[2024-01-24 10:47:10,264] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:10,267] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:10,267] [INFO] DQC Reference Directory: /var/lib/cwl/stg9d7cb356-eedd-424c-b213-a6dc1c1a6a88/dqc_reference
[2024-01-24 10:47:12,152] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,153] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,153] [INFO] Running command: gunzip -c /var/lib/cwl/stg9278a966-9434-4a80-a8ad-42fe8439e987/GCF_017776525.1_ASM1777652v1_genomic.fna.gz | prodigal -d GCF_017776525.1_ASM1777652v1_genomic.fna/cds.fna -a GCF_017776525.1_ASM1777652v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:21,888] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:21,889] [INFO] Task started: HMMsearch
[2024-01-24 10:47:21,889] [INFO] Running command: hmmsearch --tblout GCF_017776525.1_ASM1777652v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9d7cb356-eedd-424c-b213-a6dc1c1a6a88/dqc_reference/reference_markers.hmm GCF_017776525.1_ASM1777652v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:22,180] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:22,182] [INFO] Found 6/6 markers.
[2024-01-24 10:47:22,216] [INFO] Query marker FASTA was written to GCF_017776525.1_ASM1777652v1_genomic.fna/markers.fasta
[2024-01-24 10:47:22,217] [INFO] Task started: Blastn
[2024-01-24 10:47:22,217] [INFO] Running command: blastn -query GCF_017776525.1_ASM1777652v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d7cb356-eedd-424c-b213-a6dc1c1a6a88/dqc_reference/reference_markers.fasta -out GCF_017776525.1_ASM1777652v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:22,981] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:22,985] [INFO] Selected 22 target genomes.
[2024-01-24 10:47:22,986] [INFO] Target genome list was writen to GCF_017776525.1_ASM1777652v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:23,621] [INFO] Task started: fastANI
[2024-01-24 10:47:23,622] [INFO] Running command: fastANI --query /var/lib/cwl/stg9278a966-9434-4a80-a8ad-42fe8439e987/GCF_017776525.1_ASM1777652v1_genomic.fna.gz --refList GCF_017776525.1_ASM1777652v1_genomic.fna/target_genomes.txt --output GCF_017776525.1_ASM1777652v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:41,658] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:41,658] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9d7cb356-eedd-424c-b213-a6dc1c1a6a88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:41,659] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9d7cb356-eedd-424c-b213-a6dc1c1a6a88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:41,681] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:47:41,681] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:41,681] [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
Marinobacterium alkalitolerans	strain=AK62	GCA_017776525.1	1542925	1542925	type	True	100.0	1085	1088	95	conclusive
Marinobacterium stanieri	strain=DSM 7027	GCA_900155945.1	49186	49186	type	True	81.6506	711	1088	95	below_threshold
Marinobacterium halophilum	strain=DSM 17586	GCA_003014615.1	267374	267374	type	True	80.2007	540	1088	95	below_threshold
Marinobacterium georgiense	strain=DSM 11526	GCA_900107855.1	48076	48076	type	True	80.0426	459	1088	95	below_threshold
Marinobacterium mangrovicola	strain=DSM 27697	GCA_004339595.1	1476959	1476959	type	True	78.9878	291	1088	95	below_threshold
Marinobacterium lutimaris	strain=DSM 22012	GCA_900108065.1	568106	568106	type	True	78.9417	296	1088	95	below_threshold
Marinobacterium ramblicola	strain=D7	GCA_019084545.1	2849041	2849041	type	True	78.9214	336	1088	95	below_threshold
Marinobacterium zhoushanense	strain=CGMCC 1.15341	GCA_014641945.1	1679163	1679163	type	True	78.8394	296	1088	95	below_threshold
Marinobacterium arenosum	strain=CAU 1594	GCA_019795155.1	2862496	2862496	type	True	78.5433	288	1088	95	below_threshold
Marinobacterium rhizophilum	strain=DSM 18822	GCA_000378045.1	420402	420402	type	True	77.9178	249	1088	95	below_threshold
Marinobacterium aestuarii	strain=ST58-10	GCA_001651805.1	1821621	1821621	type	True	77.8787	254	1088	95	below_threshold
Marinobacterium profundum	strain=PAMC 27536	GCA_001528745.1	1714300	1714300	type	True	77.6622	221	1088	95	below_threshold
Pseudomonas yangonensis	strain=MY50	GCA_009932725.1	2579922	2579922	type	True	76.781	128	1088	95	below_threshold
Pseudomonas composti	strain=CCUG 59231	GCA_900115475.1	658457	658457	type	True	76.5735	112	1088	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	76.4211	121	1088	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	76.3489	116	1088	95	below_threshold
