[2024-01-24 15:02:36,366] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:36,369] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:36,369] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e7456b8-c32c-4df0-b0df-02f8130cff85/dqc_reference
[2024-01-24 15:02:38,278] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:38,279] [INFO] Task started: Prodigal
[2024-01-24 15:02:38,280] [INFO] Running command: gunzip -c /var/lib/cwl/stg1f4a4e81-3d85-45d2-8437-7bee44cbb16f/GCF_016755855.1_ASM1675585v1_genomic.fna.gz | prodigal -d GCF_016755855.1_ASM1675585v1_genomic.fna/cds.fna -a GCF_016755855.1_ASM1675585v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:03:05,592] [INFO] Task succeeded: Prodigal
[2024-01-24 15:03:05,593] [INFO] Task started: HMMsearch
[2024-01-24 15:03:05,593] [INFO] Running command: hmmsearch --tblout GCF_016755855.1_ASM1675585v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e7456b8-c32c-4df0-b0df-02f8130cff85/dqc_reference/reference_markers.hmm GCF_016755855.1_ASM1675585v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:03:06,045] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:03:06,047] [INFO] Found 6/6 markers.
[2024-01-24 15:03:06,124] [INFO] Query marker FASTA was written to GCF_016755855.1_ASM1675585v1_genomic.fna/markers.fasta
[2024-01-24 15:03:06,124] [INFO] Task started: Blastn
[2024-01-24 15:03:06,124] [INFO] Running command: blastn -query GCF_016755855.1_ASM1675585v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e7456b8-c32c-4df0-b0df-02f8130cff85/dqc_reference/reference_markers.fasta -out GCF_016755855.1_ASM1675585v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:07,487] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:07,491] [INFO] Selected 11 target genomes.
[2024-01-24 15:03:07,491] [INFO] Target genome list was writen to GCF_016755855.1_ASM1675585v1_genomic.fna/target_genomes.txt
[2024-01-24 15:03:07,500] [INFO] Task started: fastANI
[2024-01-24 15:03:07,501] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f4a4e81-3d85-45d2-8437-7bee44cbb16f/GCF_016755855.1_ASM1675585v1_genomic.fna.gz --refList GCF_016755855.1_ASM1675585v1_genomic.fna/target_genomes.txt --output GCF_016755855.1_ASM1675585v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:35,575] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:35,576] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e7456b8-c32c-4df0-b0df-02f8130cff85/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:35,576] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e7456b8-c32c-4df0-b0df-02f8130cff85/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:35,593] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 15:03:35,593] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:35,593] [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 nojiriensis	strain=NBRC 13794	GCA_016755855.1	66374	66374	type	True	100.0	3008	3014	95	conclusive
Streptomyces nojiriensis	strain=JCM 3382	GCA_017639205.1	66374	66374	type	True	99.9993	2994	3014	95	conclusive
Streptomyces nojiriensis	strain=JCM 3382	GCA_014648615.1	66374	66374	type	True	99.9849	2930	3014	95	conclusive
Streptomyces spororaveus	strain=NBRC 15456	GCA_016755875.1	284039	284039	type	True	93.4911	2322	3014	95	below_threshold
Streptomyces avidinii	strain=DSM 40526	GCA_017874515.1	1895	1895	type	True	92.1379	2228	3014	95	below_threshold
Streptomyces virginiae	strain=NRRL ISP-5094	GCA_000720455.1	1961	1961	suspected-type	True	89.6426	2118	3014	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	82.0307	1387	3014	95	below_threshold
Streptomyces somaliensis	strain=DSM 40738	GCA_024349285.1	78355	78355	type	True	81.5904	1040	3014	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	81.4387	1337	3014	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	81.2989	1263	3014	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	81.0757	1178	3014	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:35,595] [INFO] DFAST Taxonomy check result was written to GCF_016755855.1_ASM1675585v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:35,596] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:35,596] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:35,596] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e7456b8-c32c-4df0-b0df-02f8130cff85/dqc_reference/checkm_data
[2024-01-24 15:03:35,597] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:35,686] [INFO] Task started: CheckM
[2024-01-24 15:03:35,687] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016755855.1_ASM1675585v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016755855.1_ASM1675585v1_genomic.fna/checkm_input GCF_016755855.1_ASM1675585v1_genomic.fna/checkm_result
[2024-01-24 15:05:43,265] [INFO] Task succeeded: CheckM
[2024-01-24 15:05:43,267] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:05:43,293] [INFO] ===== Completeness check finished =====
[2024-01-24 15:05:43,294] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:05:43,294] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016755855.1_ASM1675585v1_genomic.fna/markers.fasta)
[2024-01-24 15:05:43,295] [INFO] Task started: Blastn
[2024-01-24 15:05:43,295] [INFO] Running command: blastn -query GCF_016755855.1_ASM1675585v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e7456b8-c32c-4df0-b0df-02f8130cff85/dqc_reference/reference_markers_gtdb.fasta -out GCF_016755855.1_ASM1675585v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:05:45,443] [INFO] Task succeeded: Blastn
[2024-01-24 15:05:45,446] [INFO] Selected 10 target genomes.
[2024-01-24 15:05:45,446] [INFO] Target genome list was writen to GCF_016755855.1_ASM1675585v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:05:45,471] [INFO] Task started: fastANI
[2024-01-24 15:05:45,472] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f4a4e81-3d85-45d2-8437-7bee44cbb16f/GCF_016755855.1_ASM1675585v1_genomic.fna.gz --refList GCF_016755855.1_ASM1675585v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016755855.1_ASM1675585v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:06:11,389] [INFO] Task succeeded: fastANI
[2024-01-24 15:06:11,404] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:06:11,405] [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_017639205.1	s__Streptomyces nojiriensis	99.9993	2995	3014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCF_016755875.1	s__Streptomyces spororaveus	93.4845	2325	3014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008642275.1	s__Streptomyces venezuelae_E	93.4576	2238	3014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716685.1	s__Streptomyces virginiae_A	93.3731	2327	3014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.46	95.91	0.89	0.84	3	-
GCF_003148825.1	s__Streptomyces sp003148825	92.9317	2330	3014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.84	95.84	0.87	0.86	3	-
GCF_002080455.1	s__Streptomyces sp002080455	92.332	2243	3014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.34	98.21	0.92	0.90	7	-
GCF_000725555.1	s__Streptomyces erythrochromogenes	89.9931	1966	3014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.80	95.80	0.85	0.85	2	-
GCF_014648795.1	s__Streptomyces cinnamonensis	89.5633	2088	3014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.18	96.61	0.93	0.87	24	-
GCF_001005295.1	s__Streptomyces yangpuensis	89.2181	2023	3014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.05	95.28	0.86	0.84	3	-
GCF_000612545.1	s__Streptomyces sp000612545	88.6182	1929	3014	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 15:06:11,406] [INFO] GTDB search result was written to GCF_016755855.1_ASM1675585v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:06:11,407] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:06:11,410] [INFO] DFAST_QC result json was written to GCF_016755855.1_ASM1675585v1_genomic.fna/dqc_result.json
[2024-01-24 15:06:11,410] [INFO] DFAST_QC completed!
[2024-01-24 15:06:11,410] [INFO] Total running time: 0h3m35s