[2024-01-24 11:13:04,481] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:13:04,482] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:13:04,483] [INFO] DQC Reference Directory: /var/lib/cwl/stg73921758-77de-4b28-9fd9-f25fb38f394d/dqc_reference
[2024-01-24 11:13:05,682] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:13:05,683] [INFO] Task started: Prodigal
[2024-01-24 11:13:05,683] [INFO] Running command: gunzip -c /var/lib/cwl/stg1926cfc5-5c7f-4a4e-94f5-9fe11a11f959/GCF_014646335.1_ASM1464633v1_genomic.fna.gz | prodigal -d GCF_014646335.1_ASM1464633v1_genomic.fna/cds.fna -a GCF_014646335.1_ASM1464633v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:36,409] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:36,410] [INFO] Task started: HMMsearch
[2024-01-24 11:13:36,410] [INFO] Running command: hmmsearch --tblout GCF_014646335.1_ASM1464633v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg73921758-77de-4b28-9fd9-f25fb38f394d/dqc_reference/reference_markers.hmm GCF_014646335.1_ASM1464633v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:36,901] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:36,903] [INFO] Found 6/6 markers.
[2024-01-24 11:13:36,981] [INFO] Query marker FASTA was written to GCF_014646335.1_ASM1464633v1_genomic.fna/markers.fasta
[2024-01-24 11:13:36,982] [INFO] Task started: Blastn
[2024-01-24 11:13:36,983] [INFO] Running command: blastn -query GCF_014646335.1_ASM1464633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg73921758-77de-4b28-9fd9-f25fb38f394d/dqc_reference/reference_markers.fasta -out GCF_014646335.1_ASM1464633v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:38,287] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:38,291] [INFO] Selected 19 target genomes.
[2024-01-24 11:13:38,292] [INFO] Target genome list was writen to GCF_014646335.1_ASM1464633v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:38,300] [INFO] Task started: fastANI
[2024-01-24 11:13:38,300] [INFO] Running command: fastANI --query /var/lib/cwl/stg1926cfc5-5c7f-4a4e-94f5-9fe11a11f959/GCF_014646335.1_ASM1464633v1_genomic.fna.gz --refList GCF_014646335.1_ASM1464633v1_genomic.fna/target_genomes.txt --output GCF_014646335.1_ASM1464633v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:14:25,692] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:25,693] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg73921758-77de-4b28-9fd9-f25fb38f394d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:14:25,693] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg73921758-77de-4b28-9fd9-f25fb38f394d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:14:25,711] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:14:25,711] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:14:25,711] [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 lasiicapitis	strain=CGMCC 4.7349	GCA_014646335.1	1923961	1923961	type	True	100.0	3223	3224	95	conclusive
Streptomyces aureoverticillatus	strain=JCM 4347	GCA_014649395.1	66871	66871	type	True	91.9671	2544	3224	95	below_threshold
Streptomyces alboflavus	strain=NRRL B-2373	GCA_000716675.1	67267	67267	type	True	89.7905	2442	3224	95	below_threshold
Streptomyces flavofungini	strain=JCM 4753	GCA_016411765.1	68200	68200	type	True	89.7173	2500	3224	95	below_threshold
Streptomyces flavofungini	strain=JCM 4753	GCA_014650815.1	68200	68200	type	True	89.7172	2470	3224	95	below_threshold
Streptomyces spectabilis	strain=KCTC9218	GCA_022698305.1	68270	68270	type	True	86.4542	2294	3224	95	below_threshold
Streptomyces kanamyceticus	strain=NRRL B-2535	GCA_001418465.1	1967	1967	type	True	84.6381	1832	3224	95	below_threshold
Streptomyces kanamyceticus	strain=ATCC 12853	GCA_008704495.1	1967	1967	type	True	84.4428	2115	3224	95	below_threshold
Streptomyces durmitorensis	strain=MS405	GCA_023498005.1	319947	319947	type	True	84.3782	2044	3224	95	below_threshold
Streptomyces longisporoflavus	strain=JCM 4396	GCA_014649775.1	28044	28044	type	True	84.0781	1950	3224	95	below_threshold
Streptomyces boluensis	strain=YC537	GCA_009908195.1	1775135	1775135	type	True	82.9471	1372	3224	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	82.4028	1608	3224	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	82.0633	1716	3224	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	81.9774	1564	3224	95	below_threshold
Streptomyces finlayi	strain=JCM 4637	GCA_014650515.1	67296	67296	type	True	81.4416	1560	3224	95	below_threshold
Streptomyces griseocarneus	strain=CGMCC4.1088	GCA_020093395.1	51201	51201	type	True	81.0057	1287	3224	95	below_threshold
Streptomyces griseocarneus	strain=JCM 4580	GCA_014655595.1	51201	51201	type	True	80.9986	1280	3224	95	below_threshold
