[2024-01-24 13:25:47,606] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:47,608] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:47,608] [INFO] DQC Reference Directory: /var/lib/cwl/stg84c3b0e1-a941-4958-8fe8-660b8f09ff01/dqc_reference
[2024-01-24 13:25:49,032] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:49,032] [INFO] Task started: Prodigal
[2024-01-24 13:25:49,033] [INFO] Running command: gunzip -c /var/lib/cwl/stgd8ef7c26-3a08-4abf-b191-8f4e8bcfc65b/GCF_004382795.1_ASM438279v1_genomic.fna.gz | prodigal -d GCF_004382795.1_ASM438279v1_genomic.fna/cds.fna -a GCF_004382795.1_ASM438279v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:26:01,412] [INFO] Task succeeded: Prodigal
[2024-01-24 13:26:01,412] [INFO] Task started: HMMsearch
[2024-01-24 13:26:01,413] [INFO] Running command: hmmsearch --tblout GCF_004382795.1_ASM438279v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84c3b0e1-a941-4958-8fe8-660b8f09ff01/dqc_reference/reference_markers.hmm GCF_004382795.1_ASM438279v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:26:01,682] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:26:01,683] [INFO] Found 6/6 markers.
[2024-01-24 13:26:01,724] [INFO] Query marker FASTA was written to GCF_004382795.1_ASM438279v1_genomic.fna/markers.fasta
[2024-01-24 13:26:01,724] [INFO] Task started: Blastn
[2024-01-24 13:26:01,724] [INFO] Running command: blastn -query GCF_004382795.1_ASM438279v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84c3b0e1-a941-4958-8fe8-660b8f09ff01/dqc_reference/reference_markers.fasta -out GCF_004382795.1_ASM438279v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:02,615] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:02,618] [INFO] Selected 23 target genomes.
[2024-01-24 13:26:02,619] [INFO] Target genome list was writen to GCF_004382795.1_ASM438279v1_genomic.fna/target_genomes.txt
[2024-01-24 13:26:02,673] [INFO] Task started: fastANI
[2024-01-24 13:26:02,674] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8ef7c26-3a08-4abf-b191-8f4e8bcfc65b/GCF_004382795.1_ASM438279v1_genomic.fna.gz --refList GCF_004382795.1_ASM438279v1_genomic.fna/target_genomes.txt --output GCF_004382795.1_ASM438279v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:24,507] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:24,508] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84c3b0e1-a941-4958-8fe8-660b8f09ff01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:24,508] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84c3b0e1-a941-4958-8fe8-660b8f09ff01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:24,530] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:26:24,530] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:24,531] [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
Cumulibacter soli	strain=G-1	GCA_004382795.1	2546344	2546344	type	True	100.0	1303	1305	95	conclusive
Antricoccus suffuscus	strain=DSM 100065	GCA_003003235.1	1629062	1629062	type	True	77.1479	181	1305	95	below_threshold
Rhodococcus rhodochrous	strain=NCTC10210	GCA_900187265.1	1829	1829	suspected-type	True	76.5547	112	1305	95	below_threshold
Rhodococcus kroppenstedtii	strain=DSM 44908	GCA_001646725.1	293050	293050	type	True	76.5433	95	1305	95	below_threshold
Rhodococcus rhodochrous	strain=DSM 43241	GCA_001646825.1	1829	1829	suspected-type	True	76.5081	112	1305	95	below_threshold
Actinokineospora xionganensis	strain=HBU206404	GCA_014323725.1	2684470	2684470	type	True	76.3514	119	1305	95	below_threshold
Amycolatopsis australiensis	strain=DSM 44671	GCA_900119165.1	546364	546364	type	True	76.2745	169	1305	95	below_threshold
Micromonospora deserti	strain=13K206	GCA_003236335.1	2070366	2070366	type	True	76.262	116	1305	95	below_threshold
Nocardioides szechwanensis	strain=NBRC 108562	GCA_007992395.1	1005944	1005944	type	True	76.2497	113	1305	95	below_threshold
Cellulomonas biazotea	strain=NBRC12680	GCA_004306155.1	1709	1709	type	True	76.2125	104	1305	95	below_threshold
Amycolatopsis circi	strain=DSM 45561	GCA_003385235.1	871959	871959	type	True	76.1715	138	1305	95	below_threshold
Amycolatopsis methanolica	strain=239	GCA_000739085.1	1814	1814	type	True	76.1471	161	1305	95	below_threshold
Nocardioides szechwanensis	strain=CGMCC 1.11147	GCA_900103935.1	1005944	1005944	type	True	76.1336	113	1305	95	below_threshold
Amycolatopsis nivea	strain=CFH S0261	GCA_004522235.1	1644109	1644109	type	True	76.0891	157	1305	95	below_threshold
Actinocatenispora sera	strain=NRRL B-24477	GCA_000720965.1	390989	390989	type	True	76.0669	149	1305	95	below_threshold
Prauserella muralis	strain=DSM 45305	GCA_007993965.1	588067	588067	type	True	76.0664	143	1305	95	below_threshold
Amycolatopsis tolypomycina	strain=DSM 44544	GCA_900105945.1	208445	208445	type	True	76.0639	173	1305	95	below_threshold
Actinocatenispora sera	strain=NBRC 101916	GCA_018324685.1	390989	390989	type	True	76.0547	148	1305	95	below_threshold
Amycolatopsis eburnea	strain=GLM-1	GCA_003937945.1	2267691	2267691	type	True	76.0029	173	1305	95	below_threshold
Amycolatopsis saalfeldensis	strain=DSM 44993	GCA_900110575.1	394193	394193	type	True	75.9281	160	1305	95	below_threshold
