[2024-01-24 13:31:57,474] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:57,476] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:57,476] [INFO] DQC Reference Directory: /var/lib/cwl/stgf5d3fb6f-2a70-420f-8ac6-db3a86959e30/dqc_reference
[2024-01-24 13:31:58,846] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:58,847] [INFO] Task started: Prodigal
[2024-01-24 13:31:58,847] [INFO] Running command: gunzip -c /var/lib/cwl/stg6484e551-62aa-48cf-931d-5f25fc56aa4f/GCF_014653195.1_ASM1465319v1_genomic.fna.gz | prodigal -d GCF_014653195.1_ASM1465319v1_genomic.fna/cds.fna -a GCF_014653195.1_ASM1465319v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:05,982] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:05,983] [INFO] Task started: HMMsearch
[2024-01-24 13:32:05,983] [INFO] Running command: hmmsearch --tblout GCF_014653195.1_ASM1465319v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf5d3fb6f-2a70-420f-8ac6-db3a86959e30/dqc_reference/reference_markers.hmm GCF_014653195.1_ASM1465319v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:06,228] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:06,230] [INFO] Found 6/6 markers.
[2024-01-24 13:32:06,261] [INFO] Query marker FASTA was written to GCF_014653195.1_ASM1465319v1_genomic.fna/markers.fasta
[2024-01-24 13:32:06,261] [INFO] Task started: Blastn
[2024-01-24 13:32:06,261] [INFO] Running command: blastn -query GCF_014653195.1_ASM1465319v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf5d3fb6f-2a70-420f-8ac6-db3a86959e30/dqc_reference/reference_markers.fasta -out GCF_014653195.1_ASM1465319v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:06,972] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:06,999] [INFO] Selected 20 target genomes.
[2024-01-24 13:32:07,000] [INFO] Target genome list was writen to GCF_014653195.1_ASM1465319v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:07,007] [INFO] Task started: fastANI
[2024-01-24 13:32:07,007] [INFO] Running command: fastANI --query /var/lib/cwl/stg6484e551-62aa-48cf-931d-5f25fc56aa4f/GCF_014653195.1_ASM1465319v1_genomic.fna.gz --refList GCF_014653195.1_ASM1465319v1_genomic.fna/target_genomes.txt --output GCF_014653195.1_ASM1465319v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:20,745] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:20,746] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf5d3fb6f-2a70-420f-8ac6-db3a86959e30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:20,746] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf5d3fb6f-2a70-420f-8ac6-db3a86959e30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:20,758] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:20,758] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:20,758] [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
Thalassotalea profundi	strain=CGMCC 1.15922	GCA_014653195.1	2036687	2036687	type	True	100.0	1311	1311	95	conclusive
Thalassotalea piscium	strain=DSM 26287	GCA_014207645.1	1230533	1230533	type	True	80.4307	619	1311	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_002104455.1	641665	641665	type	True	79.4869	218	1311	95	below_threshold
Thalassotalea algicola	strain=M1531	GCA_012932965.1	2716224	2716224	type	True	78.4531	177	1311	95	below_threshold
Cognaticolwellia mytili	strain=KCTC 52417	GCA_002104475.1	1888913	1888913	type	True	78.2195	242	1311	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	78.1932	197	1311	95	below_threshold
Litorilituus lipolyticus	strain=RZ04	GCA_006439335.1	2491017	2491017	type	True	78.1089	204	1311	95	below_threshold
Pseudocolwellia agarivorans	strain=QM50	GCA_002000085.1	1911682	1911682	type	True	77.9852	247	1311	95	below_threshold
Thalassotalea marina	strain=KCTC 42731	GCA_014656435.1	1673741	1673741	type	True	77.934	220	1311	95	below_threshold
Colwellia demingiae	strain=ACAM 459	GCA_007954275.1	89401	89401	type	True	77.8847	208	1311	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	77.6536	201	1311	95	below_threshold
Colwellia piezophila	strain=ATCC BAA-637	GCA_000378625.1	211668	211668	type	True	77.3628	202	1311	95	below_threshold
Shewanella inventionis	strain=KCTC 42807	GCA_023283595.1	1738770	1738770	type	True	76.0373	54	1311	95	below_threshold
Shewanella psychromarinicola	strain=JCM 32090	GCA_023283865.1	2487742	2487742	type	True	75.7998	50	1311	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:20,760] [INFO] DFAST Taxonomy check result was written to GCF_014653195.1_ASM1465319v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:20,761] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:20,761] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:20,761] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf5d3fb6f-2a70-420f-8ac6-db3a86959e30/dqc_reference/checkm_data
