[2023-06-30 05:51:13,784] [INFO] DFAST_QC pipeline started.
[2023-06-30 05:51:13,793] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 05:51:13,793] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e507b20-55c8-4e52-881e-69d78ff493c1/dqc_reference
[2023-06-30 05:51:15,439] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 05:51:15,441] [INFO] Task started: Prodigal
[2023-06-30 05:51:15,441] [INFO] Running command: gunzip -c /var/lib/cwl/stga9bc8f06-61e6-4879-a0f7-3b1cb27d85d9/GCA_016780995.1_ASM1678099v1_genomic.fna.gz | prodigal -d GCA_016780995.1_ASM1678099v1_genomic.fna/cds.fna -a GCA_016780995.1_ASM1678099v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 05:51:20,953] [INFO] Task succeeded: Prodigal
[2023-06-30 05:51:20,953] [INFO] Task started: HMMsearch
[2023-06-30 05:51:20,953] [INFO] Running command: hmmsearch --tblout GCA_016780995.1_ASM1678099v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e507b20-55c8-4e52-881e-69d78ff493c1/dqc_reference/reference_markers.hmm GCA_016780995.1_ASM1678099v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 05:51:21,179] [INFO] Task succeeded: HMMsearch
[2023-06-30 05:51:21,180] [INFO] Found 6/6 markers.
[2023-06-30 05:51:21,245] [INFO] Query marker FASTA was written to GCA_016780995.1_ASM1678099v1_genomic.fna/markers.fasta
[2023-06-30 05:51:21,245] [INFO] Task started: Blastn
[2023-06-30 05:51:21,246] [INFO] Running command: blastn -query GCA_016780995.1_ASM1678099v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e507b20-55c8-4e52-881e-69d78ff493c1/dqc_reference/reference_markers.fasta -out GCA_016780995.1_ASM1678099v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 05:51:22,032] [INFO] Task succeeded: Blastn
[2023-06-30 05:51:22,038] [INFO] Selected 21 target genomes.
[2023-06-30 05:51:22,038] [INFO] Target genome list was writen to GCA_016780995.1_ASM1678099v1_genomic.fna/target_genomes.txt
[2023-06-30 05:51:22,041] [INFO] Task started: fastANI
[2023-06-30 05:51:22,041] [INFO] Running command: fastANI --query /var/lib/cwl/stga9bc8f06-61e6-4879-a0f7-3b1cb27d85d9/GCA_016780995.1_ASM1678099v1_genomic.fna.gz --refList GCA_016780995.1_ASM1678099v1_genomic.fna/target_genomes.txt --output GCA_016780995.1_ASM1678099v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 05:51:40,566] [INFO] Task succeeded: fastANI
[2023-06-30 05:51:40,567] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e507b20-55c8-4e52-881e-69d78ff493c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 05:51:40,567] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e507b20-55c8-4e52-881e-69d78ff493c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 05:51:40,586] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 05:51:40,586] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 05:51:40,586] [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
Miltoncostaea marina	strain=SCSIO 60955	GCA_018141525.1	2843215	2843215	type	True	78.0158	218	500	95	below_threshold
Miltoncostaea oceani	strain=SCSIO 61214	GCA_018141545.1	2843216	2843216	type	True	77.5632	166	500	95	below_threshold
Gaiella occulta	strain=F2-233	GCA_003351045.1	1002870	1002870	type	True	76.1455	63	500	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	75.7873	86	500	95	below_threshold
Baekduia soli	strain=BR7-21	GCA_007970665.1	496014	496014	type	True	75.6926	132	500	95	below_threshold
Capillimicrobium parvum	strain=0166_1	GCA_021172045.1	2884022	2884022	type	True	75.6311	98	500	95	below_threshold
Acrocarpospora catenulata	strain=H8750	GCA_018476525.1	2836182	2836182	type	True	75.5042	86	500	95	below_threshold
Nonomuraea cavernae	strain=SYSU K10005	GCA_020215905.1	2045107	2045107	type	True	75.3992	95	500	95	below_threshold
Nonomuraea cavernae	strain=CGMCC 4.7368	GCA_014646355.1	2045107	2045107	type	True	75.3702	96	500	95	below_threshold
Motilibacter aurantiacus	strain=K478	GCA_011250645.1	2714955	2714955	type	True	75.3163	66	500	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	75.2159	63	500	95	below_threshold
Kitasatospora kifunensis	strain=DSM 41654	GCA_014203855.1	58351	58351	type	True	75.2153	99	500	95	below_threshold
Sphaerisporangium rufum	strain=NBRC 109079	GCA_016863395.1	1381558	1381558	type	True	75.1992	113	500	95	below_threshold
Pseudonocardia alaniniphila	strain=Y-16303	GCA_022524485.1	75291	75291	type	True	75.1967	78	500	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	75.0634	89	500	95	below_threshold
Amycolatopsis alkalitolerans	strain=SYSUP0005	GCA_006152065.1	2547244	2547244	type	True	75.0073	59	500	95	below_threshold
