[2024-01-24 13:41:40,204] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:40,206] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:40,206] [INFO] DQC Reference Directory: /var/lib/cwl/stg541c1a73-e8d6-4595-a52c-a5ad288eb80d/dqc_reference
[2024-01-24 13:41:41,410] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:41,411] [INFO] Task started: Prodigal
[2024-01-24 13:41:41,411] [INFO] Running command: gunzip -c /var/lib/cwl/stgd490d658-c3e9-4cf1-a18d-55d6161073d8/GCF_005795905.1_ASM579590v1_genomic.fna.gz | prodigal -d GCF_005795905.1_ASM579590v1_genomic.fna/cds.fna -a GCF_005795905.1_ASM579590v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:42:07,026] [INFO] Task succeeded: Prodigal
[2024-01-24 13:42:07,026] [INFO] Task started: HMMsearch
[2024-01-24 13:42:07,026] [INFO] Running command: hmmsearch --tblout GCF_005795905.1_ASM579590v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg541c1a73-e8d6-4595-a52c-a5ad288eb80d/dqc_reference/reference_markers.hmm GCF_005795905.1_ASM579590v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:42:07,389] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:42:07,390] [INFO] Found 6/6 markers.
[2024-01-24 13:42:07,457] [INFO] Query marker FASTA was written to GCF_005795905.1_ASM579590v1_genomic.fna/markers.fasta
[2024-01-24 13:42:07,458] [INFO] Task started: Blastn
[2024-01-24 13:42:07,458] [INFO] Running command: blastn -query GCF_005795905.1_ASM579590v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg541c1a73-e8d6-4595-a52c-a5ad288eb80d/dqc_reference/reference_markers.fasta -out GCF_005795905.1_ASM579590v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:08,740] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:08,744] [INFO] Selected 16 target genomes.
[2024-01-24 13:42:08,744] [INFO] Target genome list was writen to GCF_005795905.1_ASM579590v1_genomic.fna/target_genomes.txt
[2024-01-24 13:42:08,797] [INFO] Task started: fastANI
[2024-01-24 13:42:08,797] [INFO] Running command: fastANI --query /var/lib/cwl/stgd490d658-c3e9-4cf1-a18d-55d6161073d8/GCF_005795905.1_ASM579590v1_genomic.fna.gz --refList GCF_005795905.1_ASM579590v1_genomic.fna/target_genomes.txt --output GCF_005795905.1_ASM579590v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:42:38,061] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:38,061] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg541c1a73-e8d6-4595-a52c-a5ad288eb80d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:42:38,062] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg541c1a73-e8d6-4595-a52c-a5ad288eb80d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:42:38,078] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:42:38,079] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:42:38,079] [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 marianii	strain=ICN19	GCA_005795905.1	1817406	1817406	type	True	100.0	2998	2999	95	conclusive
Streptomyces wuyuanensis	strain=CGMCC 4.7042	GCA_900103455.1	1196353	1196353	type	True	91.1562	1958	2999	95	below_threshold
Streptomyces tirandamycinicus	strain=HNM0039	GCA_003097515.1	2174846	2174846	type	True	90.1008	1860	2999	95	below_threshold
Streptomyces spongiicola	strain=HNM0071	GCA_003122365.1	1690221	1690221	type	True	89.0391	1781	2999	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	84.9694	1644	2999	95	below_threshold
Streptomyces fradiae	strain=NRRL B-1195	GCA_002154445.1	1906	1906	suspected-type	True	82.5187	840	2999	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	82.3619	1108	2999	95	below_threshold
Streptomyces genisteinicus	strain=CRPJ-33	GCA_014489615.1	2768068	2768068	type	True	82.3594	1375	2999	95	below_threshold
Streptomyces fradiae	strain=DSM 40063	GCA_002119225.1	1906	1906	suspected-type	True	82.1934	1208	2999	95	below_threshold
Streptomyces fradiae	strain=ATCC 10745	GCA_008704425.1	1906	1906	suspected-type	True	82.1713	1315	2999	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	82.0947	1314	2999	95	below_threshold
Streptomyces fradiae	strain=ATCC 10745	GCA_009834665.1	1906	1906	suspected-type	True	82.0832	1290	2999	95	below_threshold
Streptomyces anulatus	strain=JCM 4721	GCA_014650675.1	1892	1892	type	True	81.7229	1375	2999	95	below_threshold
