[2023-03-16 18:40:20,527] [INFO] DFAST_QC pipeline started.
[2023-03-16 18:40:20,528] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 18:40:20,528] [INFO] DQC Reference Directory: /var/lib/cwl/stga6b28f26-a840-4838-9e2e-49ca20b2d569/dqc_reference
[2023-03-16 18:40:22,808] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 18:40:22,808] [INFO] Task started: Prodigal
[2023-03-16 18:40:22,809] [INFO] Running command: cat /var/lib/cwl/stga228f27f-a0e6-4978-b03b-815ffcbfa703/OceanDNA-b36430.fa | prodigal -d OceanDNA-b36430/cds.fna -a OceanDNA-b36430/protein.faa -g 11 -q > /dev/null
[2023-03-16 18:40:56,615] [INFO] Task succeeded: Prodigal
[2023-03-16 18:40:56,615] [INFO] Task started: HMMsearch
[2023-03-16 18:40:56,615] [INFO] Running command: hmmsearch --tblout OceanDNA-b36430/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga6b28f26-a840-4838-9e2e-49ca20b2d569/dqc_reference/reference_markers.hmm OceanDNA-b36430/protein.faa > /dev/null
[2023-03-16 18:40:56,965] [INFO] Task succeeded: HMMsearch
[2023-03-16 18:40:56,966] [INFO] Found 6/6 markers.
[2023-03-16 18:40:56,997] [INFO] Query marker FASTA was written to OceanDNA-b36430/markers.fasta
[2023-03-16 18:40:57,011] [INFO] Task started: Blastn
[2023-03-16 18:40:57,011] [INFO] Running command: blastn -query OceanDNA-b36430/markers.fasta -db /var/lib/cwl/stga6b28f26-a840-4838-9e2e-49ca20b2d569/dqc_reference/reference_markers.fasta -out OceanDNA-b36430/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:40:57,784] [INFO] Task succeeded: Blastn
[2023-03-16 18:40:57,785] [INFO] Selected 15 target genomes.
[2023-03-16 18:40:57,785] [INFO] Target genome list was writen to OceanDNA-b36430/target_genomes.txt
[2023-03-16 18:40:57,794] [INFO] Task started: fastANI
[2023-03-16 18:40:57,794] [INFO] Running command: fastANI --query /var/lib/cwl/stga228f27f-a0e6-4978-b03b-815ffcbfa703/OceanDNA-b36430.fa --refList OceanDNA-b36430/target_genomes.txt --output OceanDNA-b36430/fastani_result.tsv --threads 1
[2023-03-16 18:41:11,281] [INFO] Task succeeded: fastANI
[2023-03-16 18:41:11,281] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga6b28f26-a840-4838-9e2e-49ca20b2d569/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 18:41:11,281] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga6b28f26-a840-4838-9e2e-49ca20b2d569/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 18:41:11,290] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2023-03-16 18:41:11,291] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 18:41:11,291] [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
Alcanivorax jadensis	strain=T9	GCA_000756655.1	64988	64988	type	True	97.78	1069	1215	95	conclusive
Alcanivorax hongdengensis	strain=A-11-3	GCA_000300995.1	519051	519051	type	True	81.3434	685	1215	95	below_threshold
Alcanivorax profundi	strain=MTEO17	GCA_003597125.1	2338368	2338368	type	True	80.7104	653	1215	95	below_threshold
Alcanivorax sediminis	strain=PA15-N-34	GCA_009601165.1	2663008	2663008	type	True	80.5167	655	1215	95	below_threshold
Alcanivorax nanhaiticus	strain=19-m-6	GCA_000756665.1	1177154	1177154	type	True	80.4795	630	1215	95	below_threshold
Alcanivorax borkumensis	strain=SK2	GCA_000009365.1	59754	59754	type	True	79.8998	511	1215	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	79.1402	430	1215	95	below_threshold
Alcanivorax gelatiniphagus	strain=MEBiC 08158	GCA_005938655.1	1194167	1194167	type	True	79.1198	475	1215	95	below_threshold
Alcanivorax venustensis	strain=ISO4	GCA_015356855.1	172371	172371	type	True	79.1127	454	1215	95	below_threshold
Alcanivorax balearicus	strain=MACL04	GCA_025532145.1	413232	413232	type	True	78.6286	374	1215	95	below_threshold
Alcanivorax limicola	strain=JB21	GCA_019931215.1	2874102	2874102	type	True	77.5728	248	1215	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	76.2397	109	1215	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	76.2303	105	1215	95	below_threshold
Pseudomonas rhizoryzae	strain=RY24	GCA_005250615.1	2571129	2571129	type	True	76.1065	107	1215	95	below_threshold
