[2024-01-24 14:39:00,196] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:00,215] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:00,215] [INFO] DQC Reference Directory: /var/lib/cwl/stgf3df69a7-df7c-40f1-941a-cf80d4ca1f71/dqc_reference
[2024-01-24 14:39:01,546] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:01,547] [INFO] Task started: Prodigal
[2024-01-24 14:39:01,547] [INFO] Running command: gunzip -c /var/lib/cwl/stgbe9f91c2-21c2-4b06-a359-b884319462b5/GCF_001439665.1_ASM143966v1_genomic.fna.gz | prodigal -d GCF_001439665.1_ASM143966v1_genomic.fna/cds.fna -a GCF_001439665.1_ASM143966v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:15,045] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:15,045] [INFO] Task started: HMMsearch
[2024-01-24 14:39:15,046] [INFO] Running command: hmmsearch --tblout GCF_001439665.1_ASM143966v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf3df69a7-df7c-40f1-941a-cf80d4ca1f71/dqc_reference/reference_markers.hmm GCF_001439665.1_ASM143966v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:15,358] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:15,360] [INFO] Found 6/6 markers.
[2024-01-24 14:39:15,411] [INFO] Query marker FASTA was written to GCF_001439665.1_ASM143966v1_genomic.fna/markers.fasta
[2024-01-24 14:39:15,411] [INFO] Task started: Blastn
[2024-01-24 14:39:15,411] [INFO] Running command: blastn -query GCF_001439665.1_ASM143966v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3df69a7-df7c-40f1-941a-cf80d4ca1f71/dqc_reference/reference_markers.fasta -out GCF_001439665.1_ASM143966v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:16,180] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:16,184] [INFO] Selected 15 target genomes.
[2024-01-24 14:39:16,184] [INFO] Target genome list was writen to GCF_001439665.1_ASM143966v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:16,198] [INFO] Task started: fastANI
[2024-01-24 14:39:16,198] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe9f91c2-21c2-4b06-a359-b884319462b5/GCF_001439665.1_ASM143966v1_genomic.fna.gz --refList GCF_001439665.1_ASM143966v1_genomic.fna/target_genomes.txt --output GCF_001439665.1_ASM143966v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:26,821] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:26,821] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf3df69a7-df7c-40f1-941a-cf80d4ca1f71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:26,822] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf3df69a7-df7c-40f1-941a-cf80d4ca1f71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:26,835] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:39:26,835] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:26,836] [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 algae	strain=KMM 3553	GCA_001439665.1	225843	225843	type	True	100.0	1389	1394	95	conclusive
Formosa sediminum	strain=PS13	GCA_007197735.1	2594004	2594004	type	True	83.0357	899	1394	95	below_threshold
Formosa agariphila	strain=type strain: KMM 3901	GCA_000723205.1	320324	320324	type	True	82.273	798	1394	95	below_threshold
Formosa haliotis	strain=LMG 28520	GCA_001685485.1	1555194	1555194	type	True	80.9987	686	1394	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	78.0217	331	1394	95	below_threshold
Tamlana agarivorans	strain=JW-26	GCA_001642835.1	481183	481183	type	True	77.8166	275	1394	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.713	184	1394	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	77.5499	197	1394	95	below_threshold
Xanthomarina gelatinilytica	strain=AK20	GCA_000348685.1	1137281	1137281	type	True	77.5268	182	1394	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	77.4369	192	1394	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.4016	201	1394	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	77.2951	149	1394	95	below_threshold
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	77.2349	262	1394	95	below_threshold
Winogradskyella epiphytica	strain=KCTC 12220	GCA_014651315.1	262005	262005	type	True	77.1844	198	1394	95	below_threshold
Flavobacterium hydatis	strain=DSM 2063	GCA_000737695.1	991	991	type	True	76.466	115	1394	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:26,837] [INFO] DFAST Taxonomy check result was written to GCF_001439665.1_ASM143966v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:26,838] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:26,838] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:26,838] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf3df69a7-df7c-40f1-941a-cf80d4ca1f71/dqc_reference/checkm_data
[2024-01-24 14:39:26,840] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:26,882] [INFO] Task started: CheckM
[2024-01-24 14:39:26,883] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001439665.1_ASM143966v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001439665.1_ASM143966v1_genomic.fna/checkm_input GCF_001439665.1_ASM143966v1_genomic.fna/checkm_result
[2024-01-24 14:40:07,504] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:07,505] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:07,540] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:07,540] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:07,541] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001439665.1_ASM143966v1_genomic.fna/markers.fasta)
[2024-01-24 14:40:07,541] [INFO] Task started: Blastn
[2024-01-24 14:40:07,541] [INFO] Running command: blastn -query GCF_001439665.1_ASM143966v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3df69a7-df7c-40f1-941a-cf80d4ca1f71/dqc_reference/reference_markers_gtdb.fasta -out GCF_001439665.1_ASM143966v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:08,651] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:08,654] [INFO] Selected 6 target genomes.
[2024-01-24 14:40:08,654] [INFO] Target genome list was writen to GCF_001439665.1_ASM143966v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:08,659] [INFO] Task started: fastANI
[2024-01-24 14:40:08,659] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe9f91c2-21c2-4b06-a359-b884319462b5/GCF_001439665.1_ASM143966v1_genomic.fna.gz --refList GCF_001439665.1_ASM143966v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001439665.1_ASM143966v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:14,470] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:14,477] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:14,477] [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_001439665.1	s__Formosa algae	100.0	1389	1394	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Formosa	95.0	99.31	98.62	0.97	0.94	3	conclusive
GCF_009796865.1	s__Formosa sp009796865	84.0626	909	1394	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	83.0247	900	1394	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	82.2733	798	1394	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	80.9894	687	1394	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Formosa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148645.1	s__Xanthomarina spongicola	77.7855	274	1394	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:40:14,479] [INFO] GTDB search result was written to GCF_001439665.1_ASM143966v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:14,480] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:14,483] [INFO] DFAST_QC result json was written to GCF_001439665.1_ASM143966v1_genomic.fna/dqc_result.json
[2024-01-24 14:40:14,483] [INFO] DFAST_QC completed!
[2024-01-24 14:40:14,483] [INFO] Total running time: 0h1m14s