[2024-01-24 13:32:20,762] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:20,800] [INFO] Task started: CheckM
[2024-01-24 13:32:20,800] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014653195.1_ASM1465319v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014653195.1_ASM1465319v1_genomic.fna/checkm_input GCF_014653195.1_ASM1465319v1_genomic.fna/checkm_result
[2024-01-24 13:32:47,921] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:47,922] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:47,940] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:47,940] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:47,940] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014653195.1_ASM1465319v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:47,940] [INFO] Task started: Blastn
[2024-01-24 13:32:47,941] [INFO] Running command: blastn -query GCF_014653195.1_ASM1465319v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf5d3fb6f-2a70-420f-8ac6-db3a86959e30/dqc_reference/reference_markers_gtdb.fasta -out GCF_014653195.1_ASM1465319v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:49,025] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:49,038] [INFO] Selected 20 target genomes.
[2024-01-24 13:32:49,038] [INFO] Target genome list was writen to GCF_014653195.1_ASM1465319v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:49,052] [INFO] Task started: fastANI
[2024-01-24 13:32:49,052] [INFO] Running command: fastANI --query /var/lib/cwl/stg6484e551-62aa-48cf-931d-5f25fc56aa4f/GCF_014653195.1_ASM1465319v1_genomic.fna.gz --refList GCF_014653195.1_ASM1465319v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014653195.1_ASM1465319v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:05,372] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:05,387] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:05,387] [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_014653195.1	s__Thalassotalea_B profundi	100.0	1311	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014207645.1	s__Thalassotalea_B piscium	80.4447	618	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003971255.1	s__Cognaticolwellia sp003971255	78.2501	255	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002000025.1	s__Cognaticolwellia aestuarii	78.1255	263	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001767295.1	s__Colwellia_A sp001767295	78.1184	238	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	96.63	96.27	0.86	0.85	17	-
GCF_006439335.1	s__Litorilituus lipolyticus	78.1089	204	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Litorilituus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017168195.1	s__G2M2-11 sp017168195	78.1006	272	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__G2M2-11	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002104515.1	s__Cognaticolwellia polaris	78.0184	251	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002000085.1	s__Pseudocolwellia agarivorans	77.9992	246	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudocolwellia	95.0	95.36	95.36	0.90	0.90	2	-
GCF_001913705.1	s__Thalassotalea_C sp001913705	77.9789	231	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003545765.1	s__Litorilituus sp003545765	77.8507	214	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Litorilituus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002076895.1	s__Cognaticolwellia beringensis	77.834	255	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007197775.1	s__Thalassotalea_A sp007197775	77.8233	70	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015487235.1	s__GCA-2401725 sp015487235	77.8131	188	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__GCA-2401725	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860585.1	s__Colwellia sp018860585	77.8034	213	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215295.1	s__Colwellia_A sp013215295	77.6505	237	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836255.1	s__Colwellia sp002836255	77.588	212	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003354085.1	s__Cognaticolwellia sp003354085	77.4371	234	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:05,389] [INFO] GTDB search result was written to GCF_014653195.1_ASM1465319v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:05,389] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:05,393] [INFO] DFAST_QC result json was written to GCF_014653195.1_ASM1465319v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:05,393] [INFO] DFAST_QC completed!
[2024-01-24 13:33:05,393] [INFO] Total running time: 0h1m8s