[2023-06-30 00:10:03,931] [INFO] DFAST_QC pipeline started.
[2023-06-30 00:10:03,933] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 00:10:03,933] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c5840e3-a084-4d7d-8d95-af1f54cd496e/dqc_reference
[2023-06-30 00:10:05,315] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 00:10:05,325] [INFO] Task started: Prodigal
[2023-06-30 00:10:05,326] [INFO] Running command: gunzip -c /var/lib/cwl/stg6ab4e2aa-adf6-4fb8-aa81-546a90a19d8d/GCA_024276735.1_ASM2427673v1_genomic.fna.gz | prodigal -d GCA_024276735.1_ASM2427673v1_genomic.fna/cds.fna -a GCA_024276735.1_ASM2427673v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 00:10:09,554] [INFO] Task succeeded: Prodigal
[2023-06-30 00:10:09,554] [INFO] Task started: HMMsearch
[2023-06-30 00:10:09,554] [INFO] Running command: hmmsearch --tblout GCA_024276735.1_ASM2427673v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c5840e3-a084-4d7d-8d95-af1f54cd496e/dqc_reference/reference_markers.hmm GCA_024276735.1_ASM2427673v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 00:10:09,780] [INFO] Task succeeded: HMMsearch
[2023-06-30 00:10:09,781] [INFO] Found 6/6 markers.
[2023-06-30 00:10:09,805] [INFO] Query marker FASTA was written to GCA_024276735.1_ASM2427673v1_genomic.fna/markers.fasta
[2023-06-30 00:10:09,805] [INFO] Task started: Blastn
[2023-06-30 00:10:09,806] [INFO] Running command: blastn -query GCA_024276735.1_ASM2427673v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c5840e3-a084-4d7d-8d95-af1f54cd496e/dqc_reference/reference_markers.fasta -out GCA_024276735.1_ASM2427673v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:10:10,485] [INFO] Task succeeded: Blastn
[2023-06-30 00:10:10,490] [INFO] Selected 30 target genomes.
[2023-06-30 00:10:10,490] [INFO] Target genome list was writen to GCA_024276735.1_ASM2427673v1_genomic.fna/target_genomes.txt
[2023-06-30 00:10:10,495] [INFO] Task started: fastANI
[2023-06-30 00:10:10,495] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ab4e2aa-adf6-4fb8-aa81-546a90a19d8d/GCA_024276735.1_ASM2427673v1_genomic.fna.gz --refList GCA_024276735.1_ASM2427673v1_genomic.fna/target_genomes.txt --output GCA_024276735.1_ASM2427673v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 00:10:37,218] [INFO] Task succeeded: fastANI
[2023-06-30 00:10:37,219] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c5840e3-a084-4d7d-8d95-af1f54cd496e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 00:10:37,219] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c5840e3-a084-4d7d-8d95-af1f54cd496e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 00:10:37,237] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 00:10:37,237] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 00:10:37,237] [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 oceani	strain=SCSIO 61214	GCA_018141545.1	2843216	2843216	type	True	75.6168	68	476	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	75.4856	59	476	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	75.3869	62	476	95	below_threshold
Conexibacter arvalis	strain=DSM 23288	GCA_014199525.1	912552	912552	type	True	75.2387	84	476	95	below_threshold
Patulibacter medicamentivorans	strain=I11	GCA_000240225.2	1097667	1097667	type	True	75.1212	72	476	95	below_threshold
Pseudonocardia thermophila	strain=DSM 43832	GCA_900142365.1	1848	1848	type	True	74.9443	53	476	95	below_threshold
Nonomuraea pusilla	strain=DSM 43357	GCA_900109355.1	46177	46177	type	True	74.9032	67	476	95	below_threshold
Pyxidicoccus fallax	strain=DSM 14698	GCA_012933655.1	394095	394095	type	True	74.8806	64	476	95	below_threshold
Pyxidicoccus trucidator	strain=CA060A	GCA_010894435.1	2709662	2709662	type	True	74.8349	72	476	95	below_threshold
Pyxidicoccus caerfyrddinensis	strain=CA032A	GCA_010894405.1	2709663	2709663	type	True	74.8221	81	476	95	below_threshold
Nonomuraea africana	strain=DSM 43748	GCA_014873535.1	46171	46171	type	True	74.8	52	476	95	below_threshold
Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis	strain=AM401	GCA_006636215.1	2590453	2590453	type	True	74.7833	65	476	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 00:10:37,253] [INFO] DFAST Taxonomy check result was written to GCA_024276735.1_ASM2427673v1_genomic.fna/tc_result.tsv
[2023-06-30 00:10:37,254] [INFO] ===== Taxonomy check completed =====
