[2024-01-24 14:02:46,371] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:02:46,375] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:02:46,375] [INFO] DQC Reference Directory: /var/lib/cwl/stgace0a50b-1262-4257-9c42-42875d9a365b/dqc_reference
[2024-01-24 14:02:47,630] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:02:47,631] [INFO] Task started: Prodigal
[2024-01-24 14:02:47,631] [INFO] Running command: gunzip -c /var/lib/cwl/stgc6125767-71dd-488c-9c18-33daad00cfea/GCF_014655295.1_ASM1465529v1_genomic.fna.gz | prodigal -d GCF_014655295.1_ASM1465529v1_genomic.fna/cds.fna -a GCF_014655295.1_ASM1465529v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:03:21,561] [INFO] Task succeeded: Prodigal
[2024-01-24 14:03:21,561] [INFO] Task started: HMMsearch
[2024-01-24 14:03:21,561] [INFO] Running command: hmmsearch --tblout GCF_014655295.1_ASM1465529v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgace0a50b-1262-4257-9c42-42875d9a365b/dqc_reference/reference_markers.hmm GCF_014655295.1_ASM1465529v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:03:21,978] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:03:21,980] [INFO] Found 6/6 markers.
[2024-01-24 14:03:22,060] [INFO] Query marker FASTA was written to GCF_014655295.1_ASM1465529v1_genomic.fna/markers.fasta
[2024-01-24 14:03:22,061] [INFO] Task started: Blastn
[2024-01-24 14:03:22,061] [INFO] Running command: blastn -query GCF_014655295.1_ASM1465529v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgace0a50b-1262-4257-9c42-42875d9a365b/dqc_reference/reference_markers.fasta -out GCF_014655295.1_ASM1465529v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:23,381] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:23,384] [INFO] Selected 22 target genomes.
[2024-01-24 14:03:23,385] [INFO] Target genome list was writen to GCF_014655295.1_ASM1465529v1_genomic.fna/target_genomes.txt
[2024-01-24 14:03:23,400] [INFO] Task started: fastANI
[2024-01-24 14:03:23,400] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6125767-71dd-488c-9c18-33daad00cfea/GCF_014655295.1_ASM1465529v1_genomic.fna.gz --refList GCF_014655295.1_ASM1465529v1_genomic.fna/target_genomes.txt --output GCF_014655295.1_ASM1465529v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:04:06,945] [INFO] Task succeeded: fastANI
[2024-01-24 14:04:06,946] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgace0a50b-1262-4257-9c42-42875d9a365b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:04:06,946] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgace0a50b-1262-4257-9c42-42875d9a365b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:04:06,973] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:04:06,974] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:04:06,974] [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 fumanus	strain=JCM 4477	GCA_014655295.1	67302	67302	type	True	100.0	2691	2695	95	conclusive
Streptomyces daghestanicus	strain=JCM 4365	GCA_014649475.1	66885	66885	suspected-type	True	88.0311	1810	2695	95	below_threshold
Streptomyces daghestanicus	strain=NBRC 12762	GCA_020521275.1	66885	66885	suspected-type	True	88.0017	1829	2695	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	87.1355	1754	2695	95	below_threshold
Streptomyces solaniscabiei	strain=FS70	GCA_020312315.1	2683255	2683255	type	True	87.0387	1702	2695	95	below_threshold
Streptomyces viridiviolaceus	strain=JCM 4855	GCA_014650995.1	68282	68282	type	True	86.9611	1746	2695	95	below_threshold
Streptomyces flaveolus	strain=JCM 4032	GCA_014648815.1	67297	67297	type	True	86.8954	1739	2695	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	86.5643	1548	2695	95	below_threshold
Streptomyces rubrogriseus	strain=NBRC 15455	GCA_003112595.1	194673	194673	type	True	86.5135	1776	2695	95	below_threshold
Streptomyces ardesiacus	strain=NBRC 15402	GCA_003112575.1	285564	285564	type	True	86.5038	1737	2695	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	85.6644	1693	2695	95	below_threshold
Streptomyces griseosporeus	strain=JCM 4766	GCA_014656055.1	1910	1910	type	True	85.5895	1689	2695	95	below_threshold
Streptomyces griseoflavus	strain=JCM 4479	GCA_014649995.1	35619	35619	type	True	85.3791	1599	2695	95	below_threshold
Streptomyces djakartensis	strain=JCM 4957	GCA_014651075.1	68193	68193	type	True	85.166	1555	2695	95	below_threshold
Streptomyces cahuitamycinicus	strain=13K301	GCA_002891435.1	2070367	2070367	type	True	85.053	1411	2695	95	below_threshold
Streptomyces rubradiris	strain=NBRC 14000	GCA_016860525.1	285531	285531	type	True	84.9521	1664	2695	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	84.5286	1493	2695	95	below_threshold
Embleya hyalina	strain=NBRC 13850	GCA_003967355.1	516124	516124	type	True	77.5484	1045	2695	95	below_threshold
Knoellia remsis	strain=ATCC BAA-1496	GCA_003002895.1	407159	407159	type	True	76.7851	344	2695	95	below_threshold
Nocardioides cynanchi	strain=SB3-45	GCA_008761635.1	2558918	2558918	type	True	76.578	447	2695	95	below_threshold
Pilimelia terevasa	strain=JCM 3091	GCA_014647915.1	53372	53372	type	True	76.1514	594	2695	95	below_threshold
Nakamurella leprariae	strain=YIM 132084	GCA_016918035.1	2803911	2803911	type	True	75.9841	480	2695	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:04:06,976] [INFO] DFAST Taxonomy check result was written to GCF_014655295.1_ASM1465529v1_genomic.fna/tc_result.tsv