Agromyces mediolanus	strain=JCM 3346	GCA_014648575.1	41986	41986	type	True	75.9003	93	1305	95	below_threshold
Amycolatopsis jejuensis	strain=NRRL B-24427	GCA_000717335.1	330084	330084	type	True	75.8733	142	1305	95	below_threshold
Agromyces lapidis	strain=JCM 14321	GCA_009749405.1	279574	279574	type	True	75.7739	99	1305	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:24,534] [INFO] DFAST Taxonomy check result was written to GCF_004382795.1_ASM438279v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:24,535] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:24,535] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:24,536] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84c3b0e1-a941-4958-8fe8-660b8f09ff01/dqc_reference/checkm_data
[2024-01-24 13:26:24,537] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:24,577] [INFO] Task started: CheckM
[2024-01-24 13:26:24,577] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004382795.1_ASM438279v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004382795.1_ASM438279v1_genomic.fna/checkm_input GCF_004382795.1_ASM438279v1_genomic.fna/checkm_result
[2024-01-24 13:27:01,964] [INFO] Task succeeded: CheckM
[2024-01-24 13:27:01,965] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:27:01,985] [INFO] ===== Completeness check finished =====
[2024-01-24 13:27:01,985] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:27:01,986] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004382795.1_ASM438279v1_genomic.fna/markers.fasta)
[2024-01-24 13:27:01,986] [INFO] Task started: Blastn
[2024-01-24 13:27:01,986] [INFO] Running command: blastn -query GCF_004382795.1_ASM438279v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84c3b0e1-a941-4958-8fe8-660b8f09ff01/dqc_reference/reference_markers_gtdb.fasta -out GCF_004382795.1_ASM438279v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:03,203] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:03,207] [INFO] Selected 13 target genomes.
[2024-01-24 13:27:03,207] [INFO] Target genome list was writen to GCF_004382795.1_ASM438279v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:27:03,218] [INFO] Task started: fastANI
[2024-01-24 13:27:03,218] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8ef7c26-3a08-4abf-b191-8f4e8bcfc65b/GCF_004382795.1_ASM438279v1_genomic.fna.gz --refList GCF_004382795.1_ASM438279v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004382795.1_ASM438279v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:27:13,951] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:13,966] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:27:13,967] [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_004382795.1	s__Cumulibacter soli	100.0	1303	1305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Antricoccaceae;g__Cumulibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900292035.1	s__Cumulibacter sp900292035	78.6987	385	1305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Antricoccaceae;g__Cumulibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009602465.1	s__Cumulibacter manganitolerans	78.4513	470	1305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Antricoccaceae;g__Cumulibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009834025.1	s__Epidermidibacterium keratini	78.0066	305	1305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Antricoccaceae;g__Epidermidibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003235.1	s__Antricoccus suffuscus	77.1479	181	1305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Antricoccaceae;g__Antricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014218295.1	s__Mycobacterium litorale_B	76.2874	116	1305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103935.1	s__Nocardioides szechwanensis	76.1343	113	1305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCA_012530535.1	s__Yonghaparkia sp012530535	76.0848	74	1305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016861975.1	s__Actinocatenispora rupis	76.0627	150	1305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinocatenispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174495.1	s__Amycolatopsis echigonensis	76.0591	153	1305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	98.67	98.67	0.88	0.88	2	-
GCF_018324685.1	s__Actinocatenispora sera	76.0547	148	1305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinocatenispora	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003937945.1	s__Amycolatopsis eburnea	76.0018	173	1305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004959775.1	s__Agromyces sp004959775	75.7049	101	1305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:27:13,968] [INFO] GTDB search result was written to GCF_004382795.1_ASM438279v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:27:13,969] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:27:13,973] [INFO] DFAST_QC result json was written to GCF_004382795.1_ASM438279v1_genomic.fna/dqc_result.json
[2024-01-24 13:27:13,973] [INFO] DFAST_QC completed!
[2024-01-24 13:27:13,973] [INFO] Total running time: 0h1m26s