[2024-01-24 14:02:50,593] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:02:50,601] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:02:50,601] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c87e008-b1e3-4d48-8b3b-efd6246a083c/dqc_reference
[2024-01-24 14:02:51,982] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:02:51,983] [INFO] Task started: Prodigal
[2024-01-24 14:02:51,984] [INFO] Running command: gunzip -c /var/lib/cwl/stg6c3395f3-3d23-4e73-a55d-0f6b165320be/GCF_014656155.1_ASM1465615v1_genomic.fna.gz | prodigal -d GCF_014656155.1_ASM1465615v1_genomic.fna/cds.fna -a GCF_014656155.1_ASM1465615v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:03:14,410] [INFO] Task succeeded: Prodigal
[2024-01-24 14:03:14,411] [INFO] Task started: HMMsearch
[2024-01-24 14:03:14,411] [INFO] Running command: hmmsearch --tblout GCF_014656155.1_ASM1465615v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c87e008-b1e3-4d48-8b3b-efd6246a083c/dqc_reference/reference_markers.hmm GCF_014656155.1_ASM1465615v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:03:14,825] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:03:14,827] [INFO] Found 6/6 markers.
[2024-01-24 14:03:14,887] [INFO] Query marker FASTA was written to GCF_014656155.1_ASM1465615v1_genomic.fna/markers.fasta
[2024-01-24 14:03:14,887] [INFO] Task started: Blastn
[2024-01-24 14:03:14,887] [INFO] Running command: blastn -query GCF_014656155.1_ASM1465615v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c87e008-b1e3-4d48-8b3b-efd6246a083c/dqc_reference/reference_markers.fasta -out GCF_014656155.1_ASM1465615v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:16,213] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:16,216] [INFO] Selected 17 target genomes.
[2024-01-24 14:03:16,216] [INFO] Target genome list was writen to GCF_014656155.1_ASM1465615v1_genomic.fna/target_genomes.txt
[2024-01-24 14:03:16,228] [INFO] Task started: fastANI
[2024-01-24 14:03:16,229] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c3395f3-3d23-4e73-a55d-0f6b165320be/GCF_014656155.1_ASM1465615v1_genomic.fna.gz --refList GCF_014656155.1_ASM1465615v1_genomic.fna/target_genomes.txt --output GCF_014656155.1_ASM1465615v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:03:49,975] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:49,975] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c87e008-b1e3-4d48-8b3b-efd6246a083c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:03:49,976] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c87e008-b1e3-4d48-8b3b-efd6246a083c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:03:49,996] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:03:49,996] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:03:49,996] [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 vinaceus	strain=JCM 4849	GCA_014656155.1	1960	1960	type	True	100.0	2661	2666	95	conclusive
Streptomyces vinaceus	strain=ATCC 27476	GCA_008704935.1	1960	1960	type	True	99.9946	2524	2666	95	conclusive
Streptomyces goshikiensis	strain=JCM 4640	GCA_014650555.1	1942	1942	type	True	87.8318	1853	2666	95	below_threshold
Streptomyces nojiriensis	strain=JCM 3382	GCA_014648615.1	66374	66374	type	True	87.5398	1893	2666	95	below_threshold
Streptomyces nojiriensis	strain=NBRC 13794	GCA_016755855.1	66374	66374	type	True	87.5007	1933	2666	95	below_threshold
Streptomyces nojiriensis	strain=JCM 3382	GCA_017639205.1	66374	66374	type	True	87.4535	1930	2666	95	below_threshold
Streptomyces spororaveus	strain=NBRC 15456	GCA_016755875.1	284039	284039	type	True	87.3659	1881	2666	95	below_threshold
Streptomyces avidinii	strain=JCM 4726	GCA_014650695.1	1895	1895	type	True	87.3358	1869	2666	95	below_threshold
Streptomyces virginiae	strain=NRRL ISP-5094	GCA_000720455.1	1961	1961	suspected-type	True	87.2746	1875	2666	95	below_threshold
Streptomyces avidinii	strain=DSM 40526	GCA_017874515.1	1895	1895	type	True	87.2668	1883	2666	95	below_threshold
Streptomyces amritsarensis	strain=MTCC 11845	GCA_001953875.1	681158	681158	type	True	87.017	1744	2666	95	below_threshold
Streptomyces yangpuensis	strain=fd2-tb	GCA_001005295.1	1648182	1648182	type	True	86.8756	1783	2666	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	82.0016	1342	2666	95	below_threshold
