[2024-01-25 17:44:20,586] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:44:20,588] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:44:20,588] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ae3a48a-6a06-4255-a948-4ef563ddb6cb/dqc_reference
[2024-01-25 17:44:21,732] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:44:21,733] [INFO] Task started: Prodigal
[2024-01-25 17:44:21,733] [INFO] Running command: gunzip -c /var/lib/cwl/stg1ff1c676-dac6-495f-85c4-2242b934c1b8/GCF_000024785.1_ASM2478v1_genomic.fna.gz | prodigal -d GCF_000024785.1_ASM2478v1_genomic.fna/cds.fna -a GCF_000024785.1_ASM2478v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:44:49,447] [INFO] Task succeeded: Prodigal
[2024-01-25 17:44:49,447] [INFO] Task started: HMMsearch
[2024-01-25 17:44:49,447] [INFO] Running command: hmmsearch --tblout GCF_000024785.1_ASM2478v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ae3a48a-6a06-4255-a948-4ef563ddb6cb/dqc_reference/reference_markers.hmm GCF_000024785.1_ASM2478v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:44:49,704] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:44:49,704] [INFO] Found 6/6 markers.
[2024-01-25 17:44:49,752] [INFO] Query marker FASTA was written to GCF_000024785.1_ASM2478v1_genomic.fna/markers.fasta
[2024-01-25 17:44:49,752] [INFO] Task started: Blastn
[2024-01-25 17:44:49,752] [INFO] Running command: blastn -query GCF_000024785.1_ASM2478v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ae3a48a-6a06-4255-a948-4ef563ddb6cb/dqc_reference/reference_markers.fasta -out GCF_000024785.1_ASM2478v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:44:50,915] [INFO] Task succeeded: Blastn
[2024-01-25 17:44:50,918] [INFO] Selected 14 target genomes.
[2024-01-25 17:44:50,919] [INFO] Target genome list was writen to GCF_000024785.1_ASM2478v1_genomic.fna/target_genomes.txt
[2024-01-25 17:44:50,925] [INFO] Task started: fastANI
[2024-01-25 17:44:50,925] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ff1c676-dac6-495f-85c4-2242b934c1b8/GCF_000024785.1_ASM2478v1_genomic.fna.gz --refList GCF_000024785.1_ASM2478v1_genomic.fna/target_genomes.txt --output GCF_000024785.1_ASM2478v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:45:07,260] [INFO] Task succeeded: fastANI
[2024-01-25 17:45:07,261] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ae3a48a-6a06-4255-a948-4ef563ddb6cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:45:07,261] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ae3a48a-6a06-4255-a948-4ef563ddb6cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:45:07,270] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 17:45:07,270] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:45:07,270] [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 bronchialis	strain=DSM 43247	GCA_000024785.1	2054	2054	type	True	100.0	1763	1763	95	conclusive
Gordonia bronchialis	strain=NCTC10667	GCA_900450805.1	2054	2054	type	True	99.9968	1761	1763	95	conclusive
Gordonia bronchialis	strain=FDAARGOS_1594	GCA_020731255.1	2054	2054	type	True	99.9943	1757	1763	95	conclusive
Gordonia rubripertincta	strain=NBRC 101908	GCA_000327325.1	36822	36822	type	True	80.8811	891	1763	95	below_threshold
Gordonia rubripertincta	strain=ATCC 14352	GCA_012396225.1	36822	36822	type	True	80.8282	894	1763	95	below_threshold
Gordonia amicalis	strain=DSM 44461	GCA_012395955.1	89053	89053	type	True	80.5495	907	1763	95	below_threshold
Gordonia amicalis	strain=NBRC 100051	GCA_000332995.1	89053	89053	type	True	80.5034	909	1763	95	below_threshold
Gordonia desulfuricans	strain=213E	GCA_010119475.1	89051	89051	type	True	80.3847	879	1763	95	below_threshold
Gordonia desulfuricans	strain=NBRC 100010	GCA_001485495.1	89051	89051	type	True	80.3637	866	1763	95	below_threshold
Gordonia insulae	strain=MMS17-SY073	GCA_003855095.1	2420509	2420509	type	True	80.1019	910	1763	95	below_threshold
Gordonia mangrovi	strain=HNM0687	GCA_009828195.1	2665643	2665643	type	True	80.01	821	1763	95	below_threshold
Gordonia amarae	strain=NBRC 15530	GCA_000241345.2	36821	36821	type	True	79.6304	749	1763	95	below_threshold
Gordonia hankookensis	strain=ON-33	GCA_014673215.1	589403	589403	type	True	79.4743	833	1763	95	below_threshold
Gordonia pseudamarae	strain=CON9	GCA_025273675.1	2831662	2831662	type	True	79.3916	674	1763	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:45:07,271] [INFO] DFAST Taxonomy check result was written to GCF_000024785.1_ASM2478v1_genomic.fna/tc_result.tsv
