[2024-01-24 11:05:26,323] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:26,325] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:26,326] [INFO] DQC Reference Directory: /var/lib/cwl/stgff7b5979-69b8-4576-a0e8-c7ae6d5520a6/dqc_reference
[2024-01-24 11:05:27,670] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:27,673] [INFO] Task started: Prodigal
[2024-01-24 11:05:27,673] [INFO] Running command: gunzip -c /var/lib/cwl/stg84c1d395-0dae-406e-9618-287744ed1822/GCF_022807975.1_ASM2280797v1_genomic.fna.gz | prodigal -d GCF_022807975.1_ASM2280797v1_genomic.fna/cds.fna -a GCF_022807975.1_ASM2280797v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:42,928] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:42,928] [INFO] Task started: HMMsearch
[2024-01-24 11:05:42,928] [INFO] Running command: hmmsearch --tblout GCF_022807975.1_ASM2280797v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff7b5979-69b8-4576-a0e8-c7ae6d5520a6/dqc_reference/reference_markers.hmm GCF_022807975.1_ASM2280797v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:43,261] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:43,262] [INFO] Found 6/6 markers.
[2024-01-24 11:05:43,299] [INFO] Query marker FASTA was written to GCF_022807975.1_ASM2280797v1_genomic.fna/markers.fasta
[2024-01-24 11:05:43,300] [INFO] Task started: Blastn
[2024-01-24 11:05:43,300] [INFO] Running command: blastn -query GCF_022807975.1_ASM2280797v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff7b5979-69b8-4576-a0e8-c7ae6d5520a6/dqc_reference/reference_markers.fasta -out GCF_022807975.1_ASM2280797v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:43,967] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:43,971] [INFO] Selected 24 target genomes.
[2024-01-24 11:05:43,971] [INFO] Target genome list was writen to GCF_022807975.1_ASM2280797v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:43,979] [INFO] Task started: fastANI
[2024-01-24 11:05:43,979] [INFO] Running command: fastANI --query /var/lib/cwl/stg84c1d395-0dae-406e-9618-287744ed1822/GCF_022807975.1_ASM2280797v1_genomic.fna.gz --refList GCF_022807975.1_ASM2280797v1_genomic.fna/target_genomes.txt --output GCF_022807975.1_ASM2280797v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:01,491] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:01,492] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff7b5979-69b8-4576-a0e8-c7ae6d5520a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:01,492] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff7b5979-69b8-4576-a0e8-c7ae6d5520a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:01,514] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:06:01,514] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:06:01,514] [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
Abyssalbus ytuae	strain=MT3330	GCA_022807975.1	2926907	2926907	type	True	100.0	1455	1455	95	conclusive
Joostella marina	strain=DSM 19592	GCA_000260115.1	453852	453852	type	True	77.1594	148	1455	95	below_threshold
Mangrovimonas yunxiaonensis	strain=LY01	GCA_000733475.1	1197477	1197477	type	True	77.059	64	1455	95	below_threshold
Zhouia spongiae	strain=HN-Y44	GCA_022760175.1	2202721	2202721	type	True	76.9386	115	1455	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	76.8779	73	1455	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	76.8306	71	1455	95	below_threshold
Leptobacterium flavescens	strain=KCTC 22160	GCA_010671605.1	472055	472055	type	True	76.8071	108	1455	95	below_threshold
Zhouia amylolytica	strain=CGMCC 1.6114	GCA_900116365.1	376730	376730	type	True	76.6806	110	1455	95	below_threshold
Sinomicrobium kalidii	strain=HD2P242	GCA_021183825.1	2900738	2900738	type	True	76.6787	74	1455	95	below_threshold
Galbibacter marinus	strain=ck-I2-15	GCA_000300875.1	555500	555500	type	True	76.5307	94	1455	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.5218	127	1455	95	below_threshold
Olleya aquimaris	strain=DSM 24464	GCA_003259525.1	639310	639310	type	True	76.4653	93	1455	95	below_threshold
Mesonia oceanica	strain=ISS653	GCA_902499555.1	2687242	2687242	type	True	76.4417	80	1455	95	below_threshold
Snuella sedimenti	strain=CAU 1569	GCA_016428595.1	2798802	2798802	type	True	76.3565	82	1455	95	below_threshold
Cellulophaga baltica	strain=DSM 24729	GCA_900102165.1	76594	76594	type	True	76.3271	83	1455	95	below_threshold
Aestuariivivens insulae	strain=AH-MY3	GCA_022662195.1	1621988	1621988	type	True	76.2268	75	1455	95	below_threshold
Mangrovimonas yunxiaonensis	strain=CGMCC 1.12280	GCA_014636995.1	1197477	1197477	type	True	76.2174	59	1455	95	below_threshold
Kordia periserrulae	strain=DSM 25731	GCA_003054265.1	701523	701523	type	True	76.1264	76	1455	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.1015	86	1455	95	below_threshold
Flavobacterium luteum	strain=NBRC 112527	GCA_008806775.1	2026654	2026654	type	True	75.8991	56	1455	95	below_threshold
Cellulophaga tyrosinoxydans	strain=DSM 21164	GCA_900176415.1	504486	504486	type	True	75.8849	96	1455	95	below_threshold
Aestuariivivens sediminis	strain=S-DT1-15	GCA_022662105.1	2913557	2913557	type	True	75.7706	60	1455	95	below_threshold
Maribacter arenosus	strain=CAU 1321	GCA_014610845.1	1854708	1854708	type	True	75.736	51	1455	95	below_threshold
Croceivirga lutea	strain=CGMCC 1.15761	GCA_014643615.1	1775167	1775167	type	True	75.6543	77	1455	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:01,516] [INFO] DFAST Taxonomy check result was written to GCF_022807975.1_ASM2280797v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:01,517] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:01,517] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:01,517] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff7b5979-69b8-4576-a0e8-c7ae6d5520a6/dqc_reference/checkm_data
