[2024-01-24 13:36:45,809] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:45,811] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:45,811] [INFO] DQC Reference Directory: /var/lib/cwl/stgcde67aeb-e47e-4302-86c5-40685e648407/dqc_reference
[2024-01-24 13:36:47,068] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:47,069] [INFO] Task started: Prodigal
[2024-01-24 13:36:47,070] [INFO] Running command: gunzip -c /var/lib/cwl/stg59790416-ccde-468e-8256-3d475fcaf949/GCF_013004535.1_ASM1300453v1_genomic.fna.gz | prodigal -d GCF_013004535.1_ASM1300453v1_genomic.fna/cds.fna -a GCF_013004535.1_ASM1300453v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:58,937] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:58,938] [INFO] Task started: HMMsearch
[2024-01-24 13:36:58,938] [INFO] Running command: hmmsearch --tblout GCF_013004535.1_ASM1300453v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcde67aeb-e47e-4302-86c5-40685e648407/dqc_reference/reference_markers.hmm GCF_013004535.1_ASM1300453v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:59,178] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:59,179] [INFO] Found 6/6 markers.
[2024-01-24 13:36:59,212] [INFO] Query marker FASTA was written to GCF_013004535.1_ASM1300453v1_genomic.fna/markers.fasta
[2024-01-24 13:36:59,212] [INFO] Task started: Blastn
[2024-01-24 13:36:59,212] [INFO] Running command: blastn -query GCF_013004535.1_ASM1300453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcde67aeb-e47e-4302-86c5-40685e648407/dqc_reference/reference_markers.fasta -out GCF_013004535.1_ASM1300453v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:00,365] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:00,369] [INFO] Selected 15 target genomes.
[2024-01-24 13:37:00,369] [INFO] Target genome list was writen to GCF_013004535.1_ASM1300453v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:00,376] [INFO] Task started: fastANI
[2024-01-24 13:37:00,377] [INFO] Running command: fastANI --query /var/lib/cwl/stg59790416-ccde-468e-8256-3d475fcaf949/GCF_013004535.1_ASM1300453v1_genomic.fna.gz --refList GCF_013004535.1_ASM1300453v1_genomic.fna/target_genomes.txt --output GCF_013004535.1_ASM1300453v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:15,279] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:15,280] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcde67aeb-e47e-4302-86c5-40685e648407/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:15,280] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcde67aeb-e47e-4302-86c5-40685e648407/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:15,293] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:37:15,293] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:15,293] [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
Gordonia araii	strain=IFM 10211	GCA_013004535.1	263909	263909	type	True	100.0	1272	1276	95	conclusive
Gordonia araii	strain=NBRC 100433	GCA_000241265.2	263909	263909	type	True	99.9712	1245	1276	95	conclusive
Gordonia crocea	strain=NBRC 107697	GCA_009932435.1	589162	589162	type	True	82.7981	892	1276	95	below_threshold
Gordonia paraffinivorans	strain=NBRC 108238	GCA_000344155.1	175628	175628	type	True	79.4383	555	1276	95	below_threshold
Gordonia bronchialis	strain=NCTC10667	GCA_900450805.1	2054	2054	type	True	79.014	504	1276	95	below_threshold
Gordonia bronchialis	strain=FDAARGOS_1594	GCA_020731255.1	2054	2054	type	True	78.9907	510	1276	95	below_threshold
Gordonia rubripertincta	strain=NBRC 101908	GCA_000327325.1	36822	36822	type	True	78.9596	534	1276	95	below_threshold
Gordonia rubripertincta	strain=ATCC 14352	GCA_012396225.1	36822	36822	type	True	78.9523	549	1276	95	below_threshold
Gordonia alkanivorans	strain=NBRC 16433	GCA_000225505.1	84096	84096	type	True	78.9344	576	1276	95	below_threshold
Gordonia amarae	strain=NBRC 15530	GCA_000241345.2	36821	36821	type	True	78.8553	507	1276	95	below_threshold
Gordonia asplenii	strain=TBRC 11910	GCA_012933505.1	2725283	2725283	type	True	78.8015	545	1276	95	below_threshold
Gordonia jinghuaiqii	strain=zg-686	GCA_024701535.1	2758710	2758710	type	True	78.7887	530	1276	95	below_threshold
Gordonia terrae	strain=3612	GCA_001698225.1	2055	2055	suspected-type	True	78.772	533	1276	95	below_threshold
Gordonia terrae	strain=NRRL B-16283	GCA_003183825.1	2055	2055	suspected-type	True	78.7634	536	1276	95	below_threshold
