[2024-01-24 15:06:36,847] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:06:36,849] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:06:36,849] [INFO] DQC Reference Directory: /var/lib/cwl/stgf90ca0c7-8a2c-4abc-8380-2c7b2dce8833/dqc_reference
[2024-01-24 15:06:38,253] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:06:38,254] [INFO] Task started: Prodigal
[2024-01-24 15:06:38,254] [INFO] Running command: gunzip -c /var/lib/cwl/stg937c625d-abd7-4073-b0b0-dddcedda085b/GCF_009711045.1_ASM971104v1_genomic.fna.gz | prodigal -d GCF_009711045.1_ASM971104v1_genomic.fna/cds.fna -a GCF_009711045.1_ASM971104v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:06:50,693] [INFO] Task succeeded: Prodigal
[2024-01-24 15:06:50,693] [INFO] Task started: HMMsearch
[2024-01-24 15:06:50,693] [INFO] Running command: hmmsearch --tblout GCF_009711045.1_ASM971104v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf90ca0c7-8a2c-4abc-8380-2c7b2dce8833/dqc_reference/reference_markers.hmm GCF_009711045.1_ASM971104v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:06:50,969] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:06:50,970] [INFO] Found 6/6 markers.
[2024-01-24 15:06:51,007] [INFO] Query marker FASTA was written to GCF_009711045.1_ASM971104v1_genomic.fna/markers.fasta
[2024-01-24 15:06:51,008] [INFO] Task started: Blastn
[2024-01-24 15:06:51,008] [INFO] Running command: blastn -query GCF_009711045.1_ASM971104v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf90ca0c7-8a2c-4abc-8380-2c7b2dce8833/dqc_reference/reference_markers.fasta -out GCF_009711045.1_ASM971104v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:06:51,754] [INFO] Task succeeded: Blastn
[2024-01-24 15:06:51,758] [INFO] Selected 18 target genomes.
[2024-01-24 15:06:51,759] [INFO] Target genome list was writen to GCF_009711045.1_ASM971104v1_genomic.fna/target_genomes.txt
[2024-01-24 15:06:51,766] [INFO] Task started: fastANI
[2024-01-24 15:06:51,767] [INFO] Running command: fastANI --query /var/lib/cwl/stg937c625d-abd7-4073-b0b0-dddcedda085b/GCF_009711045.1_ASM971104v1_genomic.fna.gz --refList GCF_009711045.1_ASM971104v1_genomic.fna/target_genomes.txt --output GCF_009711045.1_ASM971104v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:07:04,704] [INFO] Task succeeded: fastANI
[2024-01-24 15:07:04,705] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf90ca0c7-8a2c-4abc-8380-2c7b2dce8833/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:07:04,706] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf90ca0c7-8a2c-4abc-8380-2c7b2dce8833/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:07:04,725] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:07:04,725] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:07:04,725] [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 albus	strain=BIT-d1	GCA_009711045.1	2562892	2562892	type	True	100.0	1110	1119	95	conclusive
Myroides odoratimimus subsp. xuanwuensis	strain=DSM 27251	GCA_900142635.1	1324934	76832	type	True	81.5505	481	1119	95	below_threshold
Myroides odoratimimus	strain=NCTC11180	GCA_900453765.1	76832	76832	type	True	81.5126	496	1119	95	below_threshold
Myroides odoratimimus	strain=CCUG39352	GCA_001485415.1	76832	76832	type	True	81.4323	498	1119	95	below_threshold
Myroides profundi	strain=D25	GCA_000833025.1	480520	480520	type	True	81.4011	489	1119	95	below_threshold
Myroides profundi	strain=DSM 19823	GCA_900111065.1	480520	480520	type	True	81.3224	494	1119	95	below_threshold
Myroides pelagicus	strain=SM1T	GCA_009711055.1	270914	270914	type	True	80.5337	459	1119	95	below_threshold
Myroides marinus	strain=DSM 23048	GCA_900109075.1	703342	703342	type	True	80.2012	430	1119	95	below_threshold
Myroides injenensis	strain=M09-0166	GCA_000246945.2	1183151	1183151	type	True	79.5021	385	1119	95	below_threshold
Myroides odoratus	strain=FDAARGOS_1131	GCA_016726985.1	256	256	type	True	79.3082	289	1119	95	below_threshold
Myroides phaeus	strain=DSM 23313	GCA_900099675.1	702745	702745	type	True	79.2124	370	1119	95	below_threshold
Flavobacterium lutivivi	strain=CGMCC 1.15347	GCA_014642275.1	1677894	1677894	type	True	77.4296	65	1119	95	below_threshold
