[2024-01-24 13:12:52,644] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:52,646] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:52,647] [INFO] DQC Reference Directory: /var/lib/cwl/stgf1955cce-e4c3-45b6-b3f1-a4f5c2c0c6bf/dqc_reference
[2024-01-24 13:12:53,991] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:53,992] [INFO] Task started: Prodigal
[2024-01-24 13:12:53,992] [INFO] Running command: gunzip -c /var/lib/cwl/stg5057068b-7984-4276-b675-58b07451b76f/GCF_900142595.1_IMG-taxon_2667527450_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900142595.1_IMG-taxon_2667527450_annotated_assembly_genomic.fna/cds.fna -a GCF_900142595.1_IMG-taxon_2667527450_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:21,946] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:21,947] [INFO] Task started: HMMsearch
[2024-01-24 13:13:21,947] [INFO] Running command: hmmsearch --tblout GCF_900142595.1_IMG-taxon_2667527450_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf1955cce-e4c3-45b6-b3f1-a4f5c2c0c6bf/dqc_reference/reference_markers.hmm GCF_900142595.1_IMG-taxon_2667527450_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:22,357] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:22,359] [INFO] Found 6/6 markers.
[2024-01-24 13:13:22,428] [INFO] Query marker FASTA was written to GCF_900142595.1_IMG-taxon_2667527450_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:13:22,428] [INFO] Task started: Blastn
[2024-01-24 13:13:22,428] [INFO] Running command: blastn -query GCF_900142595.1_IMG-taxon_2667527450_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1955cce-e4c3-45b6-b3f1-a4f5c2c0c6bf/dqc_reference/reference_markers.fasta -out GCF_900142595.1_IMG-taxon_2667527450_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:23,846] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:23,849] [INFO] Selected 23 target genomes.
[2024-01-24 13:13:23,850] [INFO] Target genome list was writen to GCF_900142595.1_IMG-taxon_2667527450_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:13:23,865] [INFO] Task started: fastANI
[2024-01-24 13:13:23,866] [INFO] Running command: fastANI --query /var/lib/cwl/stg5057068b-7984-4276-b675-58b07451b76f/GCF_900142595.1_IMG-taxon_2667527450_annotated_assembly_genomic.fna.gz --refList GCF_900142595.1_IMG-taxon_2667527450_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900142595.1_IMG-taxon_2667527450_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:10,448] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:10,449] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf1955cce-e4c3-45b6-b3f1-a4f5c2c0c6bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:10,450] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf1955cce-e4c3-45b6-b3f1-a4f5c2c0c6bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:10,472] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:14:10,473] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:14:10,473] [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 albulus	strain=JCM 4718	GCA_014650635.1	68570	68570	suspected-type	True	96.1199	2534	3071	95	conclusive
Streptomyces albospinus	strain=JCM 3399	GCA_014648695.1	285515	285515	type	True	87.8852	2029	3071	95	below_threshold
Streptomyces lydicus	strain=ATCC 25470	GCA_004125245.1	47763	47763	suspected-type	True	85.8835	1809	3071	95	below_threshold
Streptomyces lydicus	strain=NRRL ISP-5461	GCA_000717345.1	47763	47763	suspected-type	True	85.818	1801	3071	95	below_threshold
Streptomyces kronopolitis	strain=CGMCC 4.7323	GCA_014646275.1	1612435	1612435	type	True	85.6054	1687	3071	95	below_threshold
Streptomyces decoyicus	strain=NRRL 2666	GCA_019880305.1	249567	249567	type	True	85.5385	1781	3071	95	below_threshold
Streptomyces lydicamycinicus	strain=NBRC 110027	GCA_000829715.2	1546107	1546107	type	True	85.5329	1764	3071	95	below_threshold
Streptomyces decoyicus	strain=NRRL 2666	GCA_001270575.1	249567	249567	type	True	85.5324	1711	3071	95	below_threshold
Streptomyces platensis	strain=ATCC 23948	GCA_008704855.1	58346	58346	type	True	85.4638	1750	3071	95	below_threshold
Streptomyces platensis	strain=DSM 40041	GCA_002119195.1	58346	58346	type	True	85.4546	1718	3071	95	below_threshold
Streptomyces caniferus	strain=NBRC 15389	GCA_009811555.1	285557	285557	type	True	85.4485	1816	3071	95	below_threshold
Streptomyces pinistramenti	strain=SF28	GCA_020564935.1	2884812	2884812	type	True	84.6904	1608	3071	95	below_threshold
Streptomyces benahoarensis	strain=MZ03-37	GCA_007280575.1	2595054	2595054	type	True	84.2516	1260	3071	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	83.4199	1676	3071	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	83.3027	1599	3071	95	below_threshold
Streptomyces violens	strain=NRRL ISP-5597	GCA_000717745.1	66377	66377	type	True	83.2985	1446	3071	95	below_threshold
Streptomyces paromomycinus	strain=NBRC 15454	GCA_003865155.1	92743	92743	type	True	83.2771	1633	3071	95	below_threshold
Streptomyces purpurogeneiscleroticus	strain=DSM 43156	GCA_020024005.1	68259	68259	type	True	83.2302	1327	3071	95	below_threshold