Gordonia hirsuta	strain=DSM 44140	GCA_000420685.1	53427	53427	type	True	78.6314	455	1276	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:15,295] [INFO] DFAST Taxonomy check result was written to GCF_013004535.1_ASM1300453v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:15,296] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:15,296] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:15,296] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcde67aeb-e47e-4302-86c5-40685e648407/dqc_reference/checkm_data
[2024-01-24 13:37:15,297] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:15,337] [INFO] Task started: CheckM
[2024-01-24 13:37:15,338] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013004535.1_ASM1300453v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013004535.1_ASM1300453v1_genomic.fna/checkm_input GCF_013004535.1_ASM1300453v1_genomic.fna/checkm_result
[2024-01-24 13:37:52,853] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:52,854] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:52,874] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:52,875] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:52,875] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013004535.1_ASM1300453v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:52,875] [INFO] Task started: Blastn
[2024-01-24 13:37:52,875] [INFO] Running command: blastn -query GCF_013004535.1_ASM1300453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcde67aeb-e47e-4302-86c5-40685e648407/dqc_reference/reference_markers_gtdb.fasta -out GCF_013004535.1_ASM1300453v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:54,816] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:54,824] [INFO] Selected 12 target genomes.
[2024-01-24 13:37:54,824] [INFO] Target genome list was writen to GCF_013004535.1_ASM1300453v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:54,853] [INFO] Task started: fastANI
[2024-01-24 13:37:54,853] [INFO] Running command: fastANI --query /var/lib/cwl/stg59790416-ccde-468e-8256-3d475fcaf949/GCF_013004535.1_ASM1300453v1_genomic.fna.gz --refList GCF_013004535.1_ASM1300453v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013004535.1_ASM1300453v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:06,334] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:06,345] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:06,345] [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_000241265.1	s__Gordonia araii	99.9712	1245	1276	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_009932435.1	s__Gordonia crocea	82.8079	891	1276	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013348785.1	s__Gordonia sp013348785	82.1557	868	1276	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002477755.1	s__Gordonia sp002477755	81.4648	717	1276	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.87	99.81	0.89	0.84	3	-
GCA_002414845.1	s__Gordonia sp002414845	81.013	661	1276	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000344155.1	s__Gordonia paraffinivorans	79.4922	549	1276	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.97	98.74	0.93	0.90	12	-
GCF_000024785.1	s__Gordonia bronchialis	79.003	507	1276	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	100.00	100.00	1.00	1.00	3	-
GCF_000225505.1	s__Gordonia alkanivorans	78.9481	574	1276	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.26	97.87	0.90	0.88	6	-
GCF_000327325.1	s__Gordonia rubripertincta	78.9226	539	1276	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.55	98.07	0.91	0.87	6	-
GCF_000241345.1	s__Gordonia amarae	78.8779	505	1276	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.98	99.98	0.99	0.99	3	-
GCF_012933505.1	s__Gordonia asplenii	78.7934	546	1276	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003855095.1	s__Gordonia insulae	78.5731	525	1276	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:06,348] [INFO] GTDB search result was written to GCF_013004535.1_ASM1300453v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:06,349] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:06,353] [INFO] DFAST_QC result json was written to GCF_013004535.1_ASM1300453v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:06,353] [INFO] DFAST_QC completed!
[2024-01-24 13:38:06,353] [INFO] Total running time: 0h1m21s