Streptomyces gossypiisoli	strain=TRM 44567	GCA_013433285.1	2748864	2748864	type	True	81.1757	1391	2999	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	81.0706	1336	2999	95	below_threshold
Allostreptomyces psammosilenae	strain=DSM 42178	GCA_013407765.1	1892865	1892865	type	True	78.2951	834	2999	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:42:38,081] [INFO] DFAST Taxonomy check result was written to GCF_005795905.1_ASM579590v1_genomic.fna/tc_result.tsv
[2024-01-24 13:42:38,081] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:42:38,081] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:42:38,081] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg541c1a73-e8d6-4595-a52c-a5ad288eb80d/dqc_reference/checkm_data
[2024-01-24 13:42:38,082] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:42:38,164] [INFO] Task started: CheckM
[2024-01-24 13:42:38,164] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005795905.1_ASM579590v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005795905.1_ASM579590v1_genomic.fna/checkm_input GCF_005795905.1_ASM579590v1_genomic.fna/checkm_result
[2024-01-24 13:44:55,525] [INFO] Task succeeded: CheckM
[2024-01-24 13:44:55,526] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:44:55,553] [INFO] ===== Completeness check finished =====
[2024-01-24 13:44:55,553] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:44:55,554] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005795905.1_ASM579590v1_genomic.fna/markers.fasta)
[2024-01-24 13:44:55,554] [INFO] Task started: Blastn
[2024-01-24 13:44:55,554] [INFO] Running command: blastn -query GCF_005795905.1_ASM579590v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg541c1a73-e8d6-4595-a52c-a5ad288eb80d/dqc_reference/reference_markers_gtdb.fasta -out GCF_005795905.1_ASM579590v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:44:57,641] [INFO] Task succeeded: Blastn
[2024-01-24 13:44:57,646] [INFO] Selected 9 target genomes.
[2024-01-24 13:44:57,646] [INFO] Target genome list was writen to GCF_005795905.1_ASM579590v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:44:57,666] [INFO] Task started: fastANI
[2024-01-24 13:44:57,666] [INFO] Running command: fastANI --query /var/lib/cwl/stgd490d658-c3e9-4cf1-a18d-55d6161073d8/GCF_005795905.1_ASM579590v1_genomic.fna.gz --refList GCF_005795905.1_ASM579590v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005795905.1_ASM579590v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:45:17,085] [INFO] Task succeeded: fastANI
[2024-01-24 13:45:17,096] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:45:17,096] [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_005795905.1	s__Streptomyces marianii	100.0	2998	2999	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_900103455.1	s__Streptomyces wuyuanensis	91.1648	1957	2999	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003097515.1	s__Streptomyces tirandamycinicus	90.1297	1858	2999	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.65	98.27	0.90	0.88	6	-
GCA_003725745.1	s__Streptomyces sp003725745	89.6833	1875	2999	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003122365.1	s__Streptomyces spongiicola	89.0374	1781	2999	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.39	99.39	0.96	0.96	2	-
GCF_011766325.1	s__Streptomyces sp011766325	88.3257	1606	2999	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001005295.1	s__Streptomyces yangpuensis	81.3993	1337	2999	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.05	95.28	0.86	0.84	3	-
GCF_000242715.1	s__Streptomyces acidiscabies	80.0226	1212	2999	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.11	97.67	0.95	0.89	7	-
GCF_000380165.1	s__Streptomyces_A vitaminophilus	78.5293	806	2999	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces_A	95.0	99.94	99.94	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:45:17,098] [INFO] GTDB search result was written to GCF_005795905.1_ASM579590v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:45:17,098] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:45:17,102] [INFO] DFAST_QC result json was written to GCF_005795905.1_ASM579590v1_genomic.fna/dqc_result.json
[2024-01-24 13:45:17,102] [INFO] DFAST_QC completed!
[2024-01-24 13:45:17,102] [INFO] Total running time: 0h3m37s