Flavobacterium faecale	strain=WV33	GCA_003076455.1	1355330	1355330	type	True	77.2672	82	1119	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	76.9285	113	1119	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	76.2265	58	1119	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	76.0247	56	1119	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	75.6969	63	1119	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:07:04,727] [INFO] DFAST Taxonomy check result was written to GCF_009711045.1_ASM971104v1_genomic.fna/tc_result.tsv
[2024-01-24 15:07:04,728] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:07:04,728] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:07:04,728] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf90ca0c7-8a2c-4abc-8380-2c7b2dce8833/dqc_reference/checkm_data
[2024-01-24 15:07:04,729] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:07:04,771] [INFO] Task started: CheckM
[2024-01-24 15:07:04,772] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009711045.1_ASM971104v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009711045.1_ASM971104v1_genomic.fna/checkm_input GCF_009711045.1_ASM971104v1_genomic.fna/checkm_result
[2024-01-24 15:07:42,499] [INFO] Task succeeded: CheckM
[2024-01-24 15:07:42,501] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:07:42,528] [INFO] ===== Completeness check finished =====
[2024-01-24 15:07:42,529] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:07:42,529] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009711045.1_ASM971104v1_genomic.fna/markers.fasta)
[2024-01-24 15:07:42,530] [INFO] Task started: Blastn
[2024-01-24 15:07:42,530] [INFO] Running command: blastn -query GCF_009711045.1_ASM971104v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf90ca0c7-8a2c-4abc-8380-2c7b2dce8833/dqc_reference/reference_markers_gtdb.fasta -out GCF_009711045.1_ASM971104v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:07:43,579] [INFO] Task succeeded: Blastn
[2024-01-24 15:07:43,584] [INFO] Selected 14 target genomes.
[2024-01-24 15:07:43,584] [INFO] Target genome list was writen to GCF_009711045.1_ASM971104v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:07:43,607] [INFO] Task started: fastANI
[2024-01-24 15:07:43,607] [INFO] Running command: fastANI --query /var/lib/cwl/stg937c625d-abd7-4073-b0b0-dddcedda085b/GCF_009711045.1_ASM971104v1_genomic.fna.gz --refList GCF_009711045.1_ASM971104v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009711045.1_ASM971104v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:07:53,364] [INFO] Task succeeded: fastANI
[2024-01-24 15:07:53,383] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:07:53,383] [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_009711045.1	s__Flavobacterium album_A	100.0	1110	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.30	99.30	0.90	0.90	2	conclusive
GCF_001485415.1	s__Flavobacterium odoratimimum	81.4411	497	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.35	97.00	0.91	0.88	14	-
GCF_000833025.1	s__Flavobacterium profundi	81.401	489	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_009711055.1	s__Flavobacterium pelagicum	80.5523	457	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109075.1	s__Flavobacterium marinum_A	80.203	429	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.64	97.56	0.90	0.90	4	-
GCF_002286775.1	s__Flavobacterium sp002286775	79.5438	408	1119	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	79.5134	374	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000246945.1	s__Flavobacterium injenense	79.5089	384	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001549985.1	s__Flavobacterium odoratum_A	79.3568	275	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099675.1	s__Flavobacterium phaeum	79.2255	368	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009792295.1	s__Flavobacterium sp009792295	78.8675	247	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014145665.1	s__Flavobacterium sp014145665	78.8214	242	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003865405.1	s__Flavobacterium tangerinum	78.1833	139	1119	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	77.4372	64	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:07:53,386] [INFO] GTDB search result was written to GCF_009711045.1_ASM971104v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:07:53,386] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:07:53,391] [INFO] DFAST_QC result json was written to GCF_009711045.1_ASM971104v1_genomic.fna/dqc_result.json
[2024-01-24 15:07:53,391] [INFO] DFAST_QC completed!
[2024-01-24 15:07:53,391] [INFO] Total running time: 0h1m17s