[2024-01-24 12:22:34,051] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:34,055] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:34,055] [INFO] DQC Reference Directory: /var/lib/cwl/stg231356af-9901-4c3f-8735-c69436233e36/dqc_reference
[2024-01-24 12:22:35,714] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:35,714] [INFO] Task started: Prodigal
[2024-01-24 12:22:35,715] [INFO] Running command: gunzip -c /var/lib/cwl/stg488c6dfe-cfe2-4253-b7b5-d2769c73c4cd/GCF_014653155.1_ASM1465315v1_genomic.fna.gz | prodigal -d GCF_014653155.1_ASM1465315v1_genomic.fna/cds.fna -a GCF_014653155.1_ASM1465315v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:54,846] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:54,846] [INFO] Task started: HMMsearch
[2024-01-24 12:22:54,846] [INFO] Running command: hmmsearch --tblout GCF_014653155.1_ASM1465315v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg231356af-9901-4c3f-8735-c69436233e36/dqc_reference/reference_markers.hmm GCF_014653155.1_ASM1465315v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:55,071] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:55,072] [INFO] Found 6/6 markers.
[2024-01-24 12:22:55,110] [INFO] Query marker FASTA was written to GCF_014653155.1_ASM1465315v1_genomic.fna/markers.fasta
[2024-01-24 12:22:55,110] [INFO] Task started: Blastn
[2024-01-24 12:22:55,110] [INFO] Running command: blastn -query GCF_014653155.1_ASM1465315v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg231356af-9901-4c3f-8735-c69436233e36/dqc_reference/reference_markers.fasta -out GCF_014653155.1_ASM1465315v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:55,663] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:55,665] [INFO] Selected 23 target genomes.
[2024-01-24 12:22:55,666] [INFO] Target genome list was writen to GCF_014653155.1_ASM1465315v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:55,842] [INFO] Task started: fastANI
[2024-01-24 12:22:55,842] [INFO] Running command: fastANI --query /var/lib/cwl/stg488c6dfe-cfe2-4253-b7b5-d2769c73c4cd/GCF_014653155.1_ASM1465315v1_genomic.fna.gz --refList GCF_014653155.1_ASM1465315v1_genomic.fna/target_genomes.txt --output GCF_014653155.1_ASM1465315v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:12,985] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:12,986] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg231356af-9901-4c3f-8735-c69436233e36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:12,986] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg231356af-9901-4c3f-8735-c69436233e36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:12,997] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:12,997] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:12,998] [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
Sphingobacterium griseoflavum	strain=CGMCC 1.12966	GCA_014653155.1	1474952	1474952	type	True	100.0	1461	1463	95	conclusive
Sphingobacterium paludis	strain=CGMCC 1.12801	GCA_004364125.1	1476465	1476465	type	True	78.8498	402	1463	95	below_threshold
Sphingobacterium deserti	strain=ACCC 05744	GCA_000757725.1	1229276	1229276	type	True	78.7379	383	1463	95	below_threshold
Sphingobacterium wenxiniae	strain=DSM 22789	GCA_900116225.1	683125	683125	type	True	78.5231	150	1463	95	below_threshold
Sphingobacterium psychroaquaticum	strain=DSM 22418	GCA_900177625.1	561061	561061	type	True	78.4445	161	1463	95	below_threshold
Sphingobacterium bovisgrunnientis	strain=KCTC 52685	GCA_009829085.1	1874697	1874697	type	True	78.3741	93	1463	95	below_threshold
Sphingobacterium cavernae	strain=5.0403-2	GCA_008520265.1	2592657	2592657	type	True	78.3568	95	1463	95	below_threshold
Sphingobacterium composti Ten et al. 2007 non Yoo et al. 2007	strain=KCTC 12578	GCA_009829075.1	363260	363260	type	True	78.3196	87	1463	95	below_threshold
Sphingobacterium phlebotomi	strain=SSI9	GCA_008180195.1	2605433	2605433	type	True	78.2393	163	1463	95	below_threshold
Sphingobacterium lactis	strain=DSM 22361	GCA_011046555.1	797291	797291	type	True	78.2042	103	1463	95	below_threshold
Sphingobacterium lactis	strain=DSM 22361	GCA_900107985.1	797291	797291	type	True	78.1026	104	1463	95	below_threshold
Sphingobacterium olei	strain=HAL-9	GCA_005048855.1	2571155	2571155	type	True	78.0942	113	1463	95	below_threshold
Sphingobacterium arenae	strain=KCTC 32294	GCA_014692505.1	1280598	1280598	type	True	78.0495	146	1463	95	below_threshold
Sphingobacterium chuzhouense	strain=KCTC 42746	GCA_014692525.1	1742264	1742264	type	True	78.0374	184	1463	95	below_threshold
Sphingobacterium spiritivorum	strain=ATCC 33861	GCA_000143765.1	258	258	suspected-type	True	77.9495	98	1463	95	below_threshold
Sphingobacterium spiritivorum	strain=FDAARGOS_1144	GCA_016725645.1	258	258	suspected-type	True	77.9281	98	1463	95	below_threshold
Sphingobacterium spiritivorum	strain=NCTC11386	GCA_900457435.1	258	258	suspected-type	True	77.9078	98	1463	95	below_threshold
Sphingobacterium paucimobilis	strain=HER1398	GCA_000416985.1	1385985	1385985	type	True	77.7648	104	1463	95	below_threshold
