[2024-01-24 13:27:46,489] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:46,491] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:46,491] [INFO] DQC Reference Directory: /var/lib/cwl/stg0e1a7eda-176c-427d-95a5-11003e468306/dqc_reference
[2024-01-24 13:27:47,943] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:47,944] [INFO] Task started: Prodigal
[2024-01-24 13:27:47,944] [INFO] Running command: gunzip -c /var/lib/cwl/stg78358ca5-c82d-43b6-a6ac-c5c67c6ebce9/GCF_014656295.1_ASM1465629v1_genomic.fna.gz | prodigal -d GCF_014656295.1_ASM1465629v1_genomic.fna/cds.fna -a GCF_014656295.1_ASM1465629v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:13,197] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:13,197] [INFO] Task started: HMMsearch
[2024-01-24 13:28:13,198] [INFO] Running command: hmmsearch --tblout GCF_014656295.1_ASM1465629v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0e1a7eda-176c-427d-95a5-11003e468306/dqc_reference/reference_markers.hmm GCF_014656295.1_ASM1465629v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:13,653] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:13,654] [INFO] Found 6/6 markers.
[2024-01-24 13:28:13,715] [INFO] Query marker FASTA was written to GCF_014656295.1_ASM1465629v1_genomic.fna/markers.fasta
[2024-01-24 13:28:13,716] [INFO] Task started: Blastn
[2024-01-24 13:28:13,716] [INFO] Running command: blastn -query GCF_014656295.1_ASM1465629v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e1a7eda-176c-427d-95a5-11003e468306/dqc_reference/reference_markers.fasta -out GCF_014656295.1_ASM1465629v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:15,000] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:15,003] [INFO] Selected 29 target genomes.
[2024-01-24 13:28:15,004] [INFO] Target genome list was writen to GCF_014656295.1_ASM1465629v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:15,018] [INFO] Task started: fastANI
[2024-01-24 13:28:15,018] [INFO] Running command: fastANI --query /var/lib/cwl/stg78358ca5-c82d-43b6-a6ac-c5c67c6ebce9/GCF_014656295.1_ASM1465629v1_genomic.fna.gz --refList GCF_014656295.1_ASM1465629v1_genomic.fna/target_genomes.txt --output GCF_014656295.1_ASM1465629v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:29:12,413] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:12,414] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0e1a7eda-176c-427d-95a5-11003e468306/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:29:12,414] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0e1a7eda-176c-427d-95a5-11003e468306/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:29:12,435] [INFO] Found 29 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:29:12,436] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:29:12,436] [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
Streptomyces sulfonofaciens	strain=JCM 5069	GCA_014656295.1	68272	68272	type	True	100.0	2831	2835	95	conclusive
Streptomyces minutiscleroticus	strain=JCM 4790	GCA_014650875.1	68238	68238	type	True	81.6613	1452	2835	95	below_threshold
Streptomyces fumigatiscleroticus	strain=JCM 3101	GCA_014647975.1	66371	66371	type	True	81.4061	1462	2835	95	below_threshold
Streptomyces griseostramineus	strain=CECT 3273	GCA_014203535.1	66898	66898	suspected-type	True	81.3377	1383	2835	95	below_threshold
Streptomyces griseostramineus	strain=JCM 4385	GCA_014649635.1	66898	66898	suspected-type	True	81.3092	1369	2835	95	below_threshold
Streptomyces himalayensis subsp. aureolus	strain=PSKA54	GCA_013912435.1	2758039	2820085	type	True	81.2874	1342	2835	95	below_threshold
Streptomyces griseosporeus	strain=JCM 4766	GCA_014656055.1	1910	1910	type	True	81.272	1424	2835	95	below_threshold
Streptomyces viridiviolaceus	strain=JCM 4855	GCA_014650995.1	68282	68282	type	True	81.2341	1409	2835	95	below_threshold
Streptomyces silaceus	strain=NRRL B-24166	GCA_001419745.1	545123	545123	type	True	81.2315	1238	2835	95	below_threshold
Streptomyces avermitilis	strain=DSM 46492	GCA_001514135.1	33903	33903	type	True	81.1451	1392	2835	95	below_threshold
Streptomyces corchorusii	strain=DSM 40340	GCA_001514055.1	1903	1903	type	True	81.1292	1502	2835	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	81.0941	1479	2835	95	below_threshold
Streptomyces spectabilis	strain=KCTC9218	GCA_022698305.1	68270	68270	type	True	81.0718	1375	2835	95	below_threshold
Streptomyces avermitilis	strain=NBRC 14893	GCA_005405965.1	33903	33903	type	True	81.0395	1454	2835	95	below_threshold
Streptomyces musisoli	strain=CH5-8	GCA_016741855.1	2802280	2802280	type	True	80.9811	1415	2835	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	80.966	1419	2835	95	below_threshold
Streptomyces bluensis	strain=JCM 4729	GCA_014650715.1	33897	33897	type	True	80.9386	1339	2835	95	below_threshold
Streptomyces fodineus	strain=TW1S1	GCA_001735805.1	1904616	1904616	type	True	80.9138	1400	2835	95	below_threshold
Streptomyces durmitorensis	strain=MS405	GCA_023498005.1	319947	319947	type	True	80.8567	1365	2835	95	below_threshold
Streptomyces fradiae	strain=NRRL B-1195	GCA_002154445.1	1906	1906	suspected-type	True	80.8291	770	2835	95	below_threshold
Streptomyces apocyni	strain=TRM 66233	GCA_009739465.1	2654677	2654677	type	True	80.7523	1113	2835	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	80.7042	1270	2835	95	below_threshold
Streptomyces fradiae	strain=ATCC 10745	GCA_009834665.1	1906	1906	suspected-type	True	80.2851	1172	2835	95	below_threshold
Streptomyces hydrogenans	strain=NBRC 13475	GCA_020521255.1	1873719	1873719	type	True	80.2719	1293	2835	95	below_threshold
Streptomyces camponoticapitis	strain=CGMCC 4.7275	GCA_014646115.1	1616125	1616125	type	True	80.1528	1227	2835	95	below_threshold
