[2024-01-24 12:47:05,152] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:05,153] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:05,153] [INFO] DQC Reference Directory: /var/lib/cwl/stg19870643-ba53-4d62-a8c8-38ccdc240ad5/dqc_reference
[2024-01-24 12:47:06,388] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:06,389] [INFO] Task started: Prodigal
[2024-01-24 12:47:06,389] [INFO] Running command: gunzip -c /var/lib/cwl/stg8fbd792b-e74d-4909-a0bb-ab913f7b3d19/GCF_000246945.1_ASM24694v2_genomic.fna.gz | prodigal -d GCF_000246945.1_ASM24694v2_genomic.fna/cds.fna -a GCF_000246945.1_ASM24694v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:15,351] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:15,351] [INFO] Task started: HMMsearch
[2024-01-24 12:47:15,351] [INFO] Running command: hmmsearch --tblout GCF_000246945.1_ASM24694v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg19870643-ba53-4d62-a8c8-38ccdc240ad5/dqc_reference/reference_markers.hmm GCF_000246945.1_ASM24694v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:15,617] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:15,618] [INFO] Found 6/6 markers.
[2024-01-24 12:47:15,653] [INFO] Query marker FASTA was written to GCF_000246945.1_ASM24694v2_genomic.fna/markers.fasta
[2024-01-24 12:47:15,653] [INFO] Task started: Blastn
[2024-01-24 12:47:15,654] [INFO] Running command: blastn -query GCF_000246945.1_ASM24694v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg19870643-ba53-4d62-a8c8-38ccdc240ad5/dqc_reference/reference_markers.fasta -out GCF_000246945.1_ASM24694v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:16,325] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:16,329] [INFO] Selected 19 target genomes.
[2024-01-24 12:47:16,329] [INFO] Target genome list was writen to GCF_000246945.1_ASM24694v2_genomic.fna/target_genomes.txt
[2024-01-24 12:47:16,343] [INFO] Task started: fastANI
[2024-01-24 12:47:16,344] [INFO] Running command: fastANI --query /var/lib/cwl/stg8fbd792b-e74d-4909-a0bb-ab913f7b3d19/GCF_000246945.1_ASM24694v2_genomic.fna.gz --refList GCF_000246945.1_ASM24694v2_genomic.fna/target_genomes.txt --output GCF_000246945.1_ASM24694v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:26,882] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:26,883] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg19870643-ba53-4d62-a8c8-38ccdc240ad5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:26,883] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg19870643-ba53-4d62-a8c8-38ccdc240ad5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:26,900] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:47:26,901] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:26,901] [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
Myroides injenensis	strain=M09-0166	GCA_000246945.2	1183151	1183151	type	True	100.0	1051	1066	95	conclusive
Myroides albus	strain=BIT-d1	GCA_009711045.1	2562892	2562892	type	True	79.5956	382	1066	95	below_threshold
Myroides marinus	strain=DSM 23048	GCA_900109075.1	703342	703342	type	True	79.5899	409	1066	95	below_threshold
Myroides phaeus	strain=DSM 23313	GCA_900099675.1	702745	702745	type	True	79.4975	395	1066	95	below_threshold
Myroides odoratimimus	strain=NCTC11180	GCA_900453765.1	76832	76832	type	True	79.4288	435	1066	95	below_threshold
Myroides odoratimimus	strain=CCUG39352	GCA_001485415.1	76832	76832	type	True	79.3755	437	1066	95	below_threshold
Myroides odoratimimus subsp. xuanwuensis	strain=DSM 27251	GCA_900142635.1	1324934	76832	type	True	79.1846	416	1066	95	below_threshold
Myroides profundi	strain=DSM 19823	GCA_900111065.1	480520	480520	type	True	79.0646	413	1066	95	below_threshold
Myroides profundi	strain=D25	GCA_000833025.1	480520	480520	type	True	78.9513	417	1066	95	below_threshold
Myroides fluvii	strain=CJ210	GCA_009792295.1	2572594	2572594	type	True	78.7682	249	1066	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	77.1961	121	1066	95	below_threshold
Flavobacterium lutivivi	strain=CGMCC 1.15347	GCA_014642275.1	1677894	1677894	type	True	77.1205	82	1066	95	below_threshold
Flavobacterium amnicola	strain=LLJ-11	GCA_004122165.1	2506422	2506422	type	True	77.0756	69	1066	95	below_threshold
Flavobacterium haoranii	strain=DSM 22807	GCA_900142055.1	683124	683124	type	True	76.9894	122	1066	95	below_threshold
Flavobacterium frigidarium	strain=DSM 17623	GCA_000425505.1	99286	99286	type	True	76.9035	89	1066	95	below_threshold
