[2024-01-24 13:19:11,374] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:11,377] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:11,377] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc74eb7c-1863-4ee1-bc25-442f8bb34f32/dqc_reference
[2024-01-24 13:19:12,725] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:12,725] [INFO] Task started: Prodigal
[2024-01-24 13:19:12,726] [INFO] Running command: gunzip -c /var/lib/cwl/stg06c333ec-0f51-4e36-b4ab-f2b83b7be681/GCF_014649915.1_ASM1464991v1_genomic.fna.gz | prodigal -d GCF_014649915.1_ASM1464991v1_genomic.fna/cds.fna -a GCF_014649915.1_ASM1464991v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:32,843] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:32,843] [INFO] Task started: HMMsearch
[2024-01-24 13:19:32,843] [INFO] Running command: hmmsearch --tblout GCF_014649915.1_ASM1464991v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc74eb7c-1863-4ee1-bc25-442f8bb34f32/dqc_reference/reference_markers.hmm GCF_014649915.1_ASM1464991v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:33,321] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:33,322] [INFO] Found 6/6 markers.
[2024-01-24 13:19:33,395] [INFO] Query marker FASTA was written to GCF_014649915.1_ASM1464991v1_genomic.fna/markers.fasta
[2024-01-24 13:19:33,395] [INFO] Task started: Blastn
[2024-01-24 13:19:33,396] [INFO] Running command: blastn -query GCF_014649915.1_ASM1464991v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc74eb7c-1863-4ee1-bc25-442f8bb34f32/dqc_reference/reference_markers.fasta -out GCF_014649915.1_ASM1464991v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:34,844] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:34,848] [INFO] Selected 18 target genomes.
[2024-01-24 13:19:34,848] [INFO] Target genome list was writen to GCF_014649915.1_ASM1464991v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:34,857] [INFO] Task started: fastANI
[2024-01-24 13:19:34,858] [INFO] Running command: fastANI --query /var/lib/cwl/stg06c333ec-0f51-4e36-b4ab-f2b83b7be681/GCF_014649915.1_ASM1464991v1_genomic.fna.gz --refList GCF_014649915.1_ASM1464991v1_genomic.fna/target_genomes.txt --output GCF_014649915.1_ASM1464991v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:20:12,270] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:12,271] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc74eb7c-1863-4ee1-bc25-442f8bb34f32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:20:12,271] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc74eb7c-1863-4ee1-bc25-442f8bb34f32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:20:12,285] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:20:12,286] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:20:12,286] [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 toxytricini	strain=JCM 4421	GCA_014649915.1	67369	67369	type	True	100.0	2369	2373	95	conclusive
Streptomyces vinaceus	strain=ATCC 27476	GCA_008704935.1	1960	1960	type	True	86.3397	1672	2373	95	below_threshold
Streptomyces vinaceus	strain=JCM 4849	GCA_014656155.1	1960	1960	type	True	86.2417	1691	2373	95	below_threshold
Streptomyces katrae	strain=NRRL ISP-5550	GCA_000966975.1	68223	68223	type	True	85.8012	1237	2373	95	below_threshold
Streptomyces amritsarensis	strain=MTCC 11845	GCA_001953875.1	681158	681158	type	True	85.5433	1618	2373	95	below_threshold
Streptomyces yangpuensis	strain=fd2-tb	GCA_001005295.1	1648182	1648182	type	True	85.5017	1655	2373	95	below_threshold
Streptomyces subrutilus	strain=ATCC 27467	GCA_008704535.1	36818	36818	type	True	85.3776	1566	2373	95	below_threshold
Streptomyces subrutilus	strain=JCM 4834	GCA_014650935.1	36818	36818	type	True	85.356	1548	2373	95	below_threshold
Streptomyces virginiae	strain=NRRL ISP-5094	GCA_000720455.1	1961	1961	suspected-type	True	85.2805	1700	2373	95	below_threshold
Streptomyces cirratus	strain=JCM 4738	GCA_014650775.1	68187	68187	type	True	85.2286	1519	2373	95	below_threshold
Streptomyces bambusae	strain=T110	GCA_020532645.1	1550616	1550616	type	True	84.1661	1489	2373	95	below_threshold
Streptomyces roseolus	strain=JCM 4411	GCA_014649855.1	67358	67358	type	True	82.4942	1356	2373	95	below_threshold
Streptomyces rhizosphaericola	strain=1AS2c	GCA_004794175.1	2564098	2564098	type	True	81.7521	1107	2373	95	below_threshold
Streptomyces genisteinicus	strain=CRPJ-33	GCA_014489615.1	2768068	2768068	type	True	81.5431	1359	2373	95	below_threshold
Streptomyces fumanus	strain=JCM 4477	GCA_014655295.1	67302	67302	type	True	81.3133	1286	2373	95	below_threshold
Streptomyces glomeratus	strain=DSM 41457	GCA_021462825.1	284452	284452	type	True	81.0249	1152	2373	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	80.8477	1123	2373	95	below_threshold
