[2024-01-24 14:30:30,170] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:30,173] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:30,173] [INFO] DQC Reference Directory: /var/lib/cwl/stg67d7a80e-5b2f-49ff-93b3-7f2132d804b3/dqc_reference
[2024-01-24 14:30:33,676] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:33,678] [INFO] Task started: Prodigal
[2024-01-24 14:30:33,679] [INFO] Running command: gunzip -c /var/lib/cwl/stg661d1562-e6be-47bd-a871-5c4fc4529848/GCF_006716645.1_ASM671664v1_genomic.fna.gz | prodigal -d GCF_006716645.1_ASM671664v1_genomic.fna/cds.fna -a GCF_006716645.1_ASM671664v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:56,885] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:56,886] [INFO] Task started: HMMsearch
[2024-01-24 14:30:56,886] [INFO] Running command: hmmsearch --tblout GCF_006716645.1_ASM671664v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg67d7a80e-5b2f-49ff-93b3-7f2132d804b3/dqc_reference/reference_markers.hmm GCF_006716645.1_ASM671664v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:57,253] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:57,255] [INFO] Found 6/6 markers.
[2024-01-24 14:30:57,302] [INFO] Query marker FASTA was written to GCF_006716645.1_ASM671664v1_genomic.fna/markers.fasta
[2024-01-24 14:30:57,303] [INFO] Task started: Blastn
[2024-01-24 14:30:57,303] [INFO] Running command: blastn -query GCF_006716645.1_ASM671664v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67d7a80e-5b2f-49ff-93b3-7f2132d804b3/dqc_reference/reference_markers.fasta -out GCF_006716645.1_ASM671664v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:57,955] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:57,959] [INFO] Selected 22 target genomes.
[2024-01-24 14:30:57,959] [INFO] Target genome list was writen to GCF_006716645.1_ASM671664v1_genomic.fna/target_genomes.txt
[2024-01-24 14:30:58,011] [INFO] Task started: fastANI
[2024-01-24 14:30:58,012] [INFO] Running command: fastANI --query /var/lib/cwl/stg661d1562-e6be-47bd-a871-5c4fc4529848/GCF_006716645.1_ASM671664v1_genomic.fna.gz --refList GCF_006716645.1_ASM671664v1_genomic.fna/target_genomes.txt --output GCF_006716645.1_ASM671664v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:20,844] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:20,845] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg67d7a80e-5b2f-49ff-93b3-7f2132d804b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:20,845] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg67d7a80e-5b2f-49ff-93b3-7f2132d804b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:20,864] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:31:20,864] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:20,864] [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
Arcticibacter tournemirensis	strain=DSM 23085	GCA_006716645.1	699437	699437	type	True	100.0	1883	1884	95	conclusive
Arcticibacter tournemirensis	strain=TF5-37.2-LB10	GCA_008690275.1	699437	699437	type	True	99.9524	1777	1884	95	conclusive
Pararcticibacter amylolyticus	strain=FJ4-8	GCA_003130405.1	2173175	2173175	type	True	78.6935	382	1884	95	below_threshold
Pedobacter aquae	strain=CJ43	GCA_008195825.1	2605747	2605747	type	True	78.3764	53	1884	95	below_threshold
Arcticibacter pallidicorallinus	strain=CGMCC 1.9313	GCA_003002875.1	1259464	1259464	type	True	77.7024	111	1884	95	below_threshold
Pedobacter mongoliensis	strain=KCTC 52859	GCA_024436395.1	2100740	2100740	type	True	77.5728	92	1884	95	below_threshold
Pedobacter xinjiangensis	strain=CCTCC AB 208092	GCA_024436435.1	539206	539206	type	True	76.8699	121	1884	95	below_threshold
Pedobacter petrophilus	strain=LMG 29686	GCA_009674725.1	1908241	1908241	type	True	76.7502	50	1884	95	below_threshold
Mucilaginibacter ginsenosidivorax	strain=KHI28	GCA_007971525.1	862126	862126	type	True	76.6862	55	1884	95	below_threshold
Mucilaginibacter agri	strain=R11	GCA_009928685.1	2695265	2695265	type	True	76.6192	58	1884	95	below_threshold
Daejeonella lutea	strain=DSM 22385	GCA_900168015.1	572036	572036	type	True	76.5463	66	1884	95	below_threshold
Pedobacter kyonggii	strain=K-4-11-1	GCA_004310665.1	1926871	1926871	type	True	76.4792	55	1884	95	below_threshold
Pedobacter nutrimenti	strain=DSM 27372	GCA_003208655.1	1241337	1241337	type	True	76.4479	52	1884	95	below_threshold
Mucilaginibacter boryungensis	strain=KCTC 23157	GCA_015221995.1	768480	768480	type	True	76.333	54	1884	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=PP-F2FG21	GCA_004378255.1	1812349	1812349	type	True	76.2733	51	1884	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=DSM 100995	GCA_014196695.1	1812349	1812349	type	True	76.2275	50	1884	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=CCM 8625	GCA_014635525.1	1812349	1812349	type	True	76.1562	52	1884	95	below_threshold
Mucilaginibacter rubeus	strain=CGMCC 1.15913	GCA_014643835.1	2027860	2027860	suspected-type	True	76.1002	64	1884	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:20,866] [INFO] DFAST Taxonomy check result was written to GCF_006716645.1_ASM671664v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:20,867] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:20,867] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:20,867] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg67d7a80e-5b2f-49ff-93b3-7f2132d804b3/dqc_reference/checkm_data
