[2024-01-24 12:27:18,962] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:27:18,964] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:27:18,964] [INFO] DQC Reference Directory: /var/lib/cwl/stgef4e82bf-1404-4e10-a764-b512015e384c/dqc_reference
[2024-01-24 12:27:20,108] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:27:20,109] [INFO] Task started: Prodigal
[2024-01-24 12:27:20,109] [INFO] Running command: gunzip -c /var/lib/cwl/stge01c1438-17bf-4cef-ba88-e7dcbbcbb889/GCF_010993775.1_ASM1099377v1_genomic.fna.gz | prodigal -d GCF_010993775.1_ASM1099377v1_genomic.fna/cds.fna -a GCF_010993775.1_ASM1099377v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:27:45,013] [INFO] Task succeeded: Prodigal
[2024-01-24 12:27:45,014] [INFO] Task started: HMMsearch
[2024-01-24 12:27:45,014] [INFO] Running command: hmmsearch --tblout GCF_010993775.1_ASM1099377v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgef4e82bf-1404-4e10-a764-b512015e384c/dqc_reference/reference_markers.hmm GCF_010993775.1_ASM1099377v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:27:45,330] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:27:45,331] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge01c1438-17bf-4cef-ba88-e7dcbbcbb889/GCF_010993775.1_ASM1099377v1_genomic.fna.gz]
[2024-01-24 12:27:45,402] [INFO] Query marker FASTA was written to GCF_010993775.1_ASM1099377v1_genomic.fna/markers.fasta
[2024-01-24 12:27:45,402] [INFO] Task started: Blastn
[2024-01-24 12:27:45,402] [INFO] Running command: blastn -query GCF_010993775.1_ASM1099377v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgef4e82bf-1404-4e10-a764-b512015e384c/dqc_reference/reference_markers.fasta -out GCF_010993775.1_ASM1099377v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:27:46,314] [INFO] Task succeeded: Blastn
[2024-01-24 12:27:46,318] [INFO] Selected 30 target genomes.
[2024-01-24 12:27:46,318] [INFO] Target genome list was writen to GCF_010993775.1_ASM1099377v1_genomic.fna/target_genomes.txt
[2024-01-24 12:27:46,360] [INFO] Task started: fastANI
[2024-01-24 12:27:46,360] [INFO] Running command: fastANI --query /var/lib/cwl/stge01c1438-17bf-4cef-ba88-e7dcbbcbb889/GCF_010993775.1_ASM1099377v1_genomic.fna.gz --refList GCF_010993775.1_ASM1099377v1_genomic.fna/target_genomes.txt --output GCF_010993775.1_ASM1099377v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:28:19,401] [INFO] Task succeeded: fastANI
[2024-01-24 12:28:19,401] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgef4e82bf-1404-4e10-a764-b512015e384c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:28:19,402] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgef4e82bf-1404-4e10-a764-b512015e384c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:28:19,422] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:28:19,422] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:28:19,423] [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
Fodinicola acaciae	strain=GKU 173	GCA_010993745.1	2681555	2681555	type	True	80.4811	1386	2850	95	below_threshold
Modestobacter versicolor	strain=CP153-2	GCA_003226595.1	429133	429133	type	True	76.6078	318	2850	95	below_threshold
Amycolatopsis granulosa	strain=DSM 45669	GCA_011758745.1	185684	185684	type	True	76.5983	382	2850	95	below_threshold
Micromonospora coriariae	strain=DSM 44875	GCA_900091455.1	285665	285665	type	True	76.5745	454	2850	95	below_threshold
Micromonospora nigra	strain=DSM 43818	GCA_900091585.1	145857	145857	type	True	76.5201	380	2850	95	below_threshold
Micromonospora maris	strain=NRRL B-24793	GCA_001507315.1	1003110	1003110	type	True	76.4909	407	2850	95	below_threshold
Micromonospora maris	strain=AB-18-032	GCA_000204155.1	1003110	1003110	type	True	76.4679	407	2850	95	below_threshold
Kutzneria kofuensis	strain=DSM 43851	GCA_014203355.1	103725	103725	type	True	76.4491	579	2850	95	below_threshold
Kutzneria buriramensis	strain=DSM 45791	GCA_003387475.1	1045776	1045776	type	True	76.3891	599	2850	95	below_threshold
