[2024-01-25 19:59:35,308] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:59:35,310] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:59:35,310] [INFO] DQC Reference Directory: /var/lib/cwl/stg09544dbb-91c7-4766-960b-4bd139cf8897/dqc_reference
[2024-01-25 19:59:36,560] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:59:36,561] [INFO] Task started: Prodigal
[2024-01-25 19:59:36,561] [INFO] Running command: gunzip -c /var/lib/cwl/stg6ac0a238-1857-4962-8e6a-b7ab4878e274/GCF_009377205.1_ASM937720v1_genomic.fna.gz | prodigal -d GCF_009377205.1_ASM937720v1_genomic.fna/cds.fna -a GCF_009377205.1_ASM937720v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:00:00,262] [INFO] Task succeeded: Prodigal
[2024-01-25 20:00:00,262] [INFO] Task started: HMMsearch
[2024-01-25 20:00:00,262] [INFO] Running command: hmmsearch --tblout GCF_009377205.1_ASM937720v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09544dbb-91c7-4766-960b-4bd139cf8897/dqc_reference/reference_markers.hmm GCF_009377205.1_ASM937720v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:00:00,641] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:00:00,642] [INFO] Found 6/6 markers.
[2024-01-25 20:00:00,717] [INFO] Query marker FASTA was written to GCF_009377205.1_ASM937720v1_genomic.fna/markers.fasta
[2024-01-25 20:00:00,718] [INFO] Task started: Blastn
[2024-01-25 20:00:00,718] [INFO] Running command: blastn -query GCF_009377205.1_ASM937720v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09544dbb-91c7-4766-960b-4bd139cf8897/dqc_reference/reference_markers.fasta -out GCF_009377205.1_ASM937720v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:00:01,944] [INFO] Task succeeded: Blastn
[2024-01-25 20:00:01,947] [INFO] Selected 20 target genomes.
[2024-01-25 20:00:01,947] [INFO] Target genome list was writen to GCF_009377205.1_ASM937720v1_genomic.fna/target_genomes.txt
[2024-01-25 20:00:01,961] [INFO] Task started: fastANI
[2024-01-25 20:00:01,961] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ac0a238-1857-4962-8e6a-b7ab4878e274/GCF_009377205.1_ASM937720v1_genomic.fna.gz --refList GCF_009377205.1_ASM937720v1_genomic.fna/target_genomes.txt --output GCF_009377205.1_ASM937720v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:00:43,773] [INFO] Task succeeded: fastANI
[2024-01-25 20:00:43,774] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09544dbb-91c7-4766-960b-4bd139cf8897/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:00:43,774] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09544dbb-91c7-4766-960b-4bd139cf8897/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:00:43,786] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:00:43,786] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:00:43,786] [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 phyllanthi	strain=TISTR 2346	GCA_009377205.1	1803180	1803180	type	True	100.0	2905	2949	95	conclusive
Streptomyces spongiae	strain=NBRC 106415	GCA_009377185.1	565072	565072	type	True	88.1174	1786	2949	95	below_threshold
Streptomyces acidicola	strain=K1PN6	GCA_009377235.1	2596892	2596892	type	True	87.9589	1676	2949	95	below_threshold
Streptomyces bluensis	strain=JCM 4729	GCA_014650715.1	33897	33897	type	True	87.8422	1709	2949	95	below_threshold
Streptomyces poonensis	strain=JCM 4815	GCA_014650915.1	68255	68255	type	True	85.5958	1511	2949	95	below_threshold
Streptomyces capitiformicae	strain=CGMCC 4.7403	GCA_014653855.1	2014920	2014920	type	True	85.1872	1753	2949	95	below_threshold
Streptomyces capitiformicae	strain=1H-SSA4	GCA_002214185.1	2014920	2014920	type	True	85.1336	1777	2949	95	below_threshold
Streptomyces torulosus	strain=NRRL B-3889	GCA_001419765.1	68276	68276	type	True	84.9309	1521	2949	95	below_threshold
Streptomyces ruber	strain=JCM 3131	GCA_014648075.1	83378	83378	type	True	84.8695	1440	2949	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	84.8256	1845	2949	95	below_threshold
Streptomyces neyagawaensis	strain=JCM 4796	GCA_023516595.1	42238	42238	type	True	84.736	1724	2949	95	below_threshold
Streptomyces ferrugineus	strain=CCTCC AA2014009	GCA_015160855.1	1413221	1413221	type	True	84.5191	1755	2949	95	below_threshold
Streptomyces cyaneochromogenes	strain=MK-45	GCA_003963535.1	2496836	2496836	type	True	84.3093	1742	2949	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	84.1078	1727	2949	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	83.7925	1540	2949	95	below_threshold
Streptomyces triticisoli	strain=NEAU-DSCPA1-4-4	GCA_003270085.1	2182797	2182797	type	True	83.7064	1248	2949	95	below_threshold
Streptomyces galbus	strain=DSM 40089	GCA_005280195.1	33898	33898	type	True	83.3892	1400	2949	95	below_threshold
Streptomyces galbus	strain=JCM 4639	GCA_014650535.1	33898	33898	type	True	83.3797	1399	2949	95	below_threshold
Streptomyces longwoodensis	strain=DSM 41677	GCA_001514125.1	68231	68231	type	True	83.2312	1429	2949	95	below_threshold
Streptomyces filipinensis	strain=JCM 4369	GCA_014649495.1	66887	66887	type	True	82.9824	1474	2949	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:00:43,788] [INFO] DFAST Taxonomy check result was written to GCF_009377205.1_ASM937720v1_genomic.fna/tc_result.tsv