[2024-01-24 14:31:20,869] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:20,924] [INFO] Task started: CheckM
[2024-01-24 14:31:20,925] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006716645.1_ASM671664v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006716645.1_ASM671664v1_genomic.fna/checkm_input GCF_006716645.1_ASM671664v1_genomic.fna/checkm_result
[2024-01-24 14:32:31,108] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:31,110] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:31,130] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:31,130] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:31,130] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006716645.1_ASM671664v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:31,131] [INFO] Task started: Blastn
[2024-01-24 14:32:31,131] [INFO] Running command: blastn -query GCF_006716645.1_ASM671664v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67d7a80e-5b2f-49ff-93b3-7f2132d804b3/dqc_reference/reference_markers_gtdb.fasta -out GCF_006716645.1_ASM671664v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:31,951] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:31,956] [INFO] Selected 24 target genomes.
[2024-01-24 14:32:31,956] [INFO] Target genome list was writen to GCF_006716645.1_ASM671664v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:31,976] [INFO] Task started: fastANI
[2024-01-24 14:32:31,977] [INFO] Running command: fastANI --query /var/lib/cwl/stg661d1562-e6be-47bd-a871-5c4fc4529848/GCF_006716645.1_ASM671664v1_genomic.fna.gz --refList GCF_006716645.1_ASM671664v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006716645.1_ASM671664v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:54,581] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:54,598] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:54,598] [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_006716645.1	s__Pararcticibacter tournemirensis	100.0	1884	1884	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pararcticibacter	95.0	98.22	96.45	0.92	0.83	3	conclusive
GCF_003130405.1	s__Pararcticibacter amylolyticus	78.7181	381	1884	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pararcticibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015654985.1	s__Pararcticibacter sp015654985	78.032	358	1884	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pararcticibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002875.1	s__Arcticibacter pallidicorallinus	77.7024	111	1884	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Arcticibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017355855.1	s__SYSU-D00535 sp017355855	77.4108	105	1884	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__SYSU-D00535	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002454425.1	s__Pararcticibacter sp002454425	77.3598	110	1884	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pararcticibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017355835.1	s__SYSU-D00535 sp017355835	77.0958	103	1884	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__SYSU-D00535	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017355785.1	s__SYSU-D00535 sp017355785	77.0296	108	1884	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__SYSU-D00535	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142915.1	s__Mucilaginibacter sp900142915	76.9199	73	1884	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008274585.1	s__BS3 sp008274585	76.8925	84	1884	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__BS3	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900168015.1	s__Daejeonella lutea	76.5463	66	1884	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Daejeonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004310665.1	s__Pedobacter kyonggii	76.4792	55	1884	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200575.1	s__Mucilaginibacter sp014200575	76.4217	57	1884	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100945.1	s__Mucilaginibacter gossypii	76.4161	69	1884	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	96.19	95.83	0.85	0.84	10	-
GCF_900103125.1	s__Mucilaginibacter sp900103125	76.4005	61	1884	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003208075.1	s__Mucilaginibacter sp003208075	76.3868	58	1884	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000633455.1	s__Pedobacter jeongneungensis	76.3084	54	1884	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004378255.1	s__Mucilaginibacter phyllosphaerae	76.2665	50	1884	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	100.00	100.00	1.00	1.00	3	-
GCF_014643835.1	s__Mucilaginibacter rubeus	76.092	63	1884	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	97.62	97.51	0.93	0.92	3	-
GCF_001705515.1	s__Mucilaginibacter sp001705515	76.06	58	1884	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002413785.1	s__Mucilaginibacter sp002413785	75.9374	55	1884	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.87	99.70	0.98	0.97	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:54,600] [INFO] GTDB search result was written to GCF_006716645.1_ASM671664v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:54,601] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:54,606] [INFO] DFAST_QC result json was written to GCF_006716645.1_ASM671664v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:54,606] [INFO] DFAST_QC completed!
[2024-01-24 14:32:54,606] [INFO] Total running time: 0h2m24s