[2024-01-24 14:19:17,217] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:17,221] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:17,222] [INFO] DQC Reference Directory: /var/lib/cwl/stg3802494e-1421-4797-9b44-c3a744916452/dqc_reference
[2024-01-24 14:19:21,129] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:21,131] [INFO] Task started: Prodigal
[2024-01-24 14:19:21,132] [INFO] Running command: gunzip -c /var/lib/cwl/stg65b50c21-2d38-4ea9-88cf-b4e1a348adee/GCF_001685485.1_ASM168548v1_genomic.fna.gz | prodigal -d GCF_001685485.1_ASM168548v1_genomic.fna/cds.fna -a GCF_001685485.1_ASM168548v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:34,444] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:34,444] [INFO] Task started: HMMsearch
[2024-01-24 14:19:34,444] [INFO] Running command: hmmsearch --tblout GCF_001685485.1_ASM168548v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3802494e-1421-4797-9b44-c3a744916452/dqc_reference/reference_markers.hmm GCF_001685485.1_ASM168548v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:34,864] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:34,866] [INFO] Found 6/6 markers.
[2024-01-24 14:19:34,909] [INFO] Query marker FASTA was written to GCF_001685485.1_ASM168548v1_genomic.fna/markers.fasta
[2024-01-24 14:19:34,910] [INFO] Task started: Blastn
[2024-01-24 14:19:34,910] [INFO] Running command: blastn -query GCF_001685485.1_ASM168548v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3802494e-1421-4797-9b44-c3a744916452/dqc_reference/reference_markers.fasta -out GCF_001685485.1_ASM168548v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:36,346] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:36,351] [INFO] Selected 15 target genomes.
[2024-01-24 14:19:36,352] [INFO] Target genome list was writen to GCF_001685485.1_ASM168548v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:36,360] [INFO] Task started: fastANI
[2024-01-24 14:19:36,360] [INFO] Running command: fastANI --query /var/lib/cwl/stg65b50c21-2d38-4ea9-88cf-b4e1a348adee/GCF_001685485.1_ASM168548v1_genomic.fna.gz --refList GCF_001685485.1_ASM168548v1_genomic.fna/target_genomes.txt --output GCF_001685485.1_ASM168548v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:52,372] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:52,372] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3802494e-1421-4797-9b44-c3a744916452/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:52,373] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3802494e-1421-4797-9b44-c3a744916452/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:52,388] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:19:52,389] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:52,390] [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 haliotis	strain=LMG 28520	GCA_001685485.1	1555194	1555194	type	True	100.0	1435	1435	95	conclusive
Formosa agariphila	strain=type strain: KMM 3901	GCA_000723205.1	320324	320324	type	True	81.4458	754	1435	95	below_threshold
Formosa sediminum	strain=PS13	GCA_007197735.1	2594004	2594004	type	True	81.2338	665	1435	95	below_threshold
Formosa algae	strain=KMM 3553	GCA_001439665.1	225843	225843	type	True	80.9785	691	1435	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=KCTC 42117	GCA_003008435.1	1520893	393060	type	True	78.0844	269	1435	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.9946	225	1435	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.9237	218	1435	95	below_threshold
Tamlana haliotis	strain=B1N29	GCA_008806375.1	2614804	2614804	type	True	77.9116	250	1435	95	below_threshold
Tamlana sedimentorum	strain=JCM 19808	GCA_000943565.1	1435349	1435349	type	True	77.8888	287	1435	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	77.8238	305	1435	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	77.8141	211	1435	95	below_threshold
Tamlana nanhaiensis	strain=FHC16	GCA_000943555.1	1382798	1382798	type	True	77.5223	297	1435	95	below_threshold
Mariniflexile fucanivorans	strain=DSM 18792	GCA_004341235.1	264023	264023	type	True	77.4076	321	1435	95	below_threshold
Aestuariivivens insulae	strain=AH-MY3	GCA_022662195.1	1621988	1621988	type	True	77.342	189	1435	95	below_threshold
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	77.2683	253	1435	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:52,392] [INFO] DFAST Taxonomy check result was written to GCF_001685485.1_ASM168548v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:52,393] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:52,393] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:52,394] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3802494e-1421-4797-9b44-c3a744916452/dqc_reference/checkm_data
[2024-01-24 14:19:52,395] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:52,441] [INFO] Task started: CheckM
[2024-01-24 14:19:52,442] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001685485.1_ASM168548v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001685485.1_ASM168548v1_genomic.fna/checkm_input GCF_001685485.1_ASM168548v1_genomic.fna/checkm_result
[2024-01-24 14:20:39,595] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:39,597] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:39,642] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:39,642] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:39,642] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001685485.1_ASM168548v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:39,643] [INFO] Task started: Blastn
[2024-01-24 14:20:39,643] [INFO] Running command: blastn -query GCF_001685485.1_ASM168548v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3802494e-1421-4797-9b44-c3a744916452/dqc_reference/reference_markers_gtdb.fasta -out GCF_001685485.1_ASM168548v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:40,676] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:40,681] [INFO] Selected 5 target genomes.
[2024-01-24 14:20:40,681] [INFO] Target genome list was writen to GCF_001685485.1_ASM168548v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:40,686] [INFO] Task started: fastANI
[2024-01-24 14:20:40,686] [INFO] Running command: fastANI --query /var/lib/cwl/stg65b50c21-2d38-4ea9-88cf-b4e1a348adee/GCF_001685485.1_ASM168548v1_genomic.fna.gz --refList GCF_001685485.1_ASM168548v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001685485.1_ASM168548v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:46,404] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:46,434] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:46,434] [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_001685485.1	s__Formosa haliotis	100.0	1435	1435	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_000723205.1	s__Formosa agariphila	81.4593	754	1435	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Formosa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009796865.1	s__Formosa sp009796865	81.3602	667	1435	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Formosa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007197735.1	s__Formosa sediminum	81.2217	668	1435	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Formosa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001439665.1	s__Formosa algae	80.9756	692	1435	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Formosa	95.0	99.31	98.62	0.97	0.94	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:46,436] [INFO] GTDB search result was written to GCF_001685485.1_ASM168548v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:46,436] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:46,440] [INFO] DFAST_QC result json was written to GCF_001685485.1_ASM168548v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:46,440] [INFO] DFAST_QC completed!
[2024-01-24 14:20:46,441] [INFO] Total running time: 0h1m29s