDNA-b6423/result_gtdb.tsv
[2023-03-14 13:50:06,572] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:50:06,573] [INFO] DFAST_QC result json was written to OceanDNA-b6423/dqc_result.json
[2023-03-14 13:50:06,574] [INFO] DFAST_QC completed!
[2023-03-14 13:50:06,574] [INFO] Total running time: 0h1m19s