Pseudomonas kermanshahensis	strain=SWRI100	GCA_014269205.2	2745482	2745482	type	True	75.8825	88	1215	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 18:41:11,291] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36430/tc_result.tsv
[2023-03-16 18:41:11,291] [INFO] ===== Taxonomy check completed =====
[2023-03-16 18:41:11,291] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 18:41:11,291] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga6b28f26-a840-4838-9e2e-49ca20b2d569/dqc_reference/checkm_data
[2023-03-16 18:41:11,292] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 18:41:11,300] [INFO] Task started: CheckM
[2023-03-16 18:41:11,300] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36430/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36430/checkm_input OceanDNA-b36430/checkm_result
[2023-03-16 18:42:08,850] [INFO] Task succeeded: CheckM
[2023-03-16 18:42:08,851] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 18:42:08,853] [INFO] ===== Completeness check finished =====
[2023-03-16 18:42:08,853] [INFO] ===== Start GTDB Search =====
[2023-03-16 18:42:08,854] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36430/markers.fasta)
[2023-03-16 18:42:08,855] [INFO] Task started: Blastn
[2023-03-16 18:42:08,855] [INFO] Running command: blastn -query OceanDNA-b36430/markers.fasta -db /var/lib/cwl/stga6b28f26-a840-4838-9e2e-49ca20b2d569/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36430/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:42:11,958] [INFO] Task succeeded: Blastn
[2023-03-16 18:42:11,959] [INFO] Selected 13 target genomes.
[2023-03-16 18:42:11,959] [INFO] Target genome list was writen to OceanDNA-b36430/target_genomes_gtdb.txt
[2023-03-16 18:42:12,050] [INFO] Task started: fastANI
[2023-03-16 18:42:12,050] [INFO] Running command: fastANI --query /var/lib/cwl/stga228f27f-a0e6-4978-b03b-815ffcbfa703/OceanDNA-b36430.fa --refList OceanDNA-b36430/target_genomes_gtdb.txt --output OceanDNA-b36430/fastani_result_gtdb.tsv --threads 1
[2023-03-16 18:42:32,540] [INFO] Task succeeded: fastANI
[2023-03-16 18:42:32,548] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 18:42:32,548] [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_000756655.1	s__Alcanivorax jadensis	97.78	1069	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.11	97.73	0.92	0.86	7	conclusive
GCA_014762765.1	s__Alcanivorax sp014762765	89.3289	888	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003862375.1	s__Alcanivorax jadensis_A	88.9486	944	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	99.67	99.67	0.92	0.92	2	-
GCF_900107995.1	s__Alcanivorax sp900107995	87.7844	997	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.42	98.03	0.93	0.89	9	-
GCF_000155615.1	s__Alcanivorax sp000155615	82.2161	794	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.88	97.69	0.92	0.89	4	-
GCA_002733835.1	s__Alcanivorax sp002733835	82.1594	735	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009882945.1	s__Alcanivorax sp009882945	81.3553	699	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000300995.1	s__Alcanivorax hongdengensis	81.3401	685	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017794965.1	s__Alcanivorax sp017794965	81.1917	693	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015356855.1	s__Alcanivorax venustensis	79.0934	455	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.73	95.38	0.91	0.87	46	-
GCA_017794945.1	s__Alcanivorax sp009711585	79.0471	422	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	96.99	96.99	0.93	0.93	2	-
GCF_002893095.1	s__Stenotrophomonas sp002893095	75.3518	58	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.47	97.41	0.90	0.90	3	-
--------------------------------------------------------------------------------
[2023-03-16 18:42:32,548] [INFO] GTDB search result was written to OceanDNA-b36430/result_gtdb.tsv
[2023-03-16 18:42:32,548] [INFO] ===== GTDB Search completed =====
[2023-03-16 18:42:32,554] [INFO] DFAST_QC result json was written to OceanDNA-b36430/dqc_result.json
[2023-03-16 18:42:32,554] [INFO] DFAST_QC completed!
[2023-03-16 18:42:32,554] [INFO] Total running time: 0h2m12s