[2023-03-18 21:29:07,923] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:29:07,924] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:29:07,924] [INFO] DQC Reference Directory: /var/lib/cwl/stg5dec5abd-7bee-47b4-8d79-6744dbf48f1e/dqc_reference
[2023-03-18 21:29:09,057] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:29:09,057] [INFO] Task started: Prodigal
[2023-03-18 21:29:09,057] [INFO] Running command: cat /var/lib/cwl/stgceac7d83-d55b-464d-afaa-35cae2ddb2df/OceanDNA-b38376.fa | prodigal -d OceanDNA-b38376/cds.fna -a OceanDNA-b38376/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:29:55,179] [INFO] Task succeeded: Prodigal
[2023-03-18 21:29:55,179] [INFO] Task started: HMMsearch
[2023-03-18 21:29:55,179] [INFO] Running command: hmmsearch --tblout OceanDNA-b38376/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5dec5abd-7bee-47b4-8d79-6744dbf48f1e/dqc_reference/reference_markers.hmm OceanDNA-b38376/protein.faa > /dev/null
[2023-03-18 21:29:55,426] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:29:55,427] [INFO] Found 6/6 markers.
[2023-03-18 21:29:55,457] [INFO] Query marker FASTA was written to OceanDNA-b38376/markers.fasta
[2023-03-18 21:29:55,458] [INFO] Task started: Blastn
[2023-03-18 21:29:55,458] [INFO] Running command: blastn -query OceanDNA-b38376/markers.fasta -db /var/lib/cwl/stg5dec5abd-7bee-47b4-8d79-6744dbf48f1e/dqc_reference/reference_markers.fasta -out OceanDNA-b38376/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:29:56,123] [INFO] Task succeeded: Blastn
[2023-03-18 21:29:56,124] [INFO] Selected 33 target genomes.
[2023-03-18 21:29:56,124] [INFO] Target genome list was writen to OceanDNA-b38376/target_genomes.txt
[2023-03-18 21:29:56,167] [INFO] Task started: fastANI
[2023-03-18 21:29:56,167] [INFO] Running command: fastANI --query /var/lib/cwl/stgceac7d83-d55b-464d-afaa-35cae2ddb2df/OceanDNA-b38376.fa --refList OceanDNA-b38376/target_genomes.txt --output OceanDNA-b38376/fastani_result.tsv --threads 1
[2023-03-18 21:30:16,459] [INFO] Task succeeded: fastANI
[2023-03-18 21:30:16,460] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5dec5abd-7bee-47b4-8d79-6744dbf48f1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:30:16,460] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5dec5abd-7bee-47b4-8d79-6744dbf48f1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:30:16,472] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:30:16,472] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 21:30:16,472] [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
Ketobacter alkanivorans	strain=GI5	GCA_002863865.1	1917421	1917421	type	True	80.1221	634	1863	95	below_threshold
Alcanivorax jadensis	strain=T9	GCA_000756655.1	64988	64988	type	True	76.3831	89	1863	95	below_threshold
Alcanivorax hongdengensis	strain=A-11-3	GCA_000300995.1	519051	519051	type	True	76.2549	94	1863	95	below_threshold
Marinobacter nauticus	strain=DSM 50418	GCA_003634635.1	2743	2743	type	True	76.2463	63	1863	95	below_threshold
Marinobacter profundi	strain=PWS21	GCA_002744715.1	2666256	2666256	type	True	76.2251	52	1863	95	below_threshold
Alcanivorax balearicus	strain=MACL04	GCA_025532145.1	413232	413232	type	True	75.9648	88	1863	95	below_threshold
Marinobacter arenosus	strain=CAU 1620	GCA_019264345.1	2856822	2856822	type	True	75.8195	56	1863	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	75.7855	64	1863	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	75.7772	55	1863	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	75.7397	81	1863	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_012987025.1	287	287	type	True	75.6169	67	1863	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_001042925.1	287	287	type	True	75.5991	68	1863	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	75.5912	66	1863	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_900167195.1	287	287	type	True	75.5378	67	1863	95	below_threshold
Aestuariirhabdus litorea	strain=GTF13	GCA_003864255.1	2528527	2528527	type	True	75.4957	64	1863	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	75.3854	54	1863	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	75.3854	54	1863	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_002891015.1	2968968	2968968	type	True	75.3853	54	1863	95	below_threshold
