[2024-01-24 14:46:55,538] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:55,539] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:55,540] [INFO] DQC Reference Directory: /var/lib/cwl/stg87d60313-6c27-46c6-9eb6-91ee7d96129e/dqc_reference
[2024-01-24 14:46:58,016] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:58,017] [INFO] Task started: Prodigal
[2024-01-24 14:46:58,017] [INFO] Running command: gunzip -c /var/lib/cwl/stg1603dca5-2799-4dbc-a389-1f8898608e51/GCF_004217545.1_ASM421754v1_genomic.fna.gz | prodigal -d GCF_004217545.1_ASM421754v1_genomic.fna/cds.fna -a GCF_004217545.1_ASM421754v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:23,952] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:23,953] [INFO] Task started: HMMsearch
[2024-01-24 14:47:23,953] [INFO] Running command: hmmsearch --tblout GCF_004217545.1_ASM421754v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg87d60313-6c27-46c6-9eb6-91ee7d96129e/dqc_reference/reference_markers.hmm GCF_004217545.1_ASM421754v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:24,301] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:24,303] [INFO] Found 6/6 markers.
[2024-01-24 14:47:24,372] [INFO] Query marker FASTA was written to GCF_004217545.1_ASM421754v1_genomic.fna/markers.fasta
[2024-01-24 14:47:24,373] [INFO] Task started: Blastn
[2024-01-24 14:47:24,373] [INFO] Running command: blastn -query GCF_004217545.1_ASM421754v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg87d60313-6c27-46c6-9eb6-91ee7d96129e/dqc_reference/reference_markers.fasta -out GCF_004217545.1_ASM421754v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:25,570] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:25,575] [INFO] Selected 27 target genomes.
[2024-01-24 14:47:25,575] [INFO] Target genome list was writen to GCF_004217545.1_ASM421754v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:25,590] [INFO] Task started: fastANI
[2024-01-24 14:47:25,591] [INFO] Running command: fastANI --query /var/lib/cwl/stg1603dca5-2799-4dbc-a389-1f8898608e51/GCF_004217545.1_ASM421754v1_genomic.fna.gz --refList GCF_004217545.1_ASM421754v1_genomic.fna/target_genomes.txt --output GCF_004217545.1_ASM421754v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:48:16,576] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:16,577] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg87d60313-6c27-46c6-9eb6-91ee7d96129e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:48:16,577] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg87d60313-6c27-46c6-9eb6-91ee7d96129e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:48:16,602] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:48:16,603] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:48:16,603] [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
Actinoplanes nipponensis	strain=NBRC 14063	GCA_016862275.1	135950	135950	type	True	81.776	1395	2538	95	below_threshold
Actinoplanes digitatis	strain=NBRC 12512	GCA_016862155.1	1868	1868	type	True	81.7158	1394	2538	95	below_threshold
Actinoplanes digitatis	strain=DSM 43149	GCA_014205335.1	1868	1868	type	True	81.701	1427	2538	95	below_threshold
Couchioplanes caeruleus subsp. caeruleus	strain=DSM 43634	GCA_001884705.1	56427	56438	type	True	81.3402	1229	2538	95	below_threshold
Actinoplanes auranticolor	strain=NBRC 12245	GCA_018332655.1	47988	47988	type	True	81.3286	1327	2538	95	below_threshold
Couchioplanes caeruleus	strain=DSM 43634	GCA_003751945.1	56438	56438	type	True	81.2905	1345	2538	95	below_threshold
Actinoplanes teichomyceticus	strain=DSM 43866	GCA_007829915.1	1867	1867	type	True	80.8676	1260	2538	95	below_threshold
Actinoplanes teichomyceticus	strain=ATCC 31121	GCA_003711105.1	1867	1867	type	True	80.8362	1254	2538	95	below_threshold
Actinoplanes teichomyceticus	strain=NBRC 13999	GCA_016862415.1	1867	1867	type	True	80.8321	1219	2538	95	below_threshold
Actinoplanes friuliensis	strain=DSM 7358	GCA_000494755.1	196914	196914	type	True	80.6501	1266	2538	95	below_threshold
Actinoplanes subtropicus	strain=NRRL B-24665	GCA_000721705.1	543632	543632	type	True	80.4408	1317	2538	95	below_threshold
Actinoplanes octamycinicus	strain=NBRC 14524	GCA_016862295.1	135948	135948	type	True	80.4338	1311	2538	95	below_threshold
Actinoplanes deccanensis	strain=NBRC 13994	GCA_016862115.1	113561	113561	type	True	80.4	1269	2538	95	below_threshold
Actinoplanes octamycinicus	strain=DSM 45809	GCA_014205225.1	135948	135948	type	True	80.3838	1371	2538	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	80.2747	1237	2538	95	below_threshold
Actinoplanes lichenicola	strain=LDG1-01	GCA_016785085.1	2802976	2802976	type	True	80.2567	1238	2538	95	below_threshold
Actinoplanes bogorensis	strain=NBRC 110975	GCA_018829635.1	1610840	1610840	type	True	80.19	1211	2538	95	below_threshold
Actinoplanes utahensis	strain=NBRC 13244	GCA_016862455.1	1869	1869	type	True	80.0853	1188	2538	95	below_threshold
Micromonospora maritima		GCA_902825405.1	986711	986711	type	True	79.7742	796	2538	95	below_threshold
Micromonospora chersina	strain=DSM 44151	GCA_900091475.1	47854	47854	type	True	79.6867	1015	2538	95	below_threshold
Micromonospora aurantiaca	strain=ATCC 27029	GCA_000145235.1	47850	47850	type	True	79.6455	1020	2538	95	below_threshold
Micromonospora chalcea	strain=DSM 43026	GCA_002926165.1	1874	1874	type	True	79.5858	1003	2538	95	below_threshold