Micromonospora rifamycinica	strain=DSM 44983	GCA_900090265.1	291594	291594	type	True	76.3845	457	2850	95	below_threshold
Modestobacter marinus	strain=DSM 45201	GCA_011758655.1	477641	477641	type	True	76.3811	401	2850	95	below_threshold
Modestobacter versicolor	strain=DSM 16678	GCA_014195485.1	429133	429133	type	True	76.3693	403	2850	95	below_threshold
Micromonospora rifamycinica	strain=AM105	GCA_001542325.1	291594	291594	type	True	76.3297	429	2850	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	76.3167	471	2850	95	below_threshold
Mycolicibacterium fallax	strain=JCM 6405	GCA_010726955.1	1793	1793	type	True	76.3065	256	2850	95	below_threshold
Modestobacter excelsi	strain=1G6	GCA_005930495.1	2213161	2213161	type	True	76.2777	379	2850	95	below_threshold
Amycolatopsis endophytica	strain=DSM 104006	GCA_013410405.1	860233	860233	type	True	76.2674	409	2850	95	below_threshold
Cryptosporangium phraense	strain=A-T 5661	GCA_006912135.1	2593070	2593070	type	True	76.2452	492	2850	95	below_threshold
Mycolicibacterium fallax	strain=DSM 44179	GCA_002101995.1	1793	1793	type	True	76.2198	258	2850	95	below_threshold
Micromonospora matsumotoense	strain=DSM 44100	GCA_900091525.1	121616	121616	type	True	76.2187	467	2850	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	76.2132	341	2850	95	below_threshold
Prauserella isguenensis	strain=CECT 8577	GCA_014191605.1	1470180	1470180	type	True	76.2084	240	2850	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	76.194	562	2850	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	76.1651	375	2850	95	below_threshold
Cryptosporangium arvum	strain=DSM 44712	GCA_000585375.1	80871	80871	type	True	76.1599	568	2850	95	below_threshold
Flexivirga oryzae	strain=DSM 105369	GCA_014190805.1	1794944	1794944	type	True	76.0658	218	2850	95	below_threshold
Pseudonocardia acaciae	strain=DSM 45401	GCA_000620785.1	551276	551276	type	True	76.0097	557	2850	95	below_threshold
Catellatospora citrea	strain=NBRC 14495	GCA_016862615.1	53366	53366	type	True	75.9966	512	2850	95	below_threshold
Actinoplanes tereljensis	strain=NBRC 105297	GCA_016862435.1	571912	571912	type	True	75.9273	550	2850	95	below_threshold
Antricoccus suffuscus	strain=DSM 100065	GCA_003003235.1	1629062	1629062	type	True	75.8929	134	2850	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:28:19,425] [INFO] DFAST Taxonomy check result was written to GCF_010993775.1_ASM1099377v1_genomic.fna/tc_result.tsv
[2024-01-24 12:28:19,425] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:28:19,425] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:28:19,425] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgef4e82bf-1404-4e10-a764-b512015e384c/dqc_reference/checkm_data
[2024-01-24 12:28:19,426] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:28:19,503] [INFO] Task started: CheckM
[2024-01-24 12:28:19,503] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010993775.1_ASM1099377v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010993775.1_ASM1099377v1_genomic.fna/checkm_input GCF_010993775.1_ASM1099377v1_genomic.fna/checkm_result
[2024-01-24 12:29:26,113] [INFO] Task succeeded: CheckM
[2024-01-24 12:29:26,114] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:29:26,133] [INFO] ===== Completeness check finished =====
[2024-01-24 12:29:26,134] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:29:26,134] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010993775.1_ASM1099377v1_genomic.fna/markers.fasta)
[2024-01-24 12:29:26,134] [INFO] Task started: Blastn
[2024-01-24 12:29:26,134] [INFO] Running command: blastn -query GCF_010993775.1_ASM1099377v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgef4e82bf-1404-4e10-a764-b512015e384c/dqc_reference/reference_markers_gtdb.fasta -out GCF_010993775.1_ASM1099377v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:27,611] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:27,614] [INFO] Selected 24 target genomes.
