[2024-01-24 15:02:23,111] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:23,115] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:23,115] [INFO] DQC Reference Directory: /var/lib/cwl/stgb9105911-d868-4396-a52e-b41750aae06f/dqc_reference
[2024-01-24 15:02:24,340] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:24,341] [INFO] Task started: Prodigal
[2024-01-24 15:02:24,341] [INFO] Running command: gunzip -c /var/lib/cwl/stg8f124069-5b07-484c-81c7-c8ac0eabda2c/GCF_014645895.1_ASM1464589v1_genomic.fna.gz | prodigal -d GCF_014645895.1_ASM1464589v1_genomic.fna/cds.fna -a GCF_014645895.1_ASM1464589v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:41,945] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:41,945] [INFO] Task started: HMMsearch
[2024-01-24 15:02:41,945] [INFO] Running command: hmmsearch --tblout GCF_014645895.1_ASM1464589v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb9105911-d868-4396-a52e-b41750aae06f/dqc_reference/reference_markers.hmm GCF_014645895.1_ASM1464589v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:42,241] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:42,242] [INFO] Found 6/6 markers.
[2024-01-24 15:02:42,297] [INFO] Query marker FASTA was written to GCF_014645895.1_ASM1464589v1_genomic.fna/markers.fasta
[2024-01-24 15:02:42,297] [INFO] Task started: Blastn
[2024-01-24 15:02:42,298] [INFO] Running command: blastn -query GCF_014645895.1_ASM1464589v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9105911-d868-4396-a52e-b41750aae06f/dqc_reference/reference_markers.fasta -out GCF_014645895.1_ASM1464589v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:43,530] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:43,539] [INFO] Selected 21 target genomes.
[2024-01-24 15:02:43,539] [INFO] Target genome list was writen to GCF_014645895.1_ASM1464589v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:43,594] [INFO] Task started: fastANI
[2024-01-24 15:02:43,595] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f124069-5b07-484c-81c7-c8ac0eabda2c/GCF_014645895.1_ASM1464589v1_genomic.fna.gz --refList GCF_014645895.1_ASM1464589v1_genomic.fna/target_genomes.txt --output GCF_014645895.1_ASM1464589v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:23,247] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:23,247] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb9105911-d868-4396-a52e-b41750aae06f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:23,248] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb9105911-d868-4396-a52e-b41750aae06f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:23,265] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:03:23,266] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:23,266] [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 daqingensis	strain=CGMCC 4.7178	GCA_014645895.1	1472640	1472640	type	True	100.0	2160	2162	95	conclusive
Streptomyces albidus (ex Kaewkla and Franco 2021)	strain=CAP215	GCA_013870515.1	722709	722709	type	True	84.4499	1413	2162	95	below_threshold
Streptomyces bathyalis	strain=ASO4wet	GCA_015910445.1	2710756	2710756	type	True	83.6273	1544	2162	95	below_threshold
Streptomyces qinglanensis	strain=172205	GCA_003265665.1	943816	943816	type	True	80.8901	1040	2162	95	below_threshold
Streptomyces oryzae	strain=S16-07	GCA_017676365.1	1434886	1434886	type	True	80.7702	1014	2162	95	below_threshold
Streptomyces qinglanensis	strain=CGMCC 4.6825	GCA_900111245.1	943816	943816	type	True	80.766	1065	2162	95	below_threshold
Streptomyces albus subsp. albus	strain=NRRL B-1811	GCA_000725885.1	67257	1888	suspected-type	True	80.62	1050	2162	95	below_threshold
Streptomyces albus	strain=NBRC 13014	GCA_000813365.1	1888	1888	suspected-type	True	80.5783	1044	2162	95	below_threshold
Streptomyces spirodelae	strain=DW4-2	GCA_017676385.1	2812904	2812904	type	True	80.4729	1073	2162	95	below_threshold
Streptomyces radiopugnans	strain=CGMCC 4.3519	GCA_900110735.1	403935	403935	type	True	80.4723	978	2162	95	below_threshold
Streptomyces pini	strain=PL19	GCA_900114215.1	1520580	1520580	type	True	80.4619	925	2162	95	below_threshold
Streptomyces benahoarensis	strain=MZ03-37	GCA_007280575.1	2595054	2595054	type	True	80.1039	809	2162	95	below_threshold
Streptomyces niger	strain=NRRL B-3857	GCA_000718305.1	66373	66373	type	True	80.0127	1055	2162	95	below_threshold
Streptomyces pinistramenti	strain=SF28	GCA_020564935.1	2884812	2884812	type	True	79.8735	959	2162	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	79.7915	1010	2162	95	below_threshold
Streptomyces bauhiniae	strain=Bv016	GCA_004784475.1	2340725	2340725	type	True	79.4896	920	2162	95	below_threshold
