[2024-01-24 14:50:04,218] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:50:04,220] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:50:04,220] [INFO] DQC Reference Directory: /var/lib/cwl/stg6e3ab795-edfc-4a16-9fbd-ccc1ba096922/dqc_reference
[2024-01-24 14:50:05,659] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:50:05,660] [INFO] Task started: Prodigal
[2024-01-24 14:50:05,661] [INFO] Running command: gunzip -c /var/lib/cwl/stg93e8be35-644b-4329-8151-25c6eb0cd213/GCF_030295955.1_ASM3029595v1_genomic.fna.gz | prodigal -d GCF_030295955.1_ASM3029595v1_genomic.fna/cds.fna -a GCF_030295955.1_ASM3029595v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:50:13,955] [INFO] Task succeeded: Prodigal
[2024-01-24 14:50:13,956] [INFO] Task started: HMMsearch
[2024-01-24 14:50:13,956] [INFO] Running command: hmmsearch --tblout GCF_030295955.1_ASM3029595v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6e3ab795-edfc-4a16-9fbd-ccc1ba096922/dqc_reference/reference_markers.hmm GCF_030295955.1_ASM3029595v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:50:14,252] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:50:14,253] [INFO] Found 6/6 markers.
[2024-01-24 14:50:14,284] [INFO] Query marker FASTA was written to GCF_030295955.1_ASM3029595v1_genomic.fna/markers.fasta
[2024-01-24 14:50:14,285] [INFO] Task started: Blastn
[2024-01-24 14:50:14,285] [INFO] Running command: blastn -query GCF_030295955.1_ASM3029595v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e3ab795-edfc-4a16-9fbd-ccc1ba096922/dqc_reference/reference_markers.fasta -out GCF_030295955.1_ASM3029595v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:50:15,091] [INFO] Task succeeded: Blastn
[2024-01-24 14:50:15,095] [INFO] Selected 20 target genomes.
[2024-01-24 14:50:15,095] [INFO] Target genome list was writen to GCF_030295955.1_ASM3029595v1_genomic.fna/target_genomes.txt
[2024-01-24 14:50:15,106] [INFO] Task started: fastANI
[2024-01-24 14:50:15,107] [INFO] Running command: fastANI --query /var/lib/cwl/stg93e8be35-644b-4329-8151-25c6eb0cd213/GCF_030295955.1_ASM3029595v1_genomic.fna.gz --refList GCF_030295955.1_ASM3029595v1_genomic.fna/target_genomes.txt --output GCF_030295955.1_ASM3029595v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:50:29,328] [INFO] Task succeeded: fastANI
[2024-01-24 14:50:29,329] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6e3ab795-edfc-4a16-9fbd-ccc1ba096922/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:50:29,330] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6e3ab795-edfc-4a16-9fbd-ccc1ba096922/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:50:29,347] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:50:29,347] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:50:29,348] [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 agarivorans	strain=DSM 19706	GCA_900111755.1	349064	349064	type	True	99.9721	1085	1116	95	conclusive
Thalassotalea crassostreae	strain=LPB0090	GCA_001831495.1	1763536	1763536	type	True	79.3492	115	1116	95	below_threshold
Litorilituus sediminis	strain=JCM 17549	GCA_004295665.1	718192	718192	type	True	79.0214	159	1116	95	below_threshold
Thalassotalea marina	strain=KCTC 42731	GCA_014656435.1	1673741	1673741	type	True	78.8506	141	1116	95	below_threshold
Thalassotalea algicola	strain=M1531	GCA_012932965.1	2716224	2716224	type	True	78.4132	147	1116	95	below_threshold
Pseudoalteromonas tunicata	strain=D2	GCA_002310815.1	314281	314281	type	True	78.3362	70	1116	95	below_threshold
Thalassotalea crassostreae	strain=LPB0090	GCA_001652445.1	1763536	1763536	type	True	78.1362	107	1116	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	77.8764	100	1116	95	below_threshold
Thalassotalea profundi	strain=CGMCC 1.15922	GCA_014653195.1	2036687	2036687	type	True	77.739	117	1116	95	below_threshold
Pseudoalteromonas tunicata	strain=D2	GCA_000153245.1	314281	314281	type	True	77.7086	66	1116	95	below_threshold
Litorilituus lipolyticus	strain=RZ04	GCA_006439335.1	2491017	2491017	type	True	77.6823	140	1116	95	below_threshold
Cognaticolwellia mytili	strain=KCTC 52417	GCA_002104475.1	1888913	1888913	type	True	77.6787	135	1116	95	below_threshold
Thalassotalea piscium	strain=DSM 26287	GCA_014207645.1	1230533	1230533	type	True	77.6259	122	1116	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	77.5863	115	1116	95	below_threshold
Pseudocolwellia agarivorans	strain=QM50	GCA_002000085.1	1911682	1911682	type	True	77.4055	121	1116	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:50:29,349] [INFO] DFAST Taxonomy check result was written to GCF_030295955.1_ASM3029595v1_genomic.fna/tc_result.tsv