Streptomyces somaliensis	strain=DSM 40738	GCA_024349285.1	78355	78355	type	True	81.528	1042	2666	95	below_threshold
Streptomyces genisteinicus	strain=CRPJ-33	GCA_014489615.1	2768068	2768068	type	True	81.5194	1364	2666	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	81.4896	1064	2666	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	81.089	1156	2666	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:03:49,998] [INFO] DFAST Taxonomy check result was written to GCF_014656155.1_ASM1465615v1_genomic.fna/tc_result.tsv
[2024-01-24 14:03:49,999] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:03:49,999] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:03:49,999] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c87e008-b1e3-4d48-8b3b-efd6246a083c/dqc_reference/checkm_data
[2024-01-24 14:03:50,001] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:03:50,079] [INFO] Task started: CheckM
[2024-01-24 14:03:50,079] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014656155.1_ASM1465615v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014656155.1_ASM1465615v1_genomic.fna/checkm_input GCF_014656155.1_ASM1465615v1_genomic.fna/checkm_result
[2024-01-24 14:05:28,469] [INFO] Task succeeded: CheckM
[2024-01-24 14:05:28,471] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:05:28,497] [INFO] ===== Completeness check finished =====
[2024-01-24 14:05:28,497] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:05:28,498] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014656155.1_ASM1465615v1_genomic.fna/markers.fasta)
[2024-01-24 14:05:28,498] [INFO] Task started: Blastn
[2024-01-24 14:05:28,498] [INFO] Running command: blastn -query GCF_014656155.1_ASM1465615v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c87e008-b1e3-4d48-8b3b-efd6246a083c/dqc_reference/reference_markers_gtdb.fasta -out GCF_014656155.1_ASM1465615v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:30,654] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:30,668] [INFO] Selected 9 target genomes.
[2024-01-24 14:05:30,668] [INFO] Target genome list was writen to GCF_014656155.1_ASM1465615v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:05:30,683] [INFO] Task started: fastANI
[2024-01-24 14:05:30,683] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c3395f3-3d23-4e73-a55d-0f6b165320be/GCF_014656155.1_ASM1465615v1_genomic.fna.gz --refList GCF_014656155.1_ASM1465615v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014656155.1_ASM1465615v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:05:50,689] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:50,702] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:05:50,702] [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_008704935.1	s__Streptomyces vinaceus	99.9946	2524	2666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.65	97.63	0.95	0.92	5	conclusive
GCF_000717915.1	s__Streptomyces sp000717915	93.6334	2031	2666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.92	95.47	0.90	0.89	4	-
GCF_001044425.1	s__Streptomyces roseus	93.3917	2173	2666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720145.1	s__Streptomyces sp000720145	92.9685	2226	2666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000717655.1	s__Streptomyces katrae_B	91.0825	2064	2666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.60	96.50	0.86	0.86	4	-
GCA_001298555.1	s__Streptomyces sp001298555	90.6683	2013	2666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000725555.1	s__Streptomyces erythrochromogenes	87.6009	1722	2666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.80	95.80	0.85	0.85	2	-
GCF_017639205.1	s__Streptomyces nojiriensis	87.4393	1931	2666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	3	-
GCF_001005295.1	s__Streptomyces yangpuensis	86.9216	1776	2666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.05	95.28	0.86	0.84	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:05:50,704] [INFO] GTDB search result was written to GCF_014656155.1_ASM1465615v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:05:50,705] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:05:50,708] [INFO] DFAST_QC result json was written to GCF_014656155.1_ASM1465615v1_genomic.fna/dqc_result.json
[2024-01-24 14:05:50,708] [INFO] DFAST_QC completed!
[2024-01-24 14:05:50,708] [INFO] Total running time: 0h3m0s