[2024-01-24 11:44:38,169] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:38,171] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:38,171] [INFO] DQC Reference Directory: /var/lib/cwl/stg3903958f-a062-4647-b706-5359cc2f5004/dqc_reference
[2024-01-24 11:44:41,483] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:41,484] [INFO] Task started: Prodigal
[2024-01-24 11:44:41,484] [INFO] Running command: gunzip -c /var/lib/cwl/stg01cbf872-dccd-4d48-a232-b9ec20f4f060/GCF_014649715.1_ASM1464971v1_genomic.fna.gz | prodigal -d GCF_014649715.1_ASM1464971v1_genomic.fna/cds.fna -a GCF_014649715.1_ASM1464971v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:45:02,003] [INFO] Task succeeded: Prodigal
[2024-01-24 11:45:02,004] [INFO] Task started: HMMsearch
[2024-01-24 11:45:02,004] [INFO] Running command: hmmsearch --tblout GCF_014649715.1_ASM1464971v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3903958f-a062-4647-b706-5359cc2f5004/dqc_reference/reference_markers.hmm GCF_014649715.1_ASM1464971v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:45:02,336] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:45:02,338] [INFO] Found 6/6 markers.
[2024-01-24 11:45:02,405] [INFO] Query marker FASTA was written to GCF_014649715.1_ASM1464971v1_genomic.fna/markers.fasta
[2024-01-24 11:45:02,405] [INFO] Task started: Blastn
[2024-01-24 11:45:02,405] [INFO] Running command: blastn -query GCF_014649715.1_ASM1464971v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3903958f-a062-4647-b706-5359cc2f5004/dqc_reference/reference_markers.fasta -out GCF_014649715.1_ASM1464971v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:03,725] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:03,730] [INFO] Selected 20 target genomes.
[2024-01-24 11:45:03,730] [INFO] Target genome list was writen to GCF_014649715.1_ASM1464971v1_genomic.fna/target_genomes.txt
[2024-01-24 11:45:03,740] [INFO] Task started: fastANI
[2024-01-24 11:45:03,740] [INFO] Running command: fastANI --query /var/lib/cwl/stg01cbf872-dccd-4d48-a232-b9ec20f4f060/GCF_014649715.1_ASM1464971v1_genomic.fna.gz --refList GCF_014649715.1_ASM1464971v1_genomic.fna/target_genomes.txt --output GCF_014649715.1_ASM1464971v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:45:41,474] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:41,475] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3903958f-a062-4647-b706-5359cc2f5004/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:45:41,475] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3903958f-a062-4647-b706-5359cc2f5004/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:45:41,492] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:45:41,492] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:45:41,492] [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 lateritius	strain=JCM 4389	GCA_014649715.1	67313	67313	type	True	100.0	2545	2545	95	conclusive
Streptomyces nashvillensis	strain=JCM 4498	GCA_014650095.1	67334	67334	type	True	86.2366	1711	2545	95	below_threshold
Streptomyces venezuelae	strain=ATCC 10712	GCA_021432215.1	54571	54571	type	True	86.1512	1344	2545	95	below_threshold
Streptomyces tanashiensis	strain=JCM 4086	GCA_014648895.1	67367	67367	type	True	86.1055	1717	2545	95	below_threshold
Streptomyces exfoliatus	strain=NRRL B-2924	GCA_000725545.1	1905	1905	type	True	86.0839	1715	2545	95	below_threshold
Streptomyces vietnamensis	strain=GIM4.0001	GCA_000830005.1	362257	362257	type	True	86.0673	1731	2545	95	below_threshold
Streptomyces litmocidini	strain=JCM 4394	GCA_014649755.1	67318	67318	type	True	86.0306	1652	2545	95	below_threshold
Streptomyces cinereoruber	strain=ATCC 19740	GCA_009299385.1	67260	67260	type	True	86.0124	1577	2545	95	below_threshold
Streptomyces exfoliatus	strain=NRRL B-2924	GCA_000718175.1	1905	1905	type	True	86.0094	1728	2545	95	below_threshold
Streptomyces cinereoruber	strain=JCM4205	GCA_019880525.1	67260	67260	type	True	85.9773	1570	2545	95	below_threshold
Streptomyces cinereoruber	strain=JCM 4205	GCA_014649095.1	67260	67260	type	True	85.9411	1556	2545	95	below_threshold
Streptomyces nymphaeiformis	strain=SFB5A	GCA_014203895.1	2663842	2663842	type	True	85.9173	1703	2545	95	below_threshold
Streptomyces cinereoruber	strain=NRRL ISP-5012	GCA_014197485.1	67260	67260	type	True	85.8706	1585	2545	95	below_threshold
Streptomyces purpureus	strain=JCM 3172	GCA_014648195.1	1951	1951	type	True	85.2788	1585	2545	95	below_threshold
Streptomyces termitum	strain=JCM 4518	GCA_014650175.1	67368	67368	type	True	84.7936	1522	2545	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	83.5523	1463	2545	95	below_threshold