[2024-01-24 14:50:29,350] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:50:29,350] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:50:29,350] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6e3ab795-edfc-4a16-9fbd-ccc1ba096922/dqc_reference/checkm_data
[2024-01-24 14:50:29,352] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:50:29,385] [INFO] Task started: CheckM
[2024-01-24 14:50:29,385] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030295955.1_ASM3029595v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030295955.1_ASM3029595v1_genomic.fna/checkm_input GCF_030295955.1_ASM3029595v1_genomic.fna/checkm_result
[2024-01-24 14:50:58,634] [INFO] Task succeeded: CheckM
[2024-01-24 14:50:58,635] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:50:58,653] [INFO] ===== Completeness check finished =====
[2024-01-24 14:50:58,654] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:50:58,654] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030295955.1_ASM3029595v1_genomic.fna/markers.fasta)
[2024-01-24 14:50:58,654] [INFO] Task started: Blastn
[2024-01-24 14:50:58,655] [INFO] Running command: blastn -query GCF_030295955.1_ASM3029595v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e3ab795-edfc-4a16-9fbd-ccc1ba096922/dqc_reference/reference_markers_gtdb.fasta -out GCF_030295955.1_ASM3029595v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:50:59,771] [INFO] Task succeeded: Blastn
[2024-01-24 14:50:59,776] [INFO] Selected 19 target genomes.
[2024-01-24 14:50:59,776] [INFO] Target genome list was writen to GCF_030295955.1_ASM3029595v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:50:59,790] [INFO] Task started: fastANI
[2024-01-24 14:50:59,790] [INFO] Running command: fastANI --query /var/lib/cwl/stg93e8be35-644b-4329-8151-25c6eb0cd213/GCF_030295955.1_ASM3029595v1_genomic.fna.gz --refList GCF_030295955.1_ASM3029595v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030295955.1_ASM3029595v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:51:14,809] [INFO] Task succeeded: fastANI
[2024-01-24 14:51:14,825] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:51:14,825] [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_900111755.1	s__Thalassotalea_D agarivorans	99.9721	1085	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_D	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003390375.1	s__Thalassotalea euphylliae_A	79.692	140	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014898095.1	s__Thalassotalea sp014898095	79.4046	146	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003390395.1	s__Thalassotalea euphylliae_C	79.2335	144	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000948985.1	s__Thalassomonas viridans	79.2166	63	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004295665.1	s__Litorilituus sediminis	78.9539	160	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Litorilituus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656435.1	s__Thalassotalea_C marina	78.8962	138	1116	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_017744155.1	s__Thalassotalea sp017744155	78.7696	129	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002077175.1	s__Cognaticolwellia sp002077175	78.5818	127	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002076895.1	s__Cognaticolwellia beringensis	78.5674	140	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932965.1	s__Thalassotalea algicola	78.5577	146	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009832865.1	s__Colwellia sp009832865	78.2569	132	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002104515.1	s__Cognaticolwellia polaris	77.9343	126	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001913705.1	s__Thalassotalea_C sp001913705	77.9021	125	1116	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_018860755.1	s__Colwellia sp018860755	77.6902	130	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006439335.1	s__Litorilituus lipolyticus	77.6796	141	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Litorilituus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860585.1	s__Colwellia sp018860585	77.6512	107	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860915.1	s__Colwellia sp018860915	77.371	114	1116	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	76.6949	115	1116	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 14:51:14,831] [INFO] GTDB search result was written to GCF_030295955.1_ASM3029595v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:51:14,831] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:51:14,838] [INFO] DFAST_QC result json was written to GCF_030295955.1_ASM3029595v1_genomic.fna/dqc_result.json
[2024-01-24 14:51:14,838] [INFO] DFAST_QC completed!
[2024-01-24 14:51:14,838] [INFO] Total running time: 0h1m11s