[2024-01-24 14:12:03,997] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:04,003] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:04,003] [INFO] DQC Reference Directory: /var/lib/cwl/stg2572fef6-9702-4110-8134-5496d2674f7b/dqc_reference
[2024-01-24 14:12:05,365] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:05,366] [INFO] Task started: Prodigal
[2024-01-24 14:12:05,366] [INFO] Running command: gunzip -c /var/lib/cwl/stg15741c16-6da9-4afd-a53c-a00709fb1ffd/GCF_002222055.1_ASM222205v1_genomic.fna.gz | prodigal -d GCF_002222055.1_ASM222205v1_genomic.fna/cds.fna -a GCF_002222055.1_ASM222205v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:26,685] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:26,686] [INFO] Task started: HMMsearch
[2024-01-24 14:12:26,686] [INFO] Running command: hmmsearch --tblout GCF_002222055.1_ASM222205v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2572fef6-9702-4110-8134-5496d2674f7b/dqc_reference/reference_markers.hmm GCF_002222055.1_ASM222205v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:27,038] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:27,040] [INFO] Found 6/6 markers.
[2024-01-24 14:12:27,091] [INFO] Query marker FASTA was written to GCF_002222055.1_ASM222205v1_genomic.fna/markers.fasta
[2024-01-24 14:12:27,092] [INFO] Task started: Blastn
[2024-01-24 14:12:27,092] [INFO] Running command: blastn -query GCF_002222055.1_ASM222205v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2572fef6-9702-4110-8134-5496d2674f7b/dqc_reference/reference_markers.fasta -out GCF_002222055.1_ASM222205v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:27,900] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:27,904] [INFO] Selected 21 target genomes.
[2024-01-24 14:12:27,905] [INFO] Target genome list was writen to GCF_002222055.1_ASM222205v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:27,927] [INFO] Task started: fastANI
[2024-01-24 14:12:27,928] [INFO] Running command: fastANI --query /var/lib/cwl/stg15741c16-6da9-4afd-a53c-a00709fb1ffd/GCF_002222055.1_ASM222205v1_genomic.fna.gz --refList GCF_002222055.1_ASM222205v1_genomic.fna/target_genomes.txt --output GCF_002222055.1_ASM222205v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:51,316] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:51,317] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2572fef6-9702-4110-8134-5496d2674f7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:51,317] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2572fef6-9702-4110-8134-5496d2674f7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:51,333] [INFO] Found 21 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:12:51,334] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:12:51,334] [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
Flavobacterium araucananum	strain=DSM 24704	GCA_002222055.1	946678	946678	type	True	100.0	1893	1897	95	conclusive
Flavobacterium araucananum	strain=DSM 24704	GCA_003148525.1	946678	946678	type	True	99.986	1887	1897	95	conclusive
Flavobacterium bizetiae	strain=CIP 105534	GCA_902804475.1	2704140	2704140	type	True	86.0099	1207	1897	95	below_threshold
Flavobacterium bizetiae	strain=CIP 105534	GCA_904425415.1	2704140	2704140	type	True	85.9295	1244	1897	95	below_threshold
Flavobacterium piscis	strain=CCUG 60099	GCA_001686925.1	1114874	1114874	type	True	85.3479	1209	1897	95	below_threshold
Flavobacterium psychroterrae	strain=CCM 8827	GCA_018380615.1	2133767	2133767	type	True	85.3195	1276	1897	95	below_threshold
Flavobacterium piscis	strain=CCUG 60099	GCA_002222045.1	1114874	1114874	type	True	85.2537	1203	1897	95	below_threshold
Flavobacterium aquidurense	strain=DSM 18293	GCA_002217195.1	362413	362413	type	True	85.2318	1177	1897	95	below_threshold
Flavobacterium hibernum	strain=NCTC13514	GCA_900450525.1	37752	37752	type	True	84.3083	1112	1897	95	below_threshold
Flavobacterium hibernum	strain=ATCC 51468	GCA_002217315.1	37752	37752	type	True	84.2941	1117	1897	95	below_threshold
Flavobacterium frigidimaris	strain=DSM 15937	GCA_002217275.1	262320	262320	type	True	83.3139	1046	1897	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	82.5024	1028	1897	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	81.3857	963	1897	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	81.201	1014	1897	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	81.1242	938	1897	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	77.3753	197	1897	95	below_threshold
Myroides albus	strain=BIT-d1	GCA_009711045.1	2562892	2562892	type	True	77.1323	78	1897	95	below_threshold
Flavobacterium branchiophilum	strain=ATCC 35035	GCA_002217205.1	55197	55197	type	True	77.0172	188	1897	95	below_threshold
Flavobacterium branchiophilum	strain=DSM 24789	GCA_006716585.1	55197	55197	type	True	76.9872	201	1897	95	below_threshold
Myroides profundi	strain=D25	GCA_000833025.1	480520	480520	type	True	76.9421	77	1897	95	below_threshold
