[2024-01-24 14:19:46,827] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:46,828] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:46,829] [INFO] DQC Reference Directory: /var/lib/cwl/stg318dc6e9-a83f-4161-929c-8dc00cdb517d/dqc_reference
[2024-01-24 14:19:48,166] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:48,167] [INFO] Task started: Prodigal
[2024-01-24 14:19:48,167] [INFO] Running command: gunzip -c /var/lib/cwl/stg3b88c40e-c5e6-464f-a0c4-059f918fcd06/GCF_001005405.1_ASM100540v1_genomic.fna.gz | prodigal -d GCF_001005405.1_ASM100540v1_genomic.fna/cds.fna -a GCF_001005405.1_ASM100540v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:12,878] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:12,879] [INFO] Task started: HMMsearch
[2024-01-24 14:20:12,879] [INFO] Running command: hmmsearch --tblout GCF_001005405.1_ASM100540v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg318dc6e9-a83f-4161-929c-8dc00cdb517d/dqc_reference/reference_markers.hmm GCF_001005405.1_ASM100540v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:13,370] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:13,371] [INFO] Found 6/6 markers.
[2024-01-24 14:20:13,456] [INFO] Query marker FASTA was written to GCF_001005405.1_ASM100540v1_genomic.fna/markers.fasta
[2024-01-24 14:20:13,457] [INFO] Task started: Blastn
[2024-01-24 14:20:13,457] [INFO] Running command: blastn -query GCF_001005405.1_ASM100540v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg318dc6e9-a83f-4161-929c-8dc00cdb517d/dqc_reference/reference_markers.fasta -out GCF_001005405.1_ASM100540v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:14,797] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:14,800] [INFO] Selected 18 target genomes.
[2024-01-24 14:20:14,801] [INFO] Target genome list was writen to GCF_001005405.1_ASM100540v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:14,810] [INFO] Task started: fastANI
[2024-01-24 14:20:14,810] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b88c40e-c5e6-464f-a0c4-059f918fcd06/GCF_001005405.1_ASM100540v1_genomic.fna.gz --refList GCF_001005405.1_ASM100540v1_genomic.fna/target_genomes.txt --output GCF_001005405.1_ASM100540v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:50,708] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:50,709] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg318dc6e9-a83f-4161-929c-8dc00cdb517d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:50,709] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg318dc6e9-a83f-4161-929c-8dc00cdb517d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:50,724] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:20:50,724] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:20:50,724] [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 stelliscabiei	strain=DSM 41803	GCA_014873495.1	146820	146820	type	True	92.5284	2236	2716	95	below_threshold
Streptomyces bottropensis	strain=ATCC 25435	GCA_000340335.2	42235	42235	type	True	92.1658	1931	2716	95	below_threshold
Streptomyces bottropensis	strain=ATCC 25435	GCA_000383595.1	42235	42235	type	True	92.1497	1926	2716	95	below_threshold
Streptomyces brasiliscabiei	strain=IBSBF 2867	GCA_018927715.1	2736302	2736302	type	True	90.1197	1970	2716	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	89.8662	2042	2716	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	89.695	2008	2716	95	below_threshold
Streptomyces phaeolivaceus	strain=GY16	GCA_009184865.1	2653200	2653200	type	True	89.5144	1915	2716	95	below_threshold
Streptomyces neyagawaensis	strain=JCM 4796	GCA_023516595.1	42238	42238	type	True	87.6697	1906	2716	95	below_threshold
Streptomyces torulosus	strain=NRRL B-3889	GCA_001419765.1	68276	68276	type	True	87.5396	1664	2716	95	below_threshold
Streptomyces acidicola	strain=K1PN6	GCA_009377235.1	2596892	2596892	type	True	84.5182	1464	2716	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	84.3969	1634	2716	95	below_threshold
Streptomyces ferrugineus	strain=CCTCC AA2014009	GCA_015160855.1	1413221	1413221	type	True	84.1296	1635	2716	95	below_threshold
Streptomyces durhamensis	strain=NRRL B-3309	GCA_000725475.1	68194	68194	type	True	83.1716	1414	2716	95	below_threshold
Streptomyces lunaelactis	strain=MM109	GCA_003054555.1	1535768	1535768	type	True	81.3479	1209	2716	95	below_threshold
Streptacidiphilus carbonis	strain=NBRC 100919	GCA_000787775.1	105422	105422	type	True	78.6486	910	2716	95	below_threshold
Motilibacter peucedani	strain=RP-AC37	GCA_003634695.1	598650	598650	type	True	76.6983	411	2716	95	below_threshold
Kribbella catacumbae	strain=DSM 19601	GCA_000372465.1	460086	460086	type	True	76.4468	424	2716	95	below_threshold
Parenemella sanctibonifatiensis	strain=NML 150081	GCA_002250565.1	2016505	2016505	type	True	76.2002	172	2716	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:50,726] [INFO] DFAST Taxonomy check result was written to GCF_001005405.1_ASM100540v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:50,726] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:50,727] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:50,727] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg318dc6e9-a83f-4161-929c-8dc00cdb517d/dqc_reference/checkm_data