Streptomyces roseirectus	strain=CRXT-G-22	GCA_014489635.1	2768066	2768066	type	True	80.5221	1244	2373	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:20:12,288] [INFO] DFAST Taxonomy check result was written to GCF_014649915.1_ASM1464991v1_genomic.fna/tc_result.tsv
[2024-01-24 13:20:12,288] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:20:12,288] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:20:12,288] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc74eb7c-1863-4ee1-bc25-442f8bb34f32/dqc_reference/checkm_data
[2024-01-24 13:20:12,289] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:20:12,358] [INFO] Task started: CheckM
[2024-01-24 13:20:12,358] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014649915.1_ASM1464991v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014649915.1_ASM1464991v1_genomic.fna/checkm_input GCF_014649915.1_ASM1464991v1_genomic.fna/checkm_result
[2024-01-24 13:21:42,132] [INFO] Task succeeded: CheckM
[2024-01-24 13:21:42,134] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:21:42,162] [INFO] ===== Completeness check finished =====
[2024-01-24 13:21:42,162] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:21:42,163] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014649915.1_ASM1464991v1_genomic.fna/markers.fasta)
[2024-01-24 13:21:42,163] [INFO] Task started: Blastn
[2024-01-24 13:21:42,163] [INFO] Running command: blastn -query GCF_014649915.1_ASM1464991v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc74eb7c-1863-4ee1-bc25-442f8bb34f32/dqc_reference/reference_markers_gtdb.fasta -out GCF_014649915.1_ASM1464991v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:44,458] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:44,463] [INFO] Selected 14 target genomes.
[2024-01-24 13:21:44,463] [INFO] Target genome list was writen to GCF_014649915.1_ASM1464991v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:21:44,498] [INFO] Task started: fastANI
[2024-01-24 13:21:44,498] [INFO] Running command: fastANI --query /var/lib/cwl/stg06c333ec-0f51-4e36-b4ab-f2b83b7be681/GCF_014649915.1_ASM1464991v1_genomic.fna.gz --refList GCF_014649915.1_ASM1464991v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014649915.1_ASM1464991v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:22:16,498] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:16,511] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:22:16,512] [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_014649915.1	s__Streptomyces toxytricini	100.0	2369	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.98	99.98	0.99	0.99	2	conclusive
GCF_003325375.1	s__Streptomyces globosus	94.9713	2068	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.29	95.29	0.89	0.89	2	-
GCF_013401435.1	s__Streptomyces sp013401435	87.2306	1588	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000717915.1	s__Streptomyces sp000717915	86.5845	1638	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.92	95.47	0.90	0.89	4	-
GCF_000717655.1	s__Streptomyces katrae_B	86.1947	1728	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.60	96.50	0.86	0.86	4	-
GCA_001298555.1	s__Streptomyces sp001298555	86.1821	1687	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720145.1	s__Streptomyces sp000720145	86.1735	1692	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002803845.1	s__Streptomyces lavendulae_C	85.3455	1627	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.97	0.99	0.99	3	-
GCF_002028425.1	s__Streptomyces katrae_A	85.3361	1646	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.60	99.44	0.97	0.94	4	-
GCF_018614195.1	s__Streptomyces sp018614195	85.1483	1560	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003949795.1	s__Streptomyces sp003949795	84.885	1423	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003287935.1	s__Streptomyces sp003287935	84.7967	1591	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.55	99.55	0.95	0.95	2	-
GCF_000719335.1	s__Streptomyces sp000719335	83.663	1551	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649855.1	s__Streptomyces roseolus	82.536	1349	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:22:16,514] [INFO] GTDB search result was written to GCF_014649915.1_ASM1464991v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:22:16,514] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:22:16,518] [INFO] DFAST_QC result json was written to GCF_014649915.1_ASM1464991v1_genomic.fna/dqc_result.json
[2024-01-24 13:22:16,518] [INFO] DFAST_QC completed!
[2024-01-24 13:22:16,518] [INFO] Total running time: 0h3m5s