Streptomyces kurssanovii	strain=JCM 4388	GCA_014649695.1	67312	67312	type	True	82.9333	1473	2545	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	82.8515	1113	2545	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	82.7331	1344	2545	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	81.5003	1256	2545	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:45:41,494] [INFO] DFAST Taxonomy check result was written to GCF_014649715.1_ASM1464971v1_genomic.fna/tc_result.tsv
[2024-01-24 11:45:41,495] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:45:41,495] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:45:41,495] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3903958f-a062-4647-b706-5359cc2f5004/dqc_reference/checkm_data
[2024-01-24 11:45:41,496] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:45:41,576] [INFO] Task started: CheckM
[2024-01-24 11:45:41,577] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014649715.1_ASM1464971v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014649715.1_ASM1464971v1_genomic.fna/checkm_input GCF_014649715.1_ASM1464971v1_genomic.fna/checkm_result
[2024-01-24 11:47:09,412] [INFO] Task succeeded: CheckM
[2024-01-24 11:47:09,414] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:47:09,445] [INFO] ===== Completeness check finished =====
[2024-01-24 11:47:09,446] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:47:09,446] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014649715.1_ASM1464971v1_genomic.fna/markers.fasta)
[2024-01-24 11:47:09,447] [INFO] Task started: Blastn
[2024-01-24 11:47:09,447] [INFO] Running command: blastn -query GCF_014649715.1_ASM1464971v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3903958f-a062-4647-b706-5359cc2f5004/dqc_reference/reference_markers_gtdb.fasta -out GCF_014649715.1_ASM1464971v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:47:11,520] [INFO] Task succeeded: Blastn
[2024-01-24 11:47:11,524] [INFO] Selected 15 target genomes.
[2024-01-24 11:47:11,524] [INFO] Target genome list was writen to GCF_014649715.1_ASM1464971v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:47:11,537] [INFO] Task started: fastANI
[2024-01-24 11:47:11,537] [INFO] Running command: fastANI --query /var/lib/cwl/stg01cbf872-dccd-4d48-a232-b9ec20f4f060/GCF_014649715.1_ASM1464971v1_genomic.fna.gz --refList GCF_014649715.1_ASM1464971v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014649715.1_ASM1464971v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:47:41,222] [INFO] Task succeeded: fastANI
[2024-01-24 11:47:41,239] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:47:41,240] [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_014649715.1	s__Streptomyces lateritius	100.0	2545	2545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.54	99.54	0.94	0.94	2	conclusive
GCF_018614205.1	s__Streptomyces sp018614205	91.1874	1834	2545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005517195.1	s__Streptomyces exfoliatus_B	89.2644	1810	2545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008042125.1	s__Streptomyces sp008042125	87.3911	1694	2545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648895.1	s__Streptomyces tanashiensis	86.1322	1713	2545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.78	97.78	0.91	0.91	2	-
GCF_000830005.1	s__Streptomyces vietnamensis	86.0652	1731	2545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649755.1	s__Streptomyces litmocidini	86.0641	1647	2545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.07	95.07	0.85	0.85	2	-
GCF_900105415.1	s__Streptomyces sp900105415	86.0373	1750	2545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.65	95.65	0.85	0.85	2	-
GCF_003386135.1	s__Streptomyces sp003386135	85.8771	1719	2545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.57	99.57	0.94	0.94	2	-
GCA_000716465.1	s__Streptomyces bikiniensis	85.8753	1539	2545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.67	95.67	0.86	0.82	10	-
GCF_000716445.1	s__Streptomyces wedmorensis	85.7834	1714	2545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.81	97.63	0.94	0.88	3	-
GCA_000721275.1	s__Streptomyces sp000721275	85.1686	1563	2545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014596525.1	s__Streptomyces sp014596525	84.9154	1434	2545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	0.96	0.96	2	-
GCF_014650175.1	s__Streptomyces termitum	84.7956	1522	2545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649695.1	s__Streptomyces kurssanovii	82.9008	1479	2545	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 11:47:41,241] [INFO] GTDB search result was written to GCF_014649715.1_ASM1464971v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:47:41,242] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:47:41,246] [INFO] DFAST_QC result json was written to GCF_014649715.1_ASM1464971v1_genomic.fna/dqc_result.json
[2024-01-24 11:47:41,246] [INFO] DFAST_QC completed!
[2024-01-24 11:47:41,246] [INFO] Total running time: 0h3m3s