[2024-01-24 14:04:06,976] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:04:06,976] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:04:06,977] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgace0a50b-1262-4257-9c42-42875d9a365b/dqc_reference/checkm_data
[2024-01-24 14:04:06,978] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:04:07,052] [INFO] Task started: CheckM
[2024-01-24 14:04:07,052] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014655295.1_ASM1465529v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014655295.1_ASM1465529v1_genomic.fna/checkm_input GCF_014655295.1_ASM1465529v1_genomic.fna/checkm_result
[2024-01-24 14:06:32,620] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:32,622] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:32,646] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:32,646] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:32,647] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014655295.1_ASM1465529v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:32,647] [INFO] Task started: Blastn
[2024-01-24 14:06:32,647] [INFO] Running command: blastn -query GCF_014655295.1_ASM1465529v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgace0a50b-1262-4257-9c42-42875d9a365b/dqc_reference/reference_markers_gtdb.fasta -out GCF_014655295.1_ASM1465529v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:34,949] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:34,954] [INFO] Selected 22 target genomes.
[2024-01-24 14:06:34,954] [INFO] Target genome list was writen to GCF_014655295.1_ASM1465529v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:34,969] [INFO] Task started: fastANI
[2024-01-24 14:06:34,969] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6125767-71dd-488c-9c18-33daad00cfea/GCF_014655295.1_ASM1465529v1_genomic.fna.gz --refList GCF_014655295.1_ASM1465529v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014655295.1_ASM1465529v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:22,122] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:22,143] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:22,144] [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_014655295.1	s__Streptomyces fumanus	100.0	2691	2695	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_018614415.1	s__Streptomyces sp018614415	88.0851	1745	2695	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014649155.1	s__Streptomyces griseoviridis	88.0388	1799	2695	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.52	99.48	0.96	0.96	3	-
GCF_014534645.1	s__Streptomyces sp014534645	87.1556	1751	2695	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002005565.1	s__Streptomyces sp002005565	87.0438	1650	2695	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248315.1	s__Streptomyces sp003248315	87.0068	1704	2695	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650995.1	s__Streptomyces viridiviolaceus	86.9628	1745	2695	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648815.1	s__Streptomyces flaveolus	86.9093	1738	2695	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905385.1	s__Streptomyces sp001905385	86.8472	1736	2695	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.01	96.01	0.83	0.83	2	-
GCF_000931445.1	s__Streptomyces cyaneogriseus	86.6827	1736	2695	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.603	N/A	N/A	N/A	N/A	1	-
GCF_003112595.1	s__Streptomyces rubrogriseus	86.515	1776	2695	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.9168	N/A	N/A	N/A	N/A	1	-
GCF_003112575.1	s__Streptomyces ardesiacus	86.5037	1737	2695	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.97	95.84	0.93	0.82	10	-
GCF_003112555.1	s__Streptomyces coelicoflavus	86.4337	1761	2695	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.84	97.03	0.90	0.86	6	-
GCF_000721605.1	s__Streptomyces sp000721605	85.9665	1680	2695	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018069565.1	s__Streptomyces sp018069565	85.9473	1546	2695	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001293595.1	s__Streptomyces sp001293595	85.7486	1528	2695	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.56	99.56	0.94	0.94	2	-
GCF_014656055.1	s__Streptomyces griseosporeus	85.5594	1692	2695	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.70	98.69	0.95	0.95	3	-
GCF_014651075.1	s__Streptomyces djakartensis	85.1988	1550	2695	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014596915.1	s__Streptomyces sp014596915	85.1335	1654	2695	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016860525.1	s__Streptomyces rubradiris	84.9085	1672	2695	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.184	99.99	99.99	1.00	1.00	2	-
GCF_011045025.1	s__Streptomyces ureilyticus	82.7288	1448	2695	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646055.1	s__Streptomyces_A tyrosinilyticus	79.7761	1107	2695	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:22,145] [INFO] GTDB search result was written to GCF_014655295.1_ASM1465529v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:22,146] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:22,151] [INFO] DFAST_QC result json was written to GCF_014655295.1_ASM1465529v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:22,152] [INFO] DFAST_QC completed!
[2024-01-24 14:07:22,152] [INFO] Total running time: 0h4m36s