Streptomyces ochraceiscleroticus	strain=NRRL ISP-5594	GCA_000720485.1	47761	47761	type	True	83.1016	1492	3071	95	below_threshold
Streptomyces netropsis	strain=CECT 3265	GCA_014203545.1	55404	55404	type	True	81.8209	1338	3071	95	below_threshold
Streptomyces netropsis	strain=JCM 4063	GCA_014648835.1	55404	55404	type	True	81.7907	1329	3071	95	below_threshold
Streptomyces bungoensis	strain=DSM 41781	GCA_001514215.1	285568	285568	type	True	80.8111	1306	3071	95	below_threshold
Streptomyces malachitofuscus	strain=JCM 4493	GCA_014650055.1	67322	67322	type	True	80.7983	1230	3071	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:10,475] [INFO] DFAST Taxonomy check result was written to GCF_900142595.1_IMG-taxon_2667527450_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:14:10,475] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:10,476] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:10,476] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf1955cce-e4c3-45b6-b3f1-a4f5c2c0c6bf/dqc_reference/checkm_data
[2024-01-24 13:14:10,477] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:10,565] [INFO] Task started: CheckM
[2024-01-24 13:14:10,566] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900142595.1_IMG-taxon_2667527450_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900142595.1_IMG-taxon_2667527450_annotated_assembly_genomic.fna/checkm_input GCF_900142595.1_IMG-taxon_2667527450_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:15:36,148] [INFO] Task succeeded: CheckM
[2024-01-24 13:15:36,149] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 13.54%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:15:36,175] [INFO] ===== Completeness check finished =====
[2024-01-24 13:15:36,175] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:15:36,176] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900142595.1_IMG-taxon_2667527450_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:15:36,176] [INFO] Task started: Blastn
[2024-01-24 13:15:36,176] [INFO] Running command: blastn -query GCF_900142595.1_IMG-taxon_2667527450_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1955cce-e4c3-45b6-b3f1-a4f5c2c0c6bf/dqc_reference/reference_markers_gtdb.fasta -out GCF_900142595.1_IMG-taxon_2667527450_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:15:38,332] [INFO] Task succeeded: Blastn
[2024-01-24 13:15:38,336] [INFO] Selected 10 target genomes.
[2024-01-24 13:15:38,336] [INFO] Target genome list was writen to GCF_900142595.1_IMG-taxon_2667527450_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:15:38,359] [INFO] Task started: fastANI
[2024-01-24 13:15:38,360] [INFO] Running command: fastANI --query /var/lib/cwl/stg5057068b-7984-4276-b675-58b07451b76f/GCF_900142595.1_IMG-taxon_2667527450_annotated_assembly_genomic.fna.gz --refList GCF_900142595.1_IMG-taxon_2667527450_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900142595.1_IMG-taxon_2667527450_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:16:03,873] [INFO] Task succeeded: fastANI
[2024-01-24 13:16:03,887] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:16:03,887] [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_016917755.1	s__Streptomyces yunnanensis	97.4386	2603	3071	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.5028	97.38	97.21	0.85	0.85	4	conclusive
GCA_001704275.1	s__Streptomyces noursei	96.2429	2512	3071	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.5028	97.67	97.67	0.83	0.83	2	-
GCF_002803155.1	s__Streptomyces sp002803155	90.7775	2261	3071	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000373585.1	s__Streptomyces sp000373585	90.6951	2066	3071	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCA_000963515.1	s__Streptomyces albulus_C	89.9553	2171	3071	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.74	99.39	0.98	0.95	6	-
GCF_009176265.1	s__Streptomyces angustmyceticus	85.8035	1732	3071	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	1.00	1.00	2	-
GCF_014203555.1	s__Streptomyces olivoverticillatus	82.0477	1191	3071	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000717595.1	s__Streptomyces flavochromogenes	80.7901	1318	3071	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.5951	N/A	N/A	N/A	N/A	1	-
GCF_008705135.1	s__Streptomyces coeruleorubidus	80.6196	1317	3071	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.68	95.03	0.91	0.83	4	-
GCF_014646115.1	s__Streptomyces camponoticapitis	80.285	1174	3071	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 13:16:03,889] [INFO] GTDB search result was written to GCF_900142595.1_IMG-taxon_2667527450_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:16:03,890] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:16:03,894] [INFO] DFAST_QC result json was written to GCF_900142595.1_IMG-taxon_2667527450_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:16:03,894] [INFO] DFAST_QC completed!
[2024-01-24 13:16:03,895] [INFO] Total running time: 0h3m11s