Streptomyces plumbidurans	strain=KC 17012	GCA_019857225.1	2814589	2814589	type	True	79.4827	957	2162	95	below_threshold
Streptomyces indiaensis	strain=DSM 43803	GCA_021474405.1	284033	284033	type	True	79.46	947	2162	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	79.3004	998	2162	95	below_threshold
Streptomyces sulfonofaciens	strain=JCM 5069	GCA_014656295.1	68272	68272	type	True	79.1792	955	2162	95	below_threshold
Streptomyces triticiradicis	strain=NEAU-H2	GCA_008868685.1	2651189	2651189	type	True	79.1012	1000	2162	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:23,268] [INFO] DFAST Taxonomy check result was written to GCF_014645895.1_ASM1464589v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:23,268] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:23,268] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:23,268] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb9105911-d868-4396-a52e-b41750aae06f/dqc_reference/checkm_data
[2024-01-24 15:03:23,270] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:23,339] [INFO] Task started: CheckM
[2024-01-24 15:03:23,340] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014645895.1_ASM1464589v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014645895.1_ASM1464589v1_genomic.fna/checkm_input GCF_014645895.1_ASM1464589v1_genomic.fna/checkm_result
[2024-01-24 15:04:49,221] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:49,222] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:49,246] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:49,246] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:49,247] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014645895.1_ASM1464589v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:49,247] [INFO] Task started: Blastn
[2024-01-24 15:04:49,247] [INFO] Running command: blastn -query GCF_014645895.1_ASM1464589v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9105911-d868-4396-a52e-b41750aae06f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014645895.1_ASM1464589v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:51,356] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:51,361] [INFO] Selected 11 target genomes.
[2024-01-24 15:04:51,361] [INFO] Target genome list was writen to GCF_014645895.1_ASM1464589v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:51,371] [INFO] Task started: fastANI
[2024-01-24 15:04:51,371] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f124069-5b07-484c-81c7-c8ac0eabda2c/GCF_014645895.1_ASM1464589v1_genomic.fna.gz --refList GCF_014645895.1_ASM1464589v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014645895.1_ASM1464589v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:05:11,491] [INFO] Task succeeded: fastANI
[2024-01-24 15:05:11,508] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:05:11,509] [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_014645895.1	s__Streptomyces daqingensis	100.0	2160	2162	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.38	95.38	0.92	0.92	3	conclusive
GCF_013870515.1	s__Streptomyces albidus	84.4301	1415	2162	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000424965.1	s__Streptomyces sp000424965	84.2493	1507	2162	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204855.1	s__Streptomyces haliclonae	83.9344	1554	2162	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001751255.1	s__Streptomyces nanshensis_A	83.8056	1333	2162	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.85	97.85	0.86	0.86	2	-
GCF_001751365.1	s__Streptomyces abyssalis	83.7653	1556	2162	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.91	99.91	0.99	0.99	2	-
GCF_015910445.1	s__Streptomyces bathyalis	83.6248	1545	2162	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012726265.1	s__Streptomyces sp012726265	83.504	1521	2162	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418285.1	s__Streptomyces sp001418285	83.3625	1501	2162	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.71	95.43	0.94	0.89	3	-
GCF_012726235.1	s__Streptomyces sp012726235	81.5984	1129	2162	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000497405.1	s__Streptomyces sp000497405	80.106	918	2162	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 15:05:11,510] [INFO] GTDB search result was written to GCF_014645895.1_ASM1464589v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:05:11,511] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:05:11,524] [INFO] DFAST_QC result json was written to GCF_014645895.1_ASM1464589v1_genomic.fna/dqc_result.json
[2024-01-24 15:05:11,524] [INFO] DFAST_QC completed!
[2024-01-24 15:05:11,525] [INFO] Total running time: 0h2m48s