[2024-01-24 12:36:50,192] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:50,195] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:50,195] [INFO] DQC Reference Directory: /var/lib/cwl/stgff44bd2b-484c-4989-9d8a-87a8b5faef72/dqc_reference
[2024-01-24 12:36:52,570] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:52,571] [INFO] Task started: Prodigal
[2024-01-24 12:36:52,571] [INFO] Running command: gunzip -c /var/lib/cwl/stg0323e5f9-5141-4902-b38d-bb54a6e82d81/GCF_023218175.1_ASM2321817v1_genomic.fna.gz | prodigal -d GCF_023218175.1_ASM2321817v1_genomic.fna/cds.fna -a GCF_023218175.1_ASM2321817v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:11,574] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:11,575] [INFO] Task started: HMMsearch
[2024-01-24 12:37:11,575] [INFO] Running command: hmmsearch --tblout GCF_023218175.1_ASM2321817v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff44bd2b-484c-4989-9d8a-87a8b5faef72/dqc_reference/reference_markers.hmm GCF_023218175.1_ASM2321817v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:11,844] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:11,845] [INFO] Found 6/6 markers.
[2024-01-24 12:37:11,897] [INFO] Query marker FASTA was written to GCF_023218175.1_ASM2321817v1_genomic.fna/markers.fasta
[2024-01-24 12:37:11,897] [INFO] Task started: Blastn
[2024-01-24 12:37:11,897] [INFO] Running command: blastn -query GCF_023218175.1_ASM2321817v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff44bd2b-484c-4989-9d8a-87a8b5faef72/dqc_reference/reference_markers.fasta -out GCF_023218175.1_ASM2321817v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:13,156] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:13,160] [INFO] Selected 26 target genomes.
[2024-01-24 12:37:13,160] [INFO] Target genome list was writen to GCF_023218175.1_ASM2321817v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:13,196] [INFO] Task started: fastANI
[2024-01-24 12:37:13,197] [INFO] Running command: fastANI --query /var/lib/cwl/stg0323e5f9-5141-4902-b38d-bb54a6e82d81/GCF_023218175.1_ASM2321817v1_genomic.fna.gz --refList GCF_023218175.1_ASM2321817v1_genomic.fna/target_genomes.txt --output GCF_023218175.1_ASM2321817v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:57,996] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:57,997] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff44bd2b-484c-4989-9d8a-87a8b5faef72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:57,997] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff44bd2b-484c-4989-9d8a-87a8b5faef72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:58,015] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:58,016] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:58,016] [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 lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	100.0	2341	2344	95	conclusive
Streptomyces lavendofoliae	strain=JCM 4391	GCA_014649735.1	67314	67314	type	True	84.2107	1503	2344	95	below_threshold
Streptomyces purpureus	strain=JCM 3172	GCA_014648195.1	1951	1951	type	True	83.2164	1370	2344	95	below_threshold
Streptomyces cinereoruber	strain=JCM 4205	GCA_014649095.1	67260	67260	type	True	83.0879	1351	2344	95	below_threshold
Streptomyces cinereoruber	strain=JCM4205	GCA_019880525.1	67260	67260	type	True	83.081	1371	2344	95	below_threshold
Streptomyces roseolilacinus	strain=JCM 4335	GCA_014649335.1	66904	66904	type	True	83.08	1357	2344	95	below_threshold
Streptomyces cinereoruber	strain=ATCC 19740	GCA_009299385.1	67260	67260	type	True	83.0686	1397	2344	95	below_threshold
Streptomyces fradiae	strain=ATCC 10745	GCA_009834665.1	1906	1906	suspected-type	True	82.9954	1323	2344	95	below_threshold
Streptomyces kanasensis	strain=ZX01	GCA_001484625.1	936756	936756	type	True	82.9794	1326	2344	95	below_threshold
Streptomyces somaliensis	strain=DSM 40738	GCA_024349285.1	78355	78355	type	True	82.9634	1122	2344	95	below_threshold
Streptomyces fradiae	strain=ATCC 10745	GCA_008704425.1	1906	1906	suspected-type	True	82.8814	1353	2344	95	below_threshold
Streptomyces termitum	strain=JCM 4518	GCA_014650175.1	67368	67368	type	True	82.8753	1374	2344	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	82.8279	1139	2344	95	below_threshold
Streptomyces zhihengii	strain=YIM T102	GCA_016919245.1	1818004	1818004	type	True	82.5531	1493	2344	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	82.4579	1349	2344	95	below_threshold
Streptomyces genisteinicus	strain=CRPJ-33	GCA_014489615.1	2768068	2768068	type	True	82.4418	1417	2344	95	below_threshold
Streptomyces griseus	strain=DSM 40236	GCA_900105705.1	1911	1911	type	True	82.339	1434	2344	95	below_threshold
Streptomyces griseus	strain=NCTC13033	GCA_900460065.1	1911	1911	type	True	82.3246	1405	2344	95	below_threshold
Streptomyces anulatus	strain=JCM 4721	GCA_014650675.1	1892	1892	type	True	82.2104	1414	2344	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	82.0973	1307	2344	95	below_threshold
Streptomyces griseosporeus	strain=JCM 4766	GCA_014656055.1	1910	1910	type	True	81.7532	1364	2344	95	below_threshold
Streptomyces minutiscleroticus	strain=JCM 4790	GCA_014650875.1	68238	68238	type	True	81.7503	1365	2344	95	below_threshold
Streptomyces eurythermus	strain=JCM 4206	GCA_014649115.1	42237	42237	type	True	81.7202	1376	2344	95	below_threshold
Streptomyces corchorusii	strain=DSM 40340	GCA_001514055.1	1903	1903	type	True	81.7158	1367	2344	95	below_threshold
Streptomyces olivaceoviridis	strain=JCM 4499	GCA_014650115.1	1921	1921	type	True	81.5583	1364	2344	95	below_threshold
