[2024-01-25 18:15:20,792] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:15:20,793] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:15:20,794] [INFO] DQC Reference Directory: /var/lib/cwl/stg593d0a33-ba2c-4bf2-9016-497f94986a53/dqc_reference
[2024-01-25 18:15:21,935] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:15:21,936] [INFO] Task started: Prodigal
[2024-01-25 18:15:21,936] [INFO] Running command: gunzip -c /var/lib/cwl/stgc0454043-bfbd-4b48-99bb-f3ef23d23e61/GCF_002811705.1_ASM281170v2_genomic.fna.gz | prodigal -d GCF_002811705.1_ASM281170v2_genomic.fna/cds.fna -a GCF_002811705.1_ASM281170v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:15:36,915] [INFO] Task succeeded: Prodigal
[2024-01-25 18:15:36,915] [INFO] Task started: HMMsearch
[2024-01-25 18:15:36,915] [INