[2023-03-17 00:02:20,742] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:02:20,743] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:02:20,743] [INFO] DQC Reference Directory: /var/lib/cwl/stgba5db2ba-348c-4bfc-be39-09a95adc5c29/dqc_reference
[2023-03-17 00:02:21,875] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:02:21,875] [INFO] Task started: Prodigal
[2023-03-17 00:02:21,875] [INFO] Running command: cat /var/lib/cwl/stg027020ca-f66a-41a2-a827-fb2e417091c5/OceanDNA-b7200.fa | prodigal -d OceanDNA-b7200/cds.fna -a OceanDNA-b7200/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:02:41,276] [INFO] Task succeeded: Prodigal
[2023-03-17 00:02:41,277] [INFO] Task started: HMMsearch
[2023-03-17 00:02:41,277] [INFO] Running command: hmmsearch --tblout OceanDNA-b7200/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba5db2ba-348c-4bfc-be39-09a95adc5c29/dqc_reference/reference_markers.hmm OceanDNA-b7200/protein.faa > /dev/null
[2023-03-17 00:02:41,471] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:02:41,472] [INFO] Found 6/6 markers.
[2023-03-17 00:02:41,488] [INFO] Query marker FASTA was written to OceanDNA-b7200/markers.fasta
[2023-03-17 00:02:41,489] [INFO] Task started: Blastn
[2023-03-17 00:02:41,489] [INFO] Running command: blastn -query OceanDNA-b7200/markers.fasta -db /var/lib/cwl/stgba5db2ba-348c-4bfc-be39-09a95adc5c29/dqc_reference/reference_markers.fasta -out OceanDNA-b7200/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:02:42,039] [INFO] Task succeeded: Blastn
[2023-03-17 00:02:42,113] [INFO] Selected 32 target genomes.
[2023-03-17 00:02:42,113] [INFO] Target genome list was writen to OceanDNA-b7200/target_genomes.txt
[2023-03-17 00:02:42,280] [INFO] Task started: fastANI
[2023-03-17 00:02:42,280] [INFO] Running command: fastANI --query /var/lib/cwl/stg027020ca-f66a-41a2-a827-fb2e417091c5/OceanDNA-b7200.fa --refList OceanDNA-b7200/target_genomes.txt --output OceanDNA-b7200/fastani_result.tsv --threads 1
[2023-03-17 00:03:00,719] [INFO] Task succeeded: fastANI
[2023-03-17 00:03:00,720] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba5db2ba-348c-4bfc-be39-09a95adc5c29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:03:00,720] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba5db2ba-348c-4bfc-be39-09a95adc5c29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:03:00,724] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 00:03:00,724] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 00:03:00,725] [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
Pukyongia salina	strain=RR4-38	GCA_002966125.1	2094025	2094025	type	True	76.6963	60	869	95	below_threshold
Aureitalea marina	strain=NBRC 107741	GCA_002943755.1	930804	930804	type	True	76.4609	53	869	95	below_threshold
Constantimarinum furrinae	strain=ALE3EI	GCA_014295415.1	2562285	2562285	type	True	76.4466	70	869	95	below_threshold
Marinirhabdus gelatinilytica	strain=DSM 101478	GCA_003353425.1	1703343	1703343	type	True	76.3188	54	869	95	below_threshold
Luteirhabdus pelagi	strain=A3-108	GCA_016827595.1	2792783	2792783	type	True	76.197	54	869	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 00:03:00,730] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7200/tc_result.tsv
[2023-03-17 00:03:00,731] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:03:00,731] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:03:00,731] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba5db2ba-348c-4bfc-be39-09a95adc5c29/dqc_reference/checkm_data
[2023-03-17 00:03:00,732] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:03:00,745] [INFO] Task started: CheckM
[2023-03-17 00:03:00,745] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7200/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7200/checkm_input OceanDNA-b7200/checkm_result
[2023-03-17 00:03:50,810] [INFO] Task succeeded: CheckM
[2023-03-17 00:03:50,811] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 00:03:50,878] [INFO] ===== Completeness check finished =====
[2023-03-17 00:03:50,878] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:03:50,879] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7200/markers.fasta)
[2023-03-17 00:03:50,880] [INFO] Task started: Blastn
[2023-03-17 00:03:50,880] [INFO] Running command: blastn -query OceanDNA-b7200/markers.fasta -db /var/lib/cwl/stgba5db2ba-348c-4bfc-be39-09a95adc5c29/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7200/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:03:51,663] [INFO] Task succeeded: Blastn
[2023-03-17 00:03:51,664] [INFO] Selected 23 target genomes.
[2023-03-17 00:03:51,664] [INFO] Target genome list was writen to OceanDNA-b7200/target_genomes_gtdb.txt
[2023-03-17 00:03:52,269] [INFO] Task started: fastANI
[2023-03-17 00:03:52,269] [INFO] Running command: fastANI --query /var/lib/cwl/stg027020ca-f66a-41a2-a827-fb2e417091c5/OceanDNA-b7200.fa --refList OceanDNA-b7200/target_genomes_gtdb.txt --output OceanDNA-b7200/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:04:04,377] [INFO] Task succeeded: fastANI
[2023-03-17 00:04:04,382] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 00:04:04,382] [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_002163875.1	s__Gilvibacter sp002163875	93.6304	810	869	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gilvibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214815.1	s__Gilvibacter sp013214815	81.5859	531	869	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gilvibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003229235.1	s__Gilvibacter sp003229235	76.6505	56	869	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gilvibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002943755.1	s__Aureitalea marina	76.4609	53	869	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014295415.1	s__Altibacter sp014295415	76.4466	70	869	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Altibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009827225.1	s__SMXJ01 sp009827225	76.3852	59	869	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SMXJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003353425.1	s__Marinirhabdus gelatinilytica	76.3188	54	869	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003333325.1	s__Ulvibacter_A alkanivorans	76.2663	55	869	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacter_A	95.0	98.51	98.51	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-03-17 00:04:04,385] [INFO] GTDB search result was written to OceanDNA-b7200/result_gtdb.tsv
[2023-03-17 00:04:04,389] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:04:04,393] [INFO] DFAST_QC result json was written to OceanDNA-b7200/dqc_result.json
[2023-03-17 00:04:04,393] [INFO] DFAST_QC completed!
[2023-03-17 00:04:04,393] [INFO] Total running time: 0h1m44s