Streptomyces roseifaciens	strain=MBT76	GCA_001445655.1	1488406	1488406	type	True	80.8664	1402	3224	95	below_threshold
Streptomyces hiroshimensis	strain=JCM 4586	GCA_014650335.1	66424	66424	type	True	80.8546	1370	3224	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:14:25,713] [INFO] DFAST Taxonomy check result was written to GCF_014646335.1_ASM1464633v1_genomic.fna/tc_result.tsv
[2024-01-24 11:14:25,713] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:14:25,714] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:14:25,714] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg73921758-77de-4b28-9fd9-f25fb38f394d/dqc_reference/checkm_data
[2024-01-24 11:14:25,715] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:14:25,802] [INFO] Task started: CheckM
[2024-01-24 11:14:25,803] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014646335.1_ASM1464633v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014646335.1_ASM1464633v1_genomic.fna/checkm_input GCF_014646335.1_ASM1464633v1_genomic.fna/checkm_result
[2024-01-24 11:16:16,889] [INFO] Task succeeded: CheckM
[2024-01-24 11:16:16,890] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:16:16,921] [INFO] ===== Completeness check finished =====
[2024-01-24 11:16:16,922] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:16:16,922] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014646335.1_ASM1464633v1_genomic.fna/markers.fasta)
[2024-01-24 11:16:16,923] [INFO] Task started: Blastn
[2024-01-24 11:16:16,923] [INFO] Running command: blastn -query GCF_014646335.1_ASM1464633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg73921758-77de-4b28-9fd9-f25fb38f394d/dqc_reference/reference_markers_gtdb.fasta -out GCF_014646335.1_ASM1464633v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:16:18,979] [INFO] Task succeeded: Blastn
[2024-01-24 11:16:18,983] [INFO] Selected 14 target genomes.
[2024-01-24 11:16:18,983] [INFO] Target genome list was writen to GCF_014646335.1_ASM1464633v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:16:18,994] [INFO] Task started: fastANI
[2024-01-24 11:16:18,994] [INFO] Running command: fastANI --query /var/lib/cwl/stg1926cfc5-5c7f-4a4e-94f5-9fe11a11f959/GCF_014646335.1_ASM1464633v1_genomic.fna.gz --refList GCF_014646335.1_ASM1464633v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014646335.1_ASM1464633v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:16:55,523] [INFO] Task succeeded: fastANI
[2024-01-24 11:16:55,539] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:16:55,539] [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_014646335.1	s__Streptomyces lasiicapitis	100.0	3223	3224	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.86	98.86	0.95	0.95	2	conclusive
GCF_000414115.1	s__Streptomyces aurantiacus_A	92.1102	2181	3224	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649395.1	s__Streptomyces aureoverticillatus	91.9811	2542	3224	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716675.1	s__Streptomyces alboflavus	89.7714	2445	3224	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.12	98.24	0.94	0.89	5	-
GCF_014650815.1	s__Streptomyces flavofungini	89.7197	2470	3224	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000720475.1	s__Streptomyces aureocirculatus	88.1359	2167	3224	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	0.99	0.99	2	-
GCF_009755605.1	s__Streptomyces typhae	87.845	2237	3224	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.66	98.66	0.93	0.93	2	-
GCF_008704495.1	s__Streptomyces kanamyceticus	84.4333	2117	3224	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	0.99	0.99	2	-
GCF_009908195.1	s__Streptomyces boluensis	82.9488	1373	3224	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	81.8643	1680	3224	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418565.1	s__Streptomyces graminilatus	81.6402	1313	3224	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014650415.1	s__Streptomyces spiroverticillatus	81.3975	1578	3224	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014655595.1	s__Streptomyces griseocarneus	80.9712	1287	3224	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000158915.1	s__Streptomyces himastatinicus	80.3083	1500	3224	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.59	95.41	0.86	0.82	5	-
--------------------------------------------------------------------------------
[2024-01-24 11:16:55,541] [INFO] GTDB search result was written to GCF_014646335.1_ASM1464633v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:16:55,541] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:16:55,545] [INFO] DFAST_QC result json was written to GCF_014646335.1_ASM1464633v1_genomic.fna/dqc_result.json
[2024-01-24 11:16:55,546] [INFO] DFAST_QC completed!
[2024-01-24 11:16:55,546] [INFO] Total running time: 0h3m51s