[2024-01-25 17:45:07,272] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:45:07,272] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:45:07,272] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ae3a48a-6a06-4255-a948-4ef563ddb6cb/dqc_reference/checkm_data
[2024-01-25 17:45:07,273] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:45:07,324] [INFO] Task started: CheckM
[2024-01-25 17:45:07,324] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000024785.1_ASM2478v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000024785.1_ASM2478v1_genomic.fna/checkm_input GCF_000024785.1_ASM2478v1_genomic.fna/checkm_result
[2024-01-25 17:46:55,221] [INFO] Task succeeded: CheckM
[2024-01-25 17:46:55,223] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:46:55,246] [INFO] ===== Completeness check finished =====
[2024-01-25 17:46:55,246] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:46:55,247] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000024785.1_ASM2478v1_genomic.fna/markers.fasta)
[2024-01-25 17:46:55,248] [INFO] Task started: Blastn
[2024-01-25 17:46:55,248] [INFO] Running command: blastn -query GCF_000024785.1_ASM2478v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ae3a48a-6a06-4255-a948-4ef563ddb6cb/dqc_reference/reference_markers_gtdb.fasta -out GCF_000024785.1_ASM2478v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:46:57,112] [INFO] Task succeeded: Blastn
[2024-01-25 17:46:57,115] [INFO] Selected 18 target genomes.
[2024-01-25 17:46:57,115] [INFO] Target genome list was writen to GCF_000024785.1_ASM2478v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:46:57,155] [INFO] Task started: fastANI
[2024-01-25 17:46:57,155] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ff1c676-dac6-495f-85c4-2242b934c1b8/GCF_000024785.1_ASM2478v1_genomic.fna.gz --refList GCF_000024785.1_ASM2478v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000024785.1_ASM2478v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:47:18,820] [INFO] Task succeeded: fastANI
[2024-01-25 17:47:18,832] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:47:18,832] [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_000024785.1	s__Gordonia bronchialis	100.0	1763	1763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCF_900105725.1	s__Gordonia westfalica	80.9606	967	1763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000327325.1	s__Gordonia rubripertincta	80.8581	893	1763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.55	98.07	0.91	0.87	6	-
GCF_000298235.1	s__Gordonia namibiensis	80.678	877	1763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.13	97.13	0.90	0.90	2	-
GCF_011290605.1	s__Gordonia sp002009645	80.6166	928	1763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.70	97.37	0.91	0.88	14	-
GCF_000332995.1	s__Gordonia amicalis	80.5436	903	1763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.45	97.39	0.94	0.91	7	-
GCF_001485495.1	s__Gordonia desulfuricans	80.3782	864	1763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.37	98.77	0.95	0.92	3	-
GCF_001698225.1	s__Gordonia terrae	80.33	908	1763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.37	97.67	0.96	0.87	7	-
GCA_002700145.1	s__Gordonia sp002700145	80.1643	817	1763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017654315.1	s__Gordonia polyisoprenivorans_A	80.0943	885	1763	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	80.0854	910	1763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828195.1	s__Gordonia sp009828195	80.0096	822	1763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003797825.1	s__Gordonia sp003797825	79.9051	901	1763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000241345.1	s__Gordonia amarae	79.679	742	1763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.98	99.98	0.99	0.99	3	-
GCF_009862785.1	s__Gordonia sp009862785	79.6709	787	1763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003797185.1	s__Gordonia oryzae	79.6243	725	1763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014673215.1	s__Gordonia hankookensis	79.4781	832	1763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.33	98.32	0.95	0.94	3	-
GCF_009914535.1	s__Gordonia pseudoamarae	79.2924	685	1763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.95	99.95	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:47:18,834] [INFO] GTDB search result was written to GCF_000024785.1_ASM2478v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:47:18,838] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:47:18,843] [INFO] DFAST_QC result json was written to GCF_000024785.1_ASM2478v1_genomic.fna/dqc_result.json
[2024-01-25 17:47:18,843] [INFO] DFAST_QC completed!
[2024-01-25 17:47:18,843] [INFO] Total running time: 0h2m58s