Streptomyces hydrogenans	strain=JCM 4771	GCA_014656075.1	1873719	1873719	type	True	80.1438	1280	2835	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	79.9645	1274	2835	95	below_threshold
Streptomyces varsoviensis	strain=NRRL B-3589	GCA_000719255.1	67373	67373	type	True	79.9398	1230	2835	95	below_threshold
Streptomyces varsoviensis	strain=NRRL ISP-5346	GCA_000718635.1	67373	67373	type	True	79.91	1234	2835	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:29:12,438] [INFO] DFAST Taxonomy check result was written to GCF_014656295.1_ASM1465629v1_genomic.fna/tc_result.tsv
[2024-01-24 13:29:12,439] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:29:12,439] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:29:12,439] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0e1a7eda-176c-427d-95a5-11003e468306/dqc_reference/checkm_data
[2024-01-24 13:29:12,441] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:29:12,519] [INFO] Task started: CheckM
[2024-01-24 13:29:12,519] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014656295.1_ASM1465629v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014656295.1_ASM1465629v1_genomic.fna/checkm_input GCF_014656295.1_ASM1465629v1_genomic.fna/checkm_result
[2024-01-24 13:31:22,733] [INFO] Task succeeded: CheckM
[2024-01-24 13:31:22,734] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:31:22,764] [INFO] ===== Completeness check finished =====
[2024-01-24 13:31:22,765] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:31:22,765] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014656295.1_ASM1465629v1_genomic.fna/markers.fasta)
[2024-01-24 13:31:22,765] [INFO] Task started: Blastn
[2024-01-24 13:31:22,766] [INFO] Running command: blastn -query GCF_014656295.1_ASM1465629v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e1a7eda-176c-427d-95a5-11003e468306/dqc_reference/reference_markers_gtdb.fasta -out GCF_014656295.1_ASM1465629v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:24,725] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:24,731] [INFO] Selected 22 target genomes.
[2024-01-24 13:31:24,731] [INFO] Target genome list was writen to GCF_014656295.1_ASM1465629v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:31:24,767] [INFO] Task started: fastANI
[2024-01-24 13:31:24,768] [INFO] Running command: fastANI --query /var/lib/cwl/stg78358ca5-c82d-43b6-a6ac-c5c67c6ebce9/GCF_014656295.1_ASM1465629v1_genomic.fna.gz --refList GCF_014656295.1_ASM1465629v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014656295.1_ASM1465629v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:08,504] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:08,524] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:08,524] [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_014656295.1	s__Streptomyces sulfonofaciens	100.0	2831	2835	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018327685.1	s__Streptomyces sp018327685	86.436	2059	2835	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650875.1	s__Streptomyces minutiscleroticus	81.6791	1449	2835	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.56	98.56	0.90	0.90	2	-
GCF_002920535.1	s__Streptomyces sp002920535	81.3589	1364	2835	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647975.1	s__Streptomyces fumigatiscleroticus	81.3571	1473	2835	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003664315.1	s__Streptomyces sp003664315	81.3517	1422	2835	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007176755.1	s__Streptomyces sp007176755	81.3446	1395	2835	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203535.1	s__Streptomyces griseostramineus	81.3182	1388	2835	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.88	99.76	0.99	0.98	3	-
GCF_008369065.1	s__Streptomyces sp008369065	81.312	1391	2835	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001419745.1	s__Streptomyces silaceus	81.2453	1236	2835	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.58	99.58	0.96	0.96	2	-
GCF_001509795.1	s__Streptomyces sp001509795	81.2314	1354	2835	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.33	98.67	0.96	0.93	3	-
GCF_001293595.1	s__Streptomyces sp001293595	81.2303	1264	2835	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.56	99.56	0.94	0.94	2	-
GCF_014650995.1	s__Streptomyces viridiviolaceus	81.216	1413	2835	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001417775.1	s__Streptomyces sp001417775	81.1877	1349	2835	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650715.1	s__Streptomyces bluensis	80.9775	1332	2835	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.08	99.08	0.92	0.92	2	-
GCF_002803065.1	s__Streptomyces sp002803065	80.97	1407	2835	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016741855.1	s__Streptomyces musisoli	80.9627	1421	2835	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013364195.1	s__Streptomyces sp013364195	80.8715	1212	2835	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009916105.1	s__Streptomyces sp009916105	80.5274	1126	2835	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426405.1	s__Streptomyces sp001426405	80.3671	1217	2835	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014646115.1	s__Streptomyces camponoticapitis	80.1684	1223	2835	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656075.1	s__Streptomyces hydrogenans	80.1469	1278	2835	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.17	97.53	0.88	0.87	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:08,526] [INFO] GTDB search result was written to GCF_014656295.1_ASM1465629v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:08,527] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:08,534] [INFO] DFAST_QC result json was written to GCF_014656295.1_ASM1465629v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:08,534] [INFO] DFAST_QC completed!
[2024-01-24 13:32:08,534] [INFO] Total running time: 0h4m22s