Faecalibacter rhinopitheci	strain=WQ 117	GCA_015234135.1	2779678	2779678	type	True	76.1451	51	1066	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	76.0228	65	1066	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:26,903] [INFO] DFAST Taxonomy check result was written to GCF_000246945.1_ASM24694v2_genomic.fna/tc_result.tsv
[2024-01-24 12:47:26,904] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:26,904] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:26,904] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg19870643-ba53-4d62-a8c8-38ccdc240ad5/dqc_reference/checkm_data
[2024-01-24 12:47:26,906] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:26,947] [INFO] Task started: CheckM
[2024-01-24 12:47:26,947] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000246945.1_ASM24694v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000246945.1_ASM24694v2_genomic.fna/checkm_input GCF_000246945.1_ASM24694v2_genomic.fna/checkm_result
[2024-01-24 12:47:58,914] [INFO] Task succeeded: CheckM
[2024-01-24 12:47:58,915] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:47:58,940] [INFO] ===== Completeness check finished =====
[2024-01-24 12:47:58,941] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:47:58,941] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000246945.1_ASM24694v2_genomic.fna/markers.fasta)
[2024-01-24 12:47:58,942] [INFO] Task started: Blastn
[2024-01-24 12:47:58,942] [INFO] Running command: blastn -query GCF_000246945.1_ASM24694v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg19870643-ba53-4d62-a8c8-38ccdc240ad5/dqc_reference/reference_markers_gtdb.fasta -out GCF_000246945.1_ASM24694v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:00,069] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:00,072] [INFO] Selected 15 target genomes.
[2024-01-24 12:48:00,072] [INFO] Target genome list was writen to GCF_000246945.1_ASM24694v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:00,105] [INFO] Task started: fastANI
[2024-01-24 12:48:00,105] [INFO] Running command: fastANI --query /var/lib/cwl/stg8fbd792b-e74d-4909-a0bb-ab913f7b3d19/GCF_000246945.1_ASM24694v2_genomic.fna.gz --refList GCF_000246945.1_ASM24694v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000246945.1_ASM24694v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:09,803] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:09,816] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:09,816] [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_000246945.1	s__Flavobacterium injenense	100.0	1051	1066	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009711045.1	s__Flavobacterium album_A	79.5854	383	1066	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.30	99.30	0.90	0.90	2	-
GCF_900109075.1	s__Flavobacterium marinum_A	79.571	411	1066	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.64	97.56	0.90	0.90	4	-
GCF_900099675.1	s__Flavobacterium phaeum	79.5102	394	1066	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009799805.1	s__Flavobacterium phaeum_A	79.509	402	1066	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001485415.1	s__Flavobacterium odoratimimum	79.382	436	1066	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.35	97.00	0.91	0.88	14	-
GCF_002286775.1	s__Flavobacterium sp002286775	79.2623	368	1066	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000833025.1	s__Flavobacterium profundi	78.9614	416	1066	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_009792295.1	s__Flavobacterium sp009792295	78.7542	250	1066	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014642275.1	s__Flavobacterium lutivivi	77.1205	82	1066	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004122165.1	s__Flavobacterium sp004122165	77.0756	69	1066	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425505.1	s__Flavobacterium frigidarium	76.9299	87	1066	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009926065.1	s__Flavobacterium sp009926065	76.8183	62	1066	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116115.1	s__Lutibacter maritimus	75.9888	77	1066	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003260195.1	s__Lutibacter citreus	75.955	84	1066	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:09,817] [INFO] GTDB search result was written to GCF_000246945.1_ASM24694v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:09,818] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:09,822] [INFO] DFAST_QC result json was written to GCF_000246945.1_ASM24694v2_genomic.fna/dqc_result.json
[2024-01-24 12:48:09,822] [INFO] DFAST_QC completed!
[2024-01-24 12:48:09,822] [INFO] Total running time: 0h1m5s