[2023-06-30 00:10:37,254] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 00:10:37,255] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c5840e3-a084-4d7d-8d95-af1f54cd496e/dqc_reference/checkm_data
[2023-06-30 00:10:37,257] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 00:10:37,280] [INFO] Task started: CheckM
[2023-06-30 00:10:37,280] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024276735.1_ASM2427673v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024276735.1_ASM2427673v1_genomic.fna/checkm_input GCA_024276735.1_ASM2427673v1_genomic.fna/checkm_result
[2023-06-30 00:10:56,429] [INFO] Task succeeded: CheckM
[2023-06-30 00:10:56,430] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.91%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 00:10:56,452] [INFO] ===== Completeness check finished =====
[2023-06-30 00:10:56,453] [INFO] ===== Start GTDB Search =====
[2023-06-30 00:10:56,453] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024276735.1_ASM2427673v1_genomic.fna/markers.fasta)
[2023-06-30 00:10:56,454] [INFO] Task started: Blastn
[2023-06-30 00:10:56,454] [INFO] Running command: blastn -query GCA_024276735.1_ASM2427673v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c5840e3-a084-4d7d-8d95-af1f54cd496e/dqc_reference/reference_markers_gtdb.fasta -out GCA_024276735.1_ASM2427673v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:10:57,493] [INFO] Task succeeded: Blastn
[2023-06-30 00:10:57,497] [INFO] Selected 19 target genomes.
[2023-06-30 00:10:57,497] [INFO] Target genome list was writen to GCA_024276735.1_ASM2427673v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 00:10:57,504] [INFO] Task started: fastANI
[2023-06-30 00:10:57,505] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ab4e2aa-adf6-4fb8-aa81-546a90a19d8d/GCA_024276735.1_ASM2427673v1_genomic.fna.gz --refList GCA_024276735.1_ASM2427673v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024276735.1_ASM2427673v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 00:11:06,657] [INFO] Task succeeded: fastANI
[2023-06-30 00:11:06,671] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 00:11:06,672] [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_003599855.1	s__SURF-19 sp003599855	79.3832	209	476	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__BMS3ABIN01;f__BMS3ABIN01;g__SURF-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002897715.1	s__BMS3ABIN01 sp002897715	78.8622	179	476	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__BMS3ABIN01;f__BMS3ABIN01;g__BMS3ABIN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016650015.1	s__JACRMB01 sp016650015	77.7126	122	476	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__BMS3ABIN01;f__BMS3ABIN01;g__JACRMB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235065.1	s__JACRMB01 sp016235065	77.5912	137	476	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__BMS3ABIN01;f__BMS3ABIN01;g__JACRMB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859345.1	s__Kmv30 sp014859345	77.3811	111	476	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__BMS3ABIN01;f__BMS3ABIN01;g__Kmv30	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014874175.1	s__JACWAD01 sp014874175	77.2342	113	476	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__BMS3ABIN01;f__BMS3ABIN01;g__JACWAD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002347645.1	s__UBA2241 sp002347645	76.0135	57	476	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__UBA2241;f__UBA2241;g__UBA2241	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903912585.1	s__CAIXSE01 sp903912585	75.8238	60	476	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__UBA2241;f__UBA2241;g__CAIXSE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003164655.1	s__Bog-752 sp003164655	75.5932	59	476	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__UBA2241;f__UBA2241;g__Bog-752	95.0	99.30	99.30	0.91	0.91	2	-
GCF_900142365.1	s__Pseudonocardia thermophila	74.9349	54	476	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 00:11:06,674] [INFO] GTDB search result was written to GCA_024276735.1_ASM2427673v1_genomic.fna/result_gtdb.tsv
[2023-06-30 00:11:06,674] [INFO] ===== GTDB Search completed =====
[2023-06-30 00:11:06,678] [INFO] DFAST_QC result json was written to GCA_024276735.1_ASM2427673v1_genomic.fna/dqc_result.json
[2023-06-30 00:11:06,678] [INFO] DFAST_QC completed!
[2023-06-30 00:11:06,678] [INFO] Total running time: 0h1m3s