[2024-01-24 11:06:01,519] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:01,562] [INFO] Task started: CheckM
[2024-01-24 11:06:01,563] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022807975.1_ASM2280797v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022807975.1_ASM2280797v1_genomic.fna/checkm_input GCF_022807975.1_ASM2280797v1_genomic.fna/checkm_result
[2024-01-24 11:06:48,575] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:48,577] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:48,598] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:48,598] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:48,598] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022807975.1_ASM2280797v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:48,599] [INFO] Task started: Blastn
[2024-01-24 11:06:48,599] [INFO] Running command: blastn -query GCF_022807975.1_ASM2280797v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff7b5979-69b8-4576-a0e8-c7ae6d5520a6/dqc_reference/reference_markers_gtdb.fasta -out GCF_022807975.1_ASM2280797v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:49,552] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:49,557] [INFO] Selected 27 target genomes.
[2024-01-24 11:06:49,558] [INFO] Target genome list was writen to GCF_022807975.1_ASM2280797v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:49,579] [INFO] Task started: fastANI
[2024-01-24 11:06:49,579] [INFO] Running command: fastANI --query /var/lib/cwl/stg84c1d395-0dae-406e-9618-287744ed1822/GCF_022807975.1_ASM2280797v1_genomic.fna.gz --refList GCF_022807975.1_ASM2280797v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022807975.1_ASM2280797v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:07:05,117] [INFO] Task succeeded: fastANI
[2024-01-24 11:07:05,141] [INFO] Found 25 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:07:05,141] [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_000733475.1	s__Mangrovimonas yunxiaonensis	77.1998	63	1455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mangrovimonas	95.0	98.99	97.98	0.98	0.97	3	-
GCF_000260115.1	s__Joostella marina	77.1884	148	1455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Joostella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003387355.1	s__Winogradskyella sediminis	77.0699	73	1455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.63	98.63	0.93	0.93	2	-
GCA_009901575.1	s__Leptobacterium sp009901575	76.9662	133	1455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leptobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006383075.2	s__Kordia sp006383075	76.9285	77	1455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kordia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016734785.1	s__Galbibacter_A mesophilus	76.8419	110	1455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Galbibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010671605.1	s__Leptobacterium flavescens	76.8071	108	1455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leptobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259525.1	s__Olleya aquimaris	76.6783	94	1455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116365.1	s__Zhouia amylolytica	76.6608	111	1455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zhouia	95.0	98.62	98.62	0.95	0.95	2	-
GCF_000300875.1	s__Galbibacter_B marinus	76.5307	94	1455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Galbibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111025.1	s__Jejuia jejuensis	76.3989	74	1455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001310225.1	s__Algibacter_A alginicilyticus	76.3051	90	1455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006265225.1	s__Tamlana_C fucoidanivorans	76.2159	80	1455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019021925.1	s__Cellulophaga sp019021925	76.2042	113	1455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054265.1	s__Kordia periserrulae	76.1483	75	1455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kordia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016827605.1	s__Jejuia sp016827605	76.1015	86	1455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008084905.1	s__Xanthomarina maritima	76.0732	84	1455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860565.1	s__Winogradskyella psychrotolerans_B	76.0704	71	1455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001275.1	s__Flaviramulus sp013001275	76.0196	82	1455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014698935.1	s__Muricauda sp014698935	75.9296	57	1455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008806775.1	s__Flavobacterium luteum	75.8991	56	1455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176415.1	s__Cellulophaga tyrosinoxydans	75.8849	96	1455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014610845.1	s__Maribacter_A arenosus	75.736	51	1455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004791695.1	s__Flavivirga rizhaonensis	75.7283	95	1455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014235875.1	s__Croceivirga lutea	75.5944	79	1455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceivirga	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:07:05,143] [INFO] GTDB search result was written to GCF_022807975.1_ASM2280797v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:07:05,144] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:07:05,149] [INFO] DFAST_QC result json was written to GCF_022807975.1_ASM2280797v1_genomic.fna/dqc_result.json
[2024-01-24 11:07:05,149] [INFO] DFAST_QC completed!
[2024-01-24 11:07:05,149] [INFO] Total running time: 0h1m39s