Pseudomonas ekonensis	strain=COR58	GCA_019145435.1	2842353	2842353	type	True	75.2703	60	1863	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 21:30:16,473] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38376/tc_result.tsv
[2023-03-18 21:30:16,473] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:30:16,473] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:30:16,474] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5dec5abd-7bee-47b4-8d79-6744dbf48f1e/dqc_reference/checkm_data
[2023-03-18 21:30:16,474] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:30:16,526] [INFO] Task started: CheckM
[2023-03-18 21:30:16,526] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38376/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38376/checkm_input OceanDNA-b38376/checkm_result
[2023-03-18 21:32:09,073] [INFO] Task succeeded: CheckM
[2023-03-18 21:32:09,073] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:32:09,077] [INFO] ===== Completeness check finished =====
[2023-03-18 21:32:09,077] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:32:09,077] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38376/markers.fasta)
[2023-03-18 21:32:09,078] [INFO] Task started: Blastn
[2023-03-18 21:32:09,078] [INFO] Running command: blastn -query OceanDNA-b38376/markers.fasta -db /var/lib/cwl/stg5dec5abd-7bee-47b4-8d79-6744dbf48f1e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38376/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:32:10,209] [INFO] Task succeeded: Blastn
[2023-03-18 21:32:10,210] [INFO] Selected 16 target genomes.
[2023-03-18 21:32:10,210] [INFO] Target genome list was writen to OceanDNA-b38376/target_genomes_gtdb.txt
[2023-03-18 21:32:10,231] [INFO] Task started: fastANI
[2023-03-18 21:32:10,231] [INFO] Running command: fastANI --query /var/lib/cwl/stgceac7d83-d55b-464d-afaa-35cae2ddb2df/OceanDNA-b38376.fa --refList OceanDNA-b38376/target_genomes_gtdb.txt --output OceanDNA-b38376/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:32:23,235] [INFO] Task succeeded: fastANI
[2023-03-18 21:32:23,242] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 21:32:23,242] [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
GCA_002471665.1	s__Ketobacter sp002471665	99.9448	1726	1863	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ketobacter	95.0	99.82	99.43	0.96	0.93	14	conclusive
GCF_002863865.1	s__Ketobacter alkanivorans	80.1224	634	1863	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ketobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701845.1	s__Ketobacter sp002701845	80.0996	591	1863	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ketobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003671495.1	s__Ketobacter sp003671495	79.6964	853	1863	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ketobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002708905.1	s__Ketobacter sp002708905	79.6336	801	1863	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ketobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009746715.1	s__Ketobacter sp003667185	78.0855	265	1863	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ketobacter	95.0	99.27	99.27	0.91	0.91	2	-
GCF_900112645.1	s__Pseudomonas_E straminea	75.7553	50	1863	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.06	98.06	0.94	0.94	2	-
GCA_002840055.1	s__Pseudomonas_D sp002840055	75.5349	53	1863	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003864255.1	s__Aestuariirhabdus litorea	75.4987	66	1863	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Aestuariirhabdaceae;g__Aestuariirhabdus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000380335.1	s__Azotobacter vinelandii	75.2921	50	1863	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Azotobacter	95.0	99.84	99.43	0.98	0.95	5	-
--------------------------------------------------------------------------------
[2023-03-18 21:32:23,243] [INFO] GTDB search result was written to OceanDNA-b38376/result_gtdb.tsv
[2023-03-18 21:32:23,243] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:32:23,245] [INFO] DFAST_QC result json was written to OceanDNA-b38376/dqc_result.json
[2023-03-18 21:32:23,245] [INFO] DFAST_QC completed!
[2023-03-18 21:32:23,245] [INFO] Total running time: 0h3m15s