Streptomyces canarius	strain=JCM 4733	GCA_014650735.1	285453	285453	type	True	81.5172	1360	2344	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:58,018] [INFO] DFAST Taxonomy check result was written to GCF_023218175.1_ASM2321817v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:58,018] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:58,018] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:58,018] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff44bd2b-484c-4989-9d8a-87a8b5faef72/dqc_reference/checkm_data
[2024-01-24 12:37:58,019] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:58,083] [INFO] Task started: CheckM
[2024-01-24 12:37:58,084] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023218175.1_ASM2321817v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023218175.1_ASM2321817v1_genomic.fna/checkm_input GCF_023218175.1_ASM2321817v1_genomic.fna/checkm_result
[2024-01-24 12:39:27,777] [INFO] Task succeeded: CheckM
[2024-01-24 12:39:27,778] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:39:27,801] [INFO] ===== Completeness check finished =====
[2024-01-24 12:39:27,802] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:39:27,802] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023218175.1_ASM2321817v1_genomic.fna/markers.fasta)
[2024-01-24 12:39:27,802] [INFO] Task started: Blastn
[2024-01-24 12:39:27,802] [INFO] Running command: blastn -query GCF_023218175.1_ASM2321817v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff44bd2b-484c-4989-9d8a-87a8b5faef72/dqc_reference/reference_markers_gtdb.fasta -out GCF_023218175.1_ASM2321817v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:29,864] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:29,867] [INFO] Selected 21 target genomes.
[2024-01-24 12:39:29,867] [INFO] Target genome list was writen to GCF_023218175.1_ASM2321817v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:39:29,898] [INFO] Task started: fastANI
[2024-01-24 12:39:29,898] [INFO] Running command: fastANI --query /var/lib/cwl/stg0323e5f9-5141-4902-b38d-bb54a6e82d81/GCF_023218175.1_ASM2321817v1_genomic.fna.gz --refList GCF_023218175.1_ASM2321817v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023218175.1_ASM2321817v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:40:06,747] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:06,772] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:40:06,774] [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_002982015.1	s__Streptomyces sp002982015	89.4782	1302	2344	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004353505.1	s__Streptomyces sp004353505	84.3958	1476	2344	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.95	99.86	0.97	0.92	4	-
GCF_009739905.1	s__Streptomyces ficellus	84.2621	1538	2344	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649735.1	s__Streptomyces lavendofoliae	84.2561	1496	2344	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001646665.1	s__Streptomyces albulus_A	84.252	1530	2344	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905885.1	s__Streptomyces sp001905885	84.1388	1510	2344	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.05	96.05	0.87	0.87	2	-
GCF_000716335.1	s__Streptomyces sp000716335	83.6425	1449	2344	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648195.1	s__Streptomyces purpureus	83.2415	1364	2344	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.54	99.54	0.95	0.95	2	-
GCF_014649335.1	s__Streptomyces roseolilacinus	83.0596	1360	2344	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000716465.1	s__Streptomyces bikiniensis	83.038	1374	2344	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.67	95.67	0.86	0.82	10	-
GCF_001484625.1	s__Streptomyces kanasensis	82.9695	1328	2344	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000721275.1	s__Streptomyces sp000721275	82.8602	1389	2344	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005517195.1	s__Streptomyces exfoliatus_B	82.8534	1335	2344	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008271805.1	s__Streptomyces sp008271805	82.8268	1300	2344	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016919245.1	s__Streptomyces zhihengii	82.5388	1495	2344	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001865245.1	s__Streptomyces sp001865245	82.5056	1279	2344	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.88	98.02	0.87	0.86	3	-
GCF_014489615.1	s__Streptomyces sp014489615	82.4858	1410	2344	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900460065.1	s__Streptomyces griseus	82.2985	1412	2344	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.49	99.03	0.95	0.93	10	-
GCF_014650675.1	s__Streptomyces anulatus	82.1926	1419	2344	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.62	96.42	0.89	0.81	27	-
GCF_001905845.1	s__Streptomyces sp001905845	81.8511	1374	2344	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116325.1	s__Streptomyces sp900116325	81.7426	1256	2344	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.66	95.15	0.89	0.84	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:40:06,777] [INFO] GTDB search result was written to GCF_023218175.1_ASM2321817v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:40:06,778] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:40:06,792] [INFO] DFAST_QC result json was written to GCF_023218175.1_ASM2321817v1_genomic.fna/dqc_result.json
[2024-01-24 12:40:06,792] [INFO] DFAST_QC completed!
[2024-01-24 12:40:06,792] [INFO] Total running time: 0h3m17s