[2024-01-24 14:20:50,728] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:50,816] [INFO] Task started: CheckM
[2024-01-24 14:20:50,816] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001005405.1_ASM100540v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001005405.1_ASM100540v1_genomic.fna/checkm_input GCF_001005405.1_ASM100540v1_genomic.fna/checkm_result
[2024-01-24 14:22:10,608] [INFO] Task succeeded: CheckM
[2024-01-24 14:22:10,610] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.12%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2024-01-24 14:22:10,637] [INFO] ===== Completeness check finished =====
[2024-01-24 14:22:10,637] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:22:10,637] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001005405.1_ASM100540v1_genomic.fna/markers.fasta)
[2024-01-24 14:22:10,638] [INFO] Task started: Blastn
[2024-01-24 14:22:10,638] [INFO] Running command: blastn -query GCF_001005405.1_ASM100540v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg318dc6e9-a83f-4161-929c-8dc00cdb517d/dqc_reference/reference_markers_gtdb.fasta -out GCF_001005405.1_ASM100540v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:12,689] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:12,704] [INFO] Selected 18 target genomes.
[2024-01-24 14:22:12,704] [INFO] Target genome list was writen to GCF_001005405.1_ASM100540v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:22:12,729] [INFO] Task started: fastANI
[2024-01-24 14:22:12,730] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b88c40e-c5e6-464f-a0c4-059f918fcd06/GCF_001005405.1_ASM100540v1_genomic.fna.gz --refList GCF_001005405.1_ASM100540v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001005405.1_ASM100540v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:22:51,961] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:51,976] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:22:51,976] [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_000091305.1	s__Streptomyces scabiei	99.4412	2585	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.37	97.09	0.94	0.86	16	conclusive
GCF_014873495.1	s__Streptomyces stelliscabiei	92.5133	2238	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.7549	99.87	99.68	0.98	0.96	4	-
GCF_000383595.1	s__Streptomyces bottropensis	92.1329	1928	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.7549	99.99	99.99	1.00	1.00	3	-
GCF_001550375.1	s__Streptomyces europaeiscabiei	90.4256	1897	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.72	96.30	0.83	0.82	3	-
GCF_018927715.1	s__Streptomyces brasiliscabiei	90.092	1974	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203845.1	s__Streptomyces scabiei_E	89.6753	1926	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.38	95.38	0.80	0.80	2	-
GCF_900114955.1	s__Streptomyces sp900114955	89.6458	1913	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.68	97.04	0.90	0.85	10	-
GCF_000772895.1	s__Streptomyces galbus_A	89.5445	1913	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009184865.1	s__Streptomyces phaeolivaceus	89.5384	1912	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009377235.1	s__Streptomyces acidicola	84.5221	1463	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.86	96.86	0.86	0.86	2	-
GCF_015160855.1	s__Streptomyces ferrugineus	84.1794	1625	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001509475.1	s__Streptomyces regalis	84.1714	1594	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002754715.1	s__Streptomyces sp002754715	84.0086	1631	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001896135.2	s__Streptomyces phaeoluteigriseus	83.9074	1491	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054555.1	s__Streptomyces lunaelactis	81.3591	1207	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.21	97.91	0.90	0.85	18	-
GCF_000787775.1	s__Streptacidiphilus carbonis	78.6645	905	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634695.1	s__Motilibacter peucedani	76.6962	413	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Motilibacterales;f__Motilibacteraceae;g__Motilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903918645.1	s__WLRQ01 sp903918645	76.0746	79	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__CAIYMF01;g__WLRQ01	95.0	99.73	99.52	0.94	0.91	5	-
--------------------------------------------------------------------------------
[2024-01-24 14:22:51,978] [INFO] GTDB search result was written to GCF_001005405.1_ASM100540v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:22:51,979] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:22:51,984] [INFO] DFAST_QC result json was written to GCF_001005405.1_ASM100540v1_genomic.fna/dqc_result.json
[2024-01-24 14:22:51,984] [INFO] DFAST_QC completed!
[2024-01-24 14:22:51,984] [INFO] Total running time: 0h3m5s