Sphingobacterium faecale	strain=C459-1	GCA_016746095.1	2803775	2803775	type	True	77.7455	91	1463	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:13,000] [INFO] DFAST Taxonomy check result was written to GCF_014653155.1_ASM1465315v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:13,000] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:13,001] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:13,001] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg231356af-9901-4c3f-8735-c69436233e36/dqc_reference/checkm_data
[2024-01-24 12:23:13,001] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:13,057] [INFO] Task started: CheckM
[2024-01-24 12:23:13,057] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014653155.1_ASM1465315v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014653155.1_ASM1465315v1_genomic.fna/checkm_input GCF_014653155.1_ASM1465315v1_genomic.fna/checkm_result
[2024-01-24 12:24:05,331] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:05,332] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:05,351] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:05,351] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:05,352] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014653155.1_ASM1465315v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:05,352] [INFO] Task started: Blastn
[2024-01-24 12:24:05,352] [INFO] Running command: blastn -query GCF_014653155.1_ASM1465315v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg231356af-9901-4c3f-8735-c69436233e36/dqc_reference/reference_markers_gtdb.fasta -out GCF_014653155.1_ASM1465315v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:06,149] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:06,152] [INFO] Selected 21 target genomes.
[2024-01-24 12:24:06,152] [INFO] Target genome list was writen to GCF_014653155.1_ASM1465315v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:06,186] [INFO] Task started: fastANI
[2024-01-24 12:24:06,187] [INFO] Running command: fastANI --query /var/lib/cwl/stg488c6dfe-cfe2-4253-b7b5-d2769c73c4cd/GCF_014653155.1_ASM1465315v1_genomic.fna.gz --refList GCF_014653155.1_ASM1465315v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014653155.1_ASM1465315v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:21,504] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:21,516] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:21,516] [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_014653155.1	s__Sphingobacterium griseoflavum	100.0	1461	1463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004364125.1	s__Sphingobacterium paludis	78.8609	401	1463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000757725.1	s__Sphingobacterium deserti	78.7492	382	1463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016725325.1	s__Sphingobacterium sp002418355	78.7164	94	1463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	97.65	97.65	0.92	0.92	2	-
GCF_900116225.1	s__Sphingobacterium wenxiniae	78.4966	151	1463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008520265.1	s__Sphingobacterium cavernae	78.4531	92	1463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	96.1642	N/A	N/A	N/A	N/A	1	-
GCF_900177625.1	s__Sphingobacterium psychroaquaticum	78.4385	160	1463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	99.08	99.08	0.93	0.93	2	-
GCF_009829085.1	s__Sphingobacterium bovisgrunnientis	78.414	92	1463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	96.1642	N/A	N/A	N/A	N/A	1	-
GCF_016724845.1	s__Sphingobacterium spiritivorum_A	78.3279	96	1463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	97.88	95.78	0.94	0.88	3	-
GCF_009829075.1	s__Sphingobacterium composti	78.304	88	1463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008180195.1	s__Sphingobacterium phlebotomi	78.2322	162	1463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008274825.1	s__Sphingobacterium hotanense	78.2192	107	1463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	97.82	97.82	0.91	0.91	2	-
GCF_011046555.1	s__Sphingobacterium lactis	78.1609	104	1463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011043555.1	s__Sphingobacterium sp011043555	78.1447	163	1463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005048855.1	s__Sphingobacterium olei	78.1354	111	1463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008124885.1	s__Sphingobacterium composti_A	78.0812	227	1463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015209965.1	s__Sphingobacterium sp015209965	78.0619	109	1463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014692505.1	s__Sphingobacterium arenae	78.0495	146	1463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000143765.1	s__Sphingobacterium spiritivorum	77.9453	97	1463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	99.99	99.99	1.00	1.00	3	-
GCF_002980575.1	s__Sphingobacterium gobiense	77.9285	157	1463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000416985.1	s__Sphingobacterium paucimobilis	77.7874	102	1463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:21,518] [INFO] GTDB search result was written to GCF_014653155.1_ASM1465315v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:21,518] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:21,522] [INFO] DFAST_QC result json was written to GCF_014653155.1_ASM1465315v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:21,522] [INFO] DFAST_QC completed!
[2024-01-24 12:24:21,522] [INFO] Total running time: 0h1m47s