Alcanivorax limicola	strain=JB21	GCA_019931215.1	2874102	2874102	type	True	76.3062	78	1088	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	76.2733	122	1088	95	below_threshold
Tamilnaduibacter salinus	strain=Mi-7	GCA_002287355.1	1484056	1484056	type	True	76.2162	63	1088	95	below_threshold
Tamilnaduibacter salinus	strain=DSM 28688	GCA_003096655.1	1484056	1484056	type	True	76.1626	70	1088	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	75.4668	64	1088	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:41,684] [INFO] DFAST Taxonomy check result was written to GCF_017776525.1_ASM1777652v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:41,684] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:41,685] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:41,685] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9d7cb356-eedd-424c-b213-a6dc1c1a6a88/dqc_reference/checkm_data
[2024-01-24 10:47:41,687] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:41,722] [INFO] Task started: CheckM
[2024-01-24 10:47:41,722] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017776525.1_ASM1777652v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017776525.1_ASM1777652v1_genomic.fna/checkm_input GCF_017776525.1_ASM1777652v1_genomic.fna/checkm_result
[2024-01-24 10:48:15,896] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:15,897] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:15,920] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:15,920] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:15,920] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017776525.1_ASM1777652v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:15,921] [INFO] Task started: Blastn
[2024-01-24 10:48:15,921] [INFO] Running command: blastn -query GCF_017776525.1_ASM1777652v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d7cb356-eedd-424c-b213-a6dc1c1a6a88/dqc_reference/reference_markers_gtdb.fasta -out GCF_017776525.1_ASM1777652v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:17,046] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:17,051] [INFO] Selected 10 target genomes.
[2024-01-24 10:48:17,052] [INFO] Target genome list was writen to GCF_017776525.1_ASM1777652v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:17,068] [INFO] Task started: fastANI
[2024-01-24 10:48:17,069] [INFO] Running command: fastANI --query /var/lib/cwl/stg9278a966-9434-4a80-a8ad-42fe8439e987/GCF_017776525.1_ASM1777652v1_genomic.fna.gz --refList GCF_017776525.1_ASM1777652v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017776525.1_ASM1777652v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:25,543] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:25,562] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:25,563] [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_017776525.1	s__Marinobacterium alkalitolerans	100.0	1085	1088	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900155945.1	s__Marinobacterium stanieri	81.6502	711	1088	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	96.47	96.47	0.91	0.91	2	-
GCF_019061305.1	s__Marinobacterium sp019061305	81.1093	573	1088	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013868415.1	s__Marinobacterium sp013868415	80.291	463	1088	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014615.1	s__Marinobacterium halophilum	80.197	541	1088	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	98.87	98.87	0.91	0.91	2	-
GCF_900107855.1	s__Marinobacterium georgiense	80.0249	461	1088	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	97.23	97.23	0.75	0.75	2	-
GCF_900108065.1	s__Marinobacterium lutimaris	78.9197	299	1088	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003250495.1	s__Marinobacterium sp003250495	78.5523	255	1088	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373085.1	s__Marinobacterium_A sp013373085	77.9354	253	1088	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115475.1	s__Pseudomonas_E composti	76.5539	113	1088	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.90	97.79	0.91	0.90	5	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:25,566] [INFO] GTDB search result was written to GCF_017776525.1_ASM1777652v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:25,567] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:25,571] [INFO] DFAST_QC result json was written to GCF_017776525.1_ASM1777652v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:25,571] [INFO] DFAST_QC completed!
[2024-01-24 10:48:25,571] [INFO] Total running time: 0h1m15s