Actinokineospora spheciospongiae	strain=EG49	GCA_000564855.1	909613	909613	type	True	74.9636	117	500	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 05:51:40,589] [INFO] DFAST Taxonomy check result was written to GCA_016780995.1_ASM1678099v1_genomic.fna/tc_result.tsv
[2023-06-30 05:51:40,590] [INFO] ===== Taxonomy check completed =====
[2023-06-30 05:51:40,590] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 05:51:40,590] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e507b20-55c8-4e52-881e-69d78ff493c1/dqc_reference/checkm_data
[2023-06-30 05:51:40,592] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 05:51:40,616] [INFO] Task started: CheckM
[2023-06-30 05:51:40,617] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016780995.1_ASM1678099v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016780995.1_ASM1678099v1_genomic.fna/checkm_input GCA_016780995.1_ASM1678099v1_genomic.fna/checkm_result
[2023-06-30 05:52:05,770] [INFO] Task succeeded: CheckM
[2023-06-30 05:52:05,771] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 05:52:05,794] [INFO] ===== Completeness check finished =====
[2023-06-30 05:52:05,794] [INFO] ===== Start GTDB Search =====
[2023-06-30 05:52:05,794] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016780995.1_ASM1678099v1_genomic.fna/markers.fasta)
[2023-06-30 05:52:05,795] [INFO] Task started: Blastn
[2023-06-30 05:52:05,795] [INFO] Running command: blastn -query GCA_016780995.1_ASM1678099v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e507b20-55c8-4e52-881e-69d78ff493c1/dqc_reference/reference_markers_gtdb.fasta -out GCA_016780995.1_ASM1678099v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 05:52:06,912] [INFO] Task succeeded: Blastn
[2023-06-30 05:52:06,916] [INFO] Selected 8 target genomes.
[2023-06-30 05:52:06,917] [INFO] Target genome list was writen to GCA_016780995.1_ASM1678099v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 05:52:06,918] [INFO] Task started: fastANI
[2023-06-30 05:52:06,918] [INFO] Running command: fastANI --query /var/lib/cwl/stga9bc8f06-61e6-4879-a0f7-3b1cb27d85d9/GCA_016780995.1_ASM1678099v1_genomic.fna.gz --refList GCA_016780995.1_ASM1678099v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016780995.1_ASM1678099v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 05:52:10,040] [INFO] Task succeeded: fastANI
[2023-06-30 05:52:10,048] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 05:52:10,048] [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
GCA_016780995.1	s__SYFI01 sp016780995	99.9999	497	500	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Miltoncostaeales;f__Miltoncostaeaceae;g__SYFI01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017853415.1	s__SYFI01 sp017853415	85.4944	372	500	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Miltoncostaeales;f__Miltoncostaeaceae;g__SYFI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018969105.1	s__SYFI01 sp018969105	84.8326	362	500	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Miltoncostaeales;f__Miltoncostaeaceae;g__SYFI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016870155.1	s__SYFI01 sp016870155	84.6753	413	500	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Miltoncostaeales;f__Miltoncostaeaceae;g__SYFI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903928615.1	s__SYFI01 sp903928615	84.5604	265	500	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Miltoncostaeales;f__Miltoncostaeaceae;g__SYFI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005788075.1	s__SYFI01 sp005788075	83.7939	283	500	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Miltoncostaeales;f__Miltoncostaeaceae;g__SYFI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005792725.1	s__SYFI01 sp005792725	80.8536	248	500	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Miltoncostaeales;f__Miltoncostaeaceae;g__SYFI01	95.0	99.67	99.67	0.89	0.89	2	-
GCA_903943955.1	s__SYFI01 sp903943955	79.9426	286	500	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Miltoncostaeales;f__Miltoncostaeaceae;g__SYFI01	95.0	99.59	99.47	0.92	0.89	6	-
--------------------------------------------------------------------------------
[2023-06-30 05:52:10,050] [INFO] GTDB search result was written to GCA_016780995.1_ASM1678099v1_genomic.fna/result_gtdb.tsv
[2023-06-30 05:52:10,051] [INFO] ===== GTDB Search completed =====
[2023-06-30 05:52:10,055] [INFO] DFAST_QC result json was written to GCA_016780995.1_ASM1678099v1_genomic.fna/dqc_result.json
[2023-06-30 05:52:10,055] [INFO] DFAST_QC completed!
[2023-06-30 05:52:10,055] [INFO] Total running time: 0h0m56s