[2024-01-24 14:21:44,083] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:21:44,085] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:21:44,085] [INFO] DQC Reference Directory: /var/lib/cwl/stg81ab97ec-f144-4496-b787-3a0786c54307/dqc_reference
[2024-01-24 14:21:45,292] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:21:45,292] [INFO] Task started: Prodigal
[2024-01-24 14:21:45,293] [INFO] Running command: gunzip -c /var/lib/cwl/stg03f5b7d3-c46d-4c30-827b-d4f785070444/GCF_007197735.1_ASM719773v1_genomic.fna.gz | prodigal -d GCF_007197735.1_ASM719773v1_genomic.fna/cds.fna -a GCF_007197735.1_ASM719773v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:21:56,347] [INFO] Task succeeded: Prodigal
[2024-01-24 14:21:56,347] [INFO] Task started: HMMsearch
[2024-01-24 14:21:56,347] [INFO] Running command: hmmsearch --tblout GCF_007197735.1_ASM719773v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg81ab97ec-f144-4496-b787-3a0786c54307/dqc_reference/reference_markers.hmm GCF_007197735.1_ASM719773v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:21:56,631] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:21:56,633] [INFO] Found 6/6 markers.
[2024-01-24 14:21:56,666] [INFO] Query marker FASTA was written to GCF_007197735.1_ASM719773v1_genomic.fna/markers.fasta
[2024-01-24 14:21:56,666] [INFO] Task started: Blastn
[2024-01-24 14:21:56,667] [INFO] Running command: blastn -query GCF_007197735.1_ASM719773v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81ab97ec-f144-4496-b787-3a0786c54307/dqc_reference/reference_markers.fasta -out GCF_007197735.1_ASM719773v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:57,360] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:57,365] [INFO] Selected 15 target genomes.
[2024-01-24 14:21:57,365] [INFO] Target genome list was writen to GCF_007197735.1_ASM719773v1_genomic.fna/target_genomes.txt
[2024-01-24 14:21:57,407] [INFO] Task started: fastANI
[2024-01-24 14:21:57,407] [INFO] Running command: fastANI --query /var/lib/cwl/stg03f5b7d3-c46d-4c30-827b-d4f785070444/GCF_007197735.1_ASM719773v1_genomic.fna.gz --refList GCF_007197735.1_ASM719773v1_genomic.fna/target_genomes.txt --output GCF_007197735.1_ASM719773v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:08,469] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:08,470] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg81ab97ec-f144-4496-b787-3a0786c54307/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:08,470] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg81ab97ec-f144-4496-b787-3a0786c54307/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:08,483] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:22:08,483] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:08,484] [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
Formosa sediminum	strain=PS13	GCA_007197735.1	2594004	2594004	type	True	100.0	1310	1311	95	conclusive
Formosa algae	strain=KMM 3553	GCA_001439665.1	225843	225843	type	True	82.9566	916	1311	95	below_threshold
Formosa agariphila	strain=type strain: KMM 3901	GCA_000723205.1	320324	320324	type	True	82.013	749	1311	95	below_threshold
Formosa haliotis	strain=LMG 28520	GCA_001685485.1	1555194	1555194	type	True	81.2406	656	1311	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=KCTC 42117	GCA_003008435.1	1520893	393060	type	True	78.242	267	1311	95	below_threshold
Tamlana agarivorans	strain=JW-26	GCA_001642835.1	481183	481183	type	True	78.0494	262	1311	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	77.9085	307	1311	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.6675	226	1311	95	below_threshold
Olleya namhaensis	strain=DSM 28881	GCA_900114005.1	1144750	1144750	type	True	77.6629	254	1311	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	77.6547	284	1311	95	below_threshold
Mariniflexile fucanivorans	strain=DSM 18792	GCA_004341235.1	264023	264023	type	True	77.631	266	1311	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	77.3731	153	1311	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	77.2963	186	1311	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	77.0727	142	1311	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.4814	141	1311	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:08,486] [INFO] DFAST Taxonomy check result was written to GCF_007197735.1_ASM719773v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:08,486] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:08,486] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:08,487] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg81ab97ec-f144-4496-b787-3a0786c54307/dqc_reference/checkm_data
[2024-01-24 14:22:08,488] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:08,529] [INFO] Task started: CheckM
[2024-01-24 14:22:08,529] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007197735.1_ASM719773v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007197735.1_ASM719773v1_genomic.fna/checkm_input GCF_007197735.1_ASM719773v1_genomic.fna/checkm_result
[2024-01-24 14:22:44,888] [INFO] Task succeeded: CheckM
[2024-01-24 14:22:44,890] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:22:44,909] [INFO] ===== Completeness check finished =====
[2024-01-24 14:22:44,910] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:22:44,910] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007197735.1_ASM719773v1_genomic.fna/markers.fasta)
[2024-01-24 14:22:44,911] [INFO] Task started: Blastn
[2024-01-24 14:22:44,911] [INFO] Running command: blastn -query GCF_007197735.1_ASM719773v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81ab97ec-f144-4496-b787-3a0786c54307/dqc_reference/reference_markers_gtdb.fasta -out GCF_007197735.1_ASM719773v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:45,912] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:45,916] [INFO] Selected 6 target genomes.
[2024-01-24 14:22:45,916] [INFO] Target genome list was writen to GCF_007197735.1_ASM719773v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:22:45,922] [INFO] Task started: fastANI
[2024-01-24 14:22:45,922] [INFO] Running command: fastANI --query /var/lib/cwl/stg03f5b7d3-c46d-4c30-827b-d4f785070444/GCF_007197735.1_ASM719773v1_genomic.fna.gz --refList GCF_007197735.1_ASM719773v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007197735.1_ASM719773v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:22:51,509] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:51,516] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:22:51,516] [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_007197735.1	s__Formosa sediminum	100.0	1310	1311	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Formosa	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001439665.1	s__Formosa algae	82.9313	919	1311	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Formosa	95.0	99.31	98.62	0.97	0.94	3	-
GCF_009796865.1	s__Formosa sp009796865	82.7987	869	1311	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Formosa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000723205.1	s__Formosa agariphila	82.0026	748	1311	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Formosa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001685485.1	s__Formosa haliotis	81.2067	657	1311	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Formosa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610635.1	s__Ichthyenterobacterium magnum	77.5178	264	1311	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ichthyenterobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:22:51,518] [INFO] GTDB search result was written to GCF_007197735.1_ASM719773v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:22:51,519] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:22:51,522] [INFO] DFAST_QC result json was written to GCF_007197735.1_ASM719773v1_genomic.fna/dqc_result.json
[2024-01-24 14:22:51,522] [INFO] DFAST_QC completed!
[2024-01-24 14:22:51,522] [INFO] Total running time: 0h1m7s