[2024-01-25 20:00:43,788] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:00:43,788] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:00:43,789] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09544dbb-91c7-4766-960b-4bd139cf8897/dqc_reference/checkm_data
[2024-01-25 20:00:43,789] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:00:43,883] [INFO] Task started: CheckM
[2024-01-25 20:00:43,883] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009377205.1_ASM937720v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009377205.1_ASM937720v1_genomic.fna/checkm_input GCF_009377205.1_ASM937720v1_genomic.fna/checkm_result
[2024-01-25 20:02:25,860] [INFO] Task succeeded: CheckM
[2024-01-25 20:02:25,861] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.12%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2024-01-25 20:02:25,901] [INFO] ===== Completeness check finished =====
[2024-01-25 20:02:25,901] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:02:25,902] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009377205.1_ASM937720v1_genomic.fna/markers.fasta)
[2024-01-25 20:02:25,902] [INFO] Task started: Blastn
[2024-01-25 20:02:25,902] [INFO] Running command: blastn -query GCF_009377205.1_ASM937720v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09544dbb-91c7-4766-960b-4bd139cf8897/dqc_reference/reference_markers_gtdb.fasta -out GCF_009377205.1_ASM937720v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:02:27,917] [INFO] Task succeeded: Blastn
[2024-01-25 20:02:27,920] [INFO] Selected 18 target genomes.
[2024-01-25 20:02:27,920] [INFO] Target genome list was writen to GCF_009377205.1_ASM937720v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:02:27,933] [INFO] Task started: fastANI
[2024-01-25 20:02:27,933] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ac0a238-1857-4962-8e6a-b7ab4878e274/GCF_009377205.1_ASM937720v1_genomic.fna.gz --refList GCF_009377205.1_ASM937720v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009377205.1_ASM937720v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:03:08,447] [INFO] Task succeeded: fastANI
[2024-01-25 20:03:08,458] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:03:08,458] [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_009377205.1	s__Streptomyces phyllanthi	100.0	2905	2949	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_009377235.1	s__Streptomyces acidicola	87.9429	1678	2949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.86	96.86	0.86	0.86	2	-
GCF_014650715.1	s__Streptomyces bluensis	87.8473	1709	2949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.08	99.08	0.92	0.92	2	-
GCF_014650915.1	s__Streptomyces poonensis	85.6034	1509	2949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002214185.1	s__Streptomyces capitiformicae	85.1599	1772	2949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.95	99.95	1.00	1.00	2	-
GCF_000317595.1	s__Streptomyces ipomoeae	85.1054	1709	2949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.29	98.81	0.89	0.87	4	-
GCF_001550375.1	s__Streptomyces europaeiscabiei	85.034	1669	2949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.72	96.30	0.83	0.82	3	-
GCF_000772895.1	s__Streptomyces galbus_A	84.8863	1808	2949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648075.1	s__Streptomyces ruber	84.8861	1437	2949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015160855.1	s__Streptomyces ferrugineus	84.5126	1755	2949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003963535.1	s__Streptomyces cyaneochromogenes	84.3165	1741	2949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009852415.1	s__Streptomyces sp009852415	83.8535	1523	2949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014534645.1	s__Streptomyces sp014534645	83.8464	1529	2949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129855.1	s__Streptomyces sp900129855	83.796	1596	2949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.68	99.68	0.97	0.97	2	-
GCF_011193355.1	s__Streptomyces sp011193355	83.7466	1451	2949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005280195.1	s__Streptomyces galbus	83.3996	1397	2949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.26	98.53	0.96	0.94	3	-
GCF_001514125.1	s__Streptomyces longwoodensis	83.2248	1430	2949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.95	95.95	0.86	0.86	2	-
GCF_014649495.1	s__Streptomyces filipinensis	82.9969	1471	2949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.80	96.80	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:03:08,460] [INFO] GTDB search result was written to GCF_009377205.1_ASM937720v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:03:08,460] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:03:08,464] [INFO] DFAST_QC result json was written to GCF_009377205.1_ASM937720v1_genomic.fna/dqc_result.json
[2024-01-25 20:03:08,464] [INFO] DFAST_QC completed!
[2024-01-25 20:03:08,464] [INFO] Total running time: 0h3m33s