Flavobacterium branchiophilum	strain=NBRC 15030	GCA_007990815.1	55197	55197	type	True	76.9026	189	1897	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:51,335] [INFO] DFAST Taxonomy check result was written to GCF_002222055.1_ASM222205v1_genomic.fna/tc_result.tsv
[2024-01-24 14:12:51,336] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:51,336] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:51,336] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2572fef6-9702-4110-8134-5496d2674f7b/dqc_reference/checkm_data
[2024-01-24 14:12:51,338] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:51,402] [INFO] Task started: CheckM
[2024-01-24 14:12:51,402] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002222055.1_ASM222205v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002222055.1_ASM222205v1_genomic.fna/checkm_input GCF_002222055.1_ASM222205v1_genomic.fna/checkm_result
[2024-01-24 14:13:48,380] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:48,381] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:48,404] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:48,404] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:48,405] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002222055.1_ASM222205v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:48,405] [INFO] Task started: Blastn
[2024-01-24 14:13:48,405] [INFO] Running command: blastn -query GCF_002222055.1_ASM222205v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2572fef6-9702-4110-8134-5496d2674f7b/dqc_reference/reference_markers_gtdb.fasta -out GCF_002222055.1_ASM222205v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:49,397] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:49,402] [INFO] Selected 17 target genomes.
[2024-01-24 14:13:49,402] [INFO] Target genome list was writen to GCF_002222055.1_ASM222205v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:49,431] [INFO] Task started: fastANI
[2024-01-24 14:13:49,431] [INFO] Running command: fastANI --query /var/lib/cwl/stg15741c16-6da9-4afd-a53c-a00709fb1ffd/GCF_002222055.1_ASM222205v1_genomic.fna.gz --refList GCF_002222055.1_ASM222205v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002222055.1_ASM222205v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:11,074] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:11,091] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:14:11,091] [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_002222055.1	s__Flavobacterium araucananum	100.0	1893	1897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_001422725.1	s__Flavobacterium sp001422725	86.1635	1317	1897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975985.1	s__Flavobacterium sp001975985	86.1375	1315	1897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001404985.1	s__Flavobacterium aquidurense_B	86.0141	1303	1897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009664855.1	s__Flavobacterium sp009664855	85.5101	1244	1897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.90	98.90	0.89	0.89	2	-
GCF_001686925.1	s__Flavobacterium piscis	85.3479	1209	1897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.33	97.30	0.93	0.88	4	-
GCF_018380615.1	s__Flavobacterium psychroterrae	85.3032	1278	1897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900129595.1	s__Flavobacterium frigidimaris	85.2201	1190	1897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002754195.1	s__Flavobacterium sp002754195	84.7966	1232	1897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339525.1	s__Flavobacterium sp004339525	84.7368	1257	1897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_006438875.1	s__Flavobacterium pectinovorum_A	84.5381	1222	1897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003217415.1	s__Flavobacterium sp003217415	84.4389	1196	1897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.56	98.67	0.98	0.94	4	-
GCF_000832125.1	s__Flavobacterium hibernum	84.3338	1103	1897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	0.99	0.99	3	-
GCF_000813005.1	s__Flavobacterium sp000813005	80.5373	815	1897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.28	97.24	0.92	0.92	3	-
GCF_002217205.1	s__Flavobacterium branchiophilum	76.9711	192	1897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.60	97.23	0.92	0.84	5	-
GCF_016858305.2	s__Polaribacter sp016858305	76.2159	105	1897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335085.1	s__Polaribacter sp003335085	75.9383	80	1897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:14:11,093] [INFO] GTDB search result was written to GCF_002222055.1_ASM222205v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:11,094] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:11,099] [INFO] DFAST_QC result json was written to GCF_002222055.1_ASM222205v1_genomic.fna/dqc_result.json
[2024-01-24 14:14:11,099] [INFO] DFAST_QC completed!
[2024-01-24 14:14:11,099] [INFO] Total running time: 0h2m7s