[2024-01-24 12:29:27,614] [INFO] Target genome list was writen to GCF_010993775.1_ASM1099377v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:29:27,735] [INFO] Task started: fastANI
[2024-01-24 12:29:27,736] [INFO] Running command: fastANI --query /var/lib/cwl/stge01c1438-17bf-4cef-ba88-e7dcbbcbb889/GCF_010993775.1_ASM1099377v1_genomic.fna.gz --refList GCF_010993775.1_ASM1099377v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010993775.1_ASM1099377v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:29:59,231] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:59,252] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:29:59,252] [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_010993775.1	s__Fodinicola feengrottensis	100.0	2841	2850	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__HKI-0501;g__Fodinicola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_010993745.1	s__Fodinicola acaciae	80.4189	1393	2850	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__HKI-0501;g__Fodinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011758745.1	s__Amycolatopsis granulosa	76.5919	384	2850	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.9842	N/A	N/A	N/A	N/A	1	-
GCF_014645795.1	s__Longimycelium tulufanense	76.5122	302	2850	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Longimycelium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013364215.1	s__Micromonospora sp004307965	76.4771	425	2850	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.04	99.04	0.94	0.94	2	-
GCF_003725545.1	s__Micromonospora sp003725545	76.4447	456	2850	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.98	99.95	0.98	0.97	4	-
GCF_014195485.1	s__Modestobacter versicolor	76.4002	406	2850	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	99.97	99.97	1.00	1.00	2	-
GCF_003387475.1	s__Kutzneria buriramensis	76.3828	601	2850	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kutzneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739085.1	s__Amycolatopsis methanolica	76.3751	449	2850	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	96.3446	100.00	100.00	1.00	1.00	2	-
GCF_900090265.1	s__Micromonospora rifamycinica	76.3606	455	2850	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014653945.1	s__Amycolatopsis deserti	76.3588	471	2850	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000231075.2	s__Amycolatopsis sp000231075	76.3041	497	2850	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.4849	N/A	N/A	N/A	N/A	1	-
GCF_003312875.1	s__Amycolatopsis albispora	76.285	490	2850	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017875555.1	s__Amycolatopsis magusensis	76.2533	485	2850	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006912135.1	s__Cryptosporangium phraense	76.2412	493	2850	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Cryptosporangiaceae;g__Cryptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017599305.1	s__Micromonospora sp017599305	76.2179	453	2850	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005885555.1	s__Rugosimonospora sp005885555	76.2043	442	2850	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Rugosimonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014190805.1	s__Flexivirga oryzae	76.0584	219	2850	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Flexivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862575.1	s__Catellatospora bangladeshensis	76.054	509	2850	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	95.24	95.24	0.85	0.85	2	-
GCF_000620785.1	s__Pseudonocardia acaciae	76.0004	560	2850	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003289645.1	s__Actinomadura_D craniellae	75.9877	397	2850	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Actinomadura_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862635.1	s__Catellatospora coxensis	75.9683	514	2850	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003235.1	s__Antricoccus suffuscus	75.9039	133	2850	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Antricoccaceae;g__Antricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001942415.1	s__Pseudonocardia sp001942415	75.8835	444	2850	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:29:59,254] [INFO] GTDB search result was written to GCF_010993775.1_ASM1099377v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:29:59,255] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:29:59,261] [INFO] DFAST_QC result json was written to GCF_010993775.1_ASM1099377v1_genomic.fna/dqc_result.json
[2024-01-24 12:29:59,262] [INFO] DFAST_QC completed!
[2024-01-24 12:29:59,262] [INFO] Total running time: 0h2m40s