[2024-01-24 13:13:23,735] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:23,737] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:23,737] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f7ee1ae-2613-4bf8-9007-7fc1e09c0c34/dqc_reference
[2024-01-24 13:13:25,071] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:25,072] [INFO] Task started: Prodigal
[2024-01-24 13:13:25,072] [INFO] Running command: gunzip -c /var/lib/cwl/stgf7a04a7f-12f0-4be9-a4dd-0f411cfe3f74/GCF_018145875.1_ASM1814587v1_genomic.fna.gz | prodigal -d GCF_018145875.1_ASM1814587v1_genomic.fna/cds.fna -a GCF_018145875.1_ASM1814587v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:34,943] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:34,944] [INFO] Task started: HMMsearch
[2024-01-24 13:13:34,944] [INFO] Running command: hmmsearch --tblout GCF_018145875.1_ASM1814587v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f7ee1ae-2613-4bf8-9007-7fc1e09c0c34/dqc_reference/reference_markers.hmm GCF_018145875.1_ASM1814587v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:35,369] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:35,371] [INFO] Found 6/6 markers.
[2024-01-24 13:13:35,409] [INFO] Query marker FASTA was written to GCF_018145875.1_ASM1814587v1_genomic.fna/markers.fasta
[2024-01-24 13:13:35,410] [INFO] Task started: Blastn
[2024-01-24 13:13:35,410] [INFO] Running command: blastn -query GCF_018145875.1_ASM1814587v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f7ee1ae-2613-4bf8-9007-7fc1e09c0c34/dqc_reference/reference_markers.fasta -out GCF_018145875.1_ASM1814587v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:36,172] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:36,177] [INFO] Selected 19 target genomes.
[2024-01-24 13:13:36,177] [INFO] Target genome list was writen to GCF_018145875.1_ASM1814587v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:36,296] [INFO] Task started: fastANI
[2024-01-24 13:13:36,296] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7a04a7f-12f0-4be9-a4dd-0f411cfe3f74/GCF_018145875.1_ASM1814587v1_genomic.fna.gz --refList GCF_018145875.1_ASM1814587v1_genomic.fna/target_genomes.txt --output GCF_018145875.1_ASM1814587v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:50,702] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:50,702] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f7ee1ae-2613-4bf8-9007-7fc1e09c0c34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:50,703] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f7ee1ae-2613-4bf8-9007-7fc1e09c0c34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:50,718] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:50,719] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:50,719] [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
Marinomonas vulgaris	strain=A79	GCA_018145875.1	2823372	2823372	type	True	100.0	1119	1122	95	conclusive
Marinomonas foliarum	strain=CECT 7731	GCA_003337275.1	491950	491950	type	True	80.9222	461	1122	95	below_threshold
Marinomonas alcarazii	strain=CECT 7730	GCA_003208215.1	491949	491949	type	True	79.8135	446	1122	95	below_threshold
Marinomonas lutimaris	strain=E165	GCA_019426345.1	2846746	2846746	type	True	79.7567	461	1122	95	below_threshold
Marinomonas shanghaiensis	strain=DSL-35	GCA_003259175.1	2202418	2202418	type	True	79.7557	434	1122	95	below_threshold
Marinomonas profundi	strain=M1K-6	GCA_020694005.1	2726122	2726122	type	True	79.6628	461	1122	95	below_threshold
Marinomonas profundimaris	strain=D104	GCA_000508165.1	1208321	1208321	type	True	79.6412	482	1122	95	below_threshold
Marinomonas profundi	strain=M1K-6	GCA_012584435.1	2726122	2726122	type	True	79.614	459	1122	95	below_threshold
Marinomonas primoryensis	strain=MPKMM3633	GCA_013372285.1	178399	178399	type	True	79.5567	429	1122	95	below_threshold
Marinomonas ushuaiensis	strain=DSM 15871	GCA_000521805.1	263818	263818	type	True	79.5154	354	1122	95	below_threshold
Marinomonas rhizomae	strain=IVIA-Po-145	GCA_003721275.1	491948	491948	type	True	79.4764	462	1122	95	below_threshold
Marinomonas hwangdonensis	strain=HDW-15	GCA_003721245.1	1053647	1053647	type	True	79.3899	369	1122	95	below_threshold
Marinomonas spartinae	strain=CECT 8886	GCA_900089775.1	1792290	1792290	type	True	78.9173	240	1122	95	below_threshold
Marinomonas colpomeniae	strain=SM2066	GCA_014803385.1	2774408	2774408	type	True	78.9016	345	1122	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:50,720] [INFO] DFAST Taxonomy check result was written to GCF_018145875.1_ASM1814587v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:50,721] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:50,721] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:50,721] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f7ee1ae-2613-4bf8-9007-7fc1e09c0c34/dqc_reference/checkm_data
[2024-01-24 13:13:50,722] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:50,756] [INFO] Task started: CheckM
[2024-01-24 13:13:50,757] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018145875.1_ASM1814587v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018145875.1_ASM1814587v1_genomic.fna/checkm_input GCF_018145875.1_ASM1814587v1_genomic.fna/checkm_result
[2024-01-24 13:14:25,975] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:25,977] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:25,998] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:25,998] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:25,999] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018145875.1_ASM1814587v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:25,999] [INFO] Task started: Blastn
[2024-01-24 13:14:25,999] [INFO] Running command: blastn -query GCF_018145875.1_ASM1814587v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f7ee1ae-2613-4bf8-9007-7fc1e09c0c34/dqc_reference/reference_markers_gtdb.fasta -out GCF_018145875.1_ASM1814587v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:27,157] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:27,161] [INFO] Selected 17 target genomes.
[2024-01-24 13:14:27,161] [INFO] Target genome list was writen to GCF_018145875.1_ASM1814587v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:27,183] [INFO] Task started: fastANI
[2024-01-24 13:14:27,183] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7a04a7f-12f0-4be9-a4dd-0f411cfe3f74/GCF_018145875.1_ASM1814587v1_genomic.fna.gz --refList GCF_018145875.1_ASM1814587v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018145875.1_ASM1814587v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:40,368] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:40,381] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:40,381] [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_018145875.1	s__Marinomonas sp018145875	100.0	1119	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008122525.1	s__Marinomonas sp008122525	81.4649	552	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337275.1	s__Marinomonas foliarum	80.9633	458	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.18	98.18	0.87	0.87	2	-
GCF_003208215.1	s__Marinomonas alcarazii	79.8255	445	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.70	98.70	0.93	0.93	2	-
GCF_018336955.1	s__Marinomonas sp018336955	79.7358	457	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259175.1	s__Marinomonas shanghaiensis	79.73	437	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000508165.1	s__Marinomonas profundimaris	79.6412	482	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012584435.1	s__Marinomonas sp012584435	79.6066	460	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013372285.1	s__Marinomonas primoryensis	79.5567	429	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	96.98	96.98	0.86	0.86	2	-
GCF_000521805.1	s__Marinomonas ushuaiensis	79.5297	353	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018336975.1	s__Marinomonas sp013373235	79.4584	425	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.11	98.11	0.83	0.83	2	-
GCF_003315485.1	s__Marinomonas rhizomae	79.4572	471	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003721245.1	s__Marinomonas hwangdonensis	79.3813	370	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004352855.1	s__Marinomonas sp004352855	79.2577	315	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900089775.1	s__Marinomonas spartinae	78.9065	241	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.99	98.99	0.93	0.93	2	-
GCF_014803385.1	s__Marinomonas colpomeniae	78.9016	345	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:40,383] [INFO] GTDB search result was written to GCF_018145875.1_ASM1814587v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:40,383] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:40,387] [INFO] DFAST_QC result json was written to GCF_018145875.1_ASM1814587v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:40,387] [INFO] DFAST_QC completed!
[2024-01-24 13:14:40,387] [INFO] Total running time: 0h1m17s