Micromonospora sediminicola	strain=DSM 45794	GCA_900089585.1	946078	946078	type	True	79.5445	1068	2538	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	79.4369	1056	2538	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	79.2972	999	2538	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	76.3878	643	2538	95	below_threshold
Saccharothrix obliqua	strain=SC076	GCA_019375475.1	2861747	2861747	type	True	76.345	672	2538	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:48:16,604] [INFO] DFAST Taxonomy check result was written to GCF_004217545.1_ASM421754v1_genomic.fna/tc_result.tsv
[2024-01-24 14:48:16,605] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:48:16,605] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:48:16,605] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg87d60313-6c27-46c6-9eb6-91ee7d96129e/dqc_reference/checkm_data
[2024-01-24 14:48:16,607] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:48:16,675] [INFO] Task started: CheckM
[2024-01-24 14:48:16,676] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004217545.1_ASM421754v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004217545.1_ASM421754v1_genomic.fna/checkm_input GCF_004217545.1_ASM421754v1_genomic.fna/checkm_result
[2024-01-24 14:50:05,588] [INFO] Task succeeded: CheckM
[2024-01-24 14:50:05,589] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:50:05,645] [INFO] ===== Completeness check finished =====
[2024-01-24 14:50:05,645] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:50:05,646] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004217545.1_ASM421754v1_genomic.fna/markers.fasta)
[2024-01-24 14:50:05,646] [INFO] Task started: Blastn
[2024-01-24 14:50:05,646] [INFO] Running command: blastn -query GCF_004217545.1_ASM421754v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg87d60313-6c27-46c6-9eb6-91ee7d96129e/dqc_reference/reference_markers_gtdb.fasta -out GCF_004217545.1_ASM421754v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:50:07,622] [INFO] Task succeeded: Blastn
[2024-01-24 14:50:07,626] [INFO] Selected 20 target genomes.
[2024-01-24 14:50:07,626] [INFO] Target genome list was writen to GCF_004217545.1_ASM421754v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:50:07,640] [INFO] Task started: fastANI
[2024-01-24 14:50:07,640] [INFO] Running command: fastANI --query /var/lib/cwl/stg1603dca5-2799-4dbc-a389-1f8898608e51/GCF_004217545.1_ASM421754v1_genomic.fna.gz --refList GCF_004217545.1_ASM421754v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004217545.1_ASM421754v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:50:49,536] [INFO] Task succeeded: fastANI
[2024-01-24 14:50:49,553] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:50:49,553] [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_004217545.1	s__Actinoplanes cinnamomeus	100.0	2536	2538	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016862275.1	s__Actinoplanes nipponensis	81.8055	1389	2538	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648355.1	s__Actinoplanes azureus	81.7445	1328	2538	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205335.1	s__Actinoplanes digitatis	81.7394	1421	2538	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016464385.1	s__Actinoplanes sp016464385	81.4766	1302	2538	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018332655.1	s__Actinoplanes auranticolor	81.3712	1320	2538	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751945.1	s__Actinoplanes caeruleus	81.3327	1335	2538	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.98	0.98	2	-
GCF_003002065.1	s__Actinoplanes ferrugineus_A	81.2857	1339	2538	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.31	99.31	0.94	0.94	2	-
GCF_000389965.1	s__Actinoplanes sp000389965	80.8625	1234	2538	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003711105.1	s__Actinoplanes teichomyceticus	80.8597	1252	2538	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	99.99	1.00	1.00	4	-
GCF_016862395.1	s__Actinoplanes siamensis	80.5467	1182	2538	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863475.1	s__Spirilliplanes yamanashiensis	80.532	1180	2538	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Spirilliplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000721705.1	s__Actinoplanes subtropicus	80.4594	1314	2538	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862115.1	s__Actinoplanes deccanensis	80.4114	1267	2538	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205225.1	s__Actinoplanes octamycinicus	80.4028	1365	2538	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015704865.1	s__Actinoplanes sp015704865	80.1772	1263	2538	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018829635.1	s__Actinoplanes bogorensis	80.1729	1214	2538	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002926165.1	s__Micromonospora chalcea	79.5795	1003	2538	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.52	95.31	0.89	0.84	18	-
GCF_018070045.1	s__Micromonospora sp018070045	79.2204	953	2538	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013364215.1	s__Micromonospora sp004307965	79.1149	909	2538	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.04	99.04	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:50:49,555] [INFO] GTDB search result was written to GCF_004217545.1_ASM421754v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:50:49,555] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:50:49,561] [INFO] DFAST_QC result json was written to GCF_004217545.1_ASM421754v1_genomic.fna/dqc_result.json
[2024-01-24 14:50:49,561] [INFO] DFAST_QC completed!
[2024-01-24 14:50:49,561] [INFO] Total running time: 0h3m54s