[2024-01-24 13:49:40,027] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:40,028] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:40,029] [INFO] DQC Reference Directory: /var/lib/cwl/stgc02a595e-e4b9-434a-bb9d-b5a9a9804d9c/dqc_reference
[2024-01-24 13:49:41,114] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:41,115] [INFO] Task started: Prodigal
[2024-01-24 13:49:41,115] [INFO] Running command: gunzip -c /var/lib/cwl/stg17ca36fb-1112-4321-99d5-1243adcdd8d6/GCF_017896165.1_ASM1789616v1_genomic.fna.gz | prodigal -d GCF_017896165.1_ASM1789616v1_genomic.fna/cds.fna -a GCF_017896165.1_ASM1789616v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:00,425] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:00,426] [INFO] Task started: HMMsearch
[2024-01-24 13:50:00,426] [INFO] Running command: hmmsearch --tblout GCF_017896165.1_ASM1789616v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc02a595e-e4b9-434a-bb9d-b5a9a9804d9c/dqc_reference/reference_markers.hmm GCF_017896165.1_ASM1789616v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:00,711] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:00,712] [INFO] Found 6/6 markers.
[2024-01-24 13:50:00,765] [INFO] Query marker FASTA was written to GCF_017896165.1_ASM1789616v1_genomic.fna/markers.fasta
[2024-01-24 13:50:00,765] [INFO] Task started: Blastn
[2024-01-24 13:50:00,765] [INFO] Running command: blastn -query GCF_017896165.1_ASM1789616v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc02a595e-e4b9-434a-bb9d-b5a9a9804d9c/dqc_reference/reference_markers.fasta -out GCF_017896165.1_ASM1789616v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:01,967] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:01,970] [INFO] Selected 20 target genomes.
[2024-01-24 13:50:01,970] [INFO] Target genome list was writen to GCF_017896165.1_ASM1789616v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:01,975] [INFO] Task started: fastANI
[2024-01-24 13:50:01,975] [INFO] Running command: fastANI --query /var/lib/cwl/stg17ca36fb-1112-4321-99d5-1243adcdd8d6/GCF_017896165.1_ASM1789616v1_genomic.fna.gz --refList GCF_017896165.1_ASM1789616v1_genomic.fna/target_genomes.txt --output GCF_017896165.1_ASM1789616v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:39,881] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:39,881] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc02a595e-e4b9-434a-bb9d-b5a9a9804d9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:39,882] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc02a595e-e4b9-434a-bb9d-b5a9a9804d9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:39,893] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:39,893] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:39,894] [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
Microbispora oryzae	strain=RL4-1S	GCA_017896165.1	2806554	2806554	type	True	100.0	2444	2449	95	conclusive
Microbispora corallina	strain=NBRC 16416	GCA_016863035.1	83302	83302	type	True	84.087	1647	2449	95	below_threshold
Microbispora catharanthi	strain=CR1-09	GCA_006334915.2	1712871	1712871	type	True	83.4326	1553	2449	95	below_threshold
Microbispora sitophila	strain=NEAU-D428	GCA_014892245.1	2771537	2771537	type	True	83.2602	1541	2449	95	below_threshold
Microbispora siamensis	strain=NBRC 104113	GCA_016863095.1	564413	564413	type	True	83.2413	1490	2449	95	below_threshold
Microbispora hainanensis	strain=DSM 45428	GCA_006874475.1	568844	568844	type	True	83.1978	1514	2449	95	below_threshold
Microbispora amethystogenes	strain=NBRC 101907	GCA_016863015.1	1427754	1427754	type	True	83.1769	1485	2449	95	below_threshold
Microbispora cellulosiformans	strain=Gxj-6	GCA_008728085.1	2614688	2614688	type	True	83.151	1514	2449	95	below_threshold
Microbispora fusca	strain=NEAU-HEGS1-5	GCA_005864065.1	2576905	2576905	type	True	83.1436	1464	2449	95	below_threshold
Sphaerimonospora thailandensis	strain=NBRC 107569	GCA_016863115.1	795644	795644	type	True	81.7262	1014	2449	95	below_threshold
Planotetraspora kaengkrachanensis	strain=NBRC 104272	GCA_016862895.1	575193	575193	type	True	81.4482	1296	2449	95	below_threshold
Planotetraspora thailandica	strain=NBRC 104271	GCA_016863335.1	487172	487172	type	True	81.4013	1263	2449	95	below_threshold
Microtetraspora malaysiensis	strain=NBRC 100735	GCA_001528665.1	161358	161358	type	True	80.9394	1184	2449	95	below_threshold
Sphaerisporangium melleum	strain=JCM 13064	GCA_014646695.1	321316	321316	type	True	80.1645	1243	2449	95	below_threshold
Sphaerisporangium corydalis	strain=NEAU-YHS15	GCA_025506355.1	1441875	1441875	type	True	79.7878	1153	2449	95	below_threshold
Planobispora siamensis	strain=NBRC 107568	GCA_016863175.1	936338	936338	type	True	79.6462	1168	2449	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	79.6246	1199	2449	95	below_threshold
Streptosporangium canum	strain=CGMCC 4.2126	GCA_900113865.1	324952	324952	type	True	79.5896	1107	2449	95	below_threshold
Nonomuraea maritima	strain=CGMCC 4.5681	GCA_900100395.1	683260	683260	type	True	79.3763	1053	2449	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	78.701	1094	2449	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:39,895] [INFO] DFAST Taxonomy check result was written to GCF_017896165.1_ASM1789616v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:39,895] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:39,895] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:39,896] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc02a595e-e4b9-434a-bb9d-b5a9a9804d9c/dqc_reference/checkm_data
[2024-01-24 13:50:39,896] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:39,961] [INFO] Task started: CheckM
[2024-01-24 13:50:39,961] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017896165.1_ASM1789616v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017896165.1_ASM1789616v1_genomic.fna/checkm_input GCF_017896165.1_ASM1789616v1_genomic.fna/checkm_result
[2024-01-24 13:51:44,433] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:44,433] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.31%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:44,452] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:44,452] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:44,452] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017896165.1_ASM1789616v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:44,452] [INFO] Task started: Blastn
[2024-01-24 13:51:44,452] [INFO] Running command: blastn -query GCF_017896165.1_ASM1789616v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc02a595e-e4b9-434a-bb9d-b5a9a9804d9c/dqc_reference/reference_markers_gtdb.fasta -out GCF_017896165.1_ASM1789616v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:46,412] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:46,415] [INFO] Selected 18 target genomes.
[2024-01-24 13:51:46,415] [INFO] Target genome list was writen to GCF_017896165.1_ASM1789616v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:46,466] [INFO] Task started: fastANI
[2024-01-24 13:51:46,466] [INFO] Running command: fastANI --query /var/lib/cwl/stg17ca36fb-1112-4321-99d5-1243adcdd8d6/GCF_017896165.1_ASM1789616v1_genomic.fna.gz --refList GCF_017896165.1_ASM1789616v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017896165.1_ASM1789616v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:52:19,409] [INFO] Task succeeded: fastANI
[2024-01-24 13:52:19,420] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:52:19,420] [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_017896165.1	s__Microbispora sp017896165	100.0	2444	2449	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016863035.1	s__Microbispora corallina	84.116	1642	2449	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	97.01	97.01	0.91	0.91	2	-
GCF_006334915.2	s__Microbispora catharanthi	83.4692	1546	2449	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	96.79	95.45	0.89	0.84	4	-
GCF_006874465.1	s__Microbispora bryophytorum	83.3004	1499	2449	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	99.22	97.66	0.97	0.91	4	-
GCF_016863095.1	s__Microbispora siamensis	83.2268	1494	2449	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	96.99	95.83	0.88	0.87	3	-
GCF_016863015.1	s__Microbispora amethystogenes	83.2055	1479	2449	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	97.43	97.43	0.91	0.91	2	-
GCF_006874475.1	s__Microbispora hainanensis	83.2024	1515	2449	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	95.41	95.40	0.85	0.85	4	-
GCF_014161445.1	s__Microbispora sp014161445	83.0848	1507	2449	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	98.71	98.71	0.93	0.93	2	-
GCF_014647835.1	s__Microbispora aerata	82.8276	1315	2449	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_012999535.1	s__Microbispora sp012999535	82.8008	1395	2449	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862895.1	s__Planotetraspora kaengkrachanensis	81.4424	1297	2449	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planotetraspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863335.1	s__Planotetraspora thailandica	81.418	1260	2449	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planotetraspora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001570385.1	s__Microtetraspora glauca	81.0559	1189	2449	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microtetraspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001528665.1	s__Microtetraspora malaysiensis	80.9206	1188	2449	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microtetraspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646695.1	s__Sphaerisporangium melleum	80.1596	1243	2449	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	99.98	99.98	0.99	0.99	2	-
GCF_016863175.1	s__Planobispora siamensis	79.6396	1170	2449	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.117	N/A	N/A	N/A	N/A	1	-
GCF_900113865.1	s__Streptosporangium canum	79.6196	1102	2449	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.8736	96.48	96.48	0.86	0.86	2	-
GCF_900100395.1	s__Nonomuraea maritima	79.341	1061	2449	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:52:19,422] [INFO] GTDB search result was written to GCF_017896165.1_ASM1789616v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:52:19,422] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:52:19,425] [INFO] DFAST_QC result json was written to GCF_017896165.1_ASM1789616v1_genomic.fna/dqc_result.json
[2024-01-24 13:52:19,425] [INFO] DFAST_QC completed!
[2024-01-24 13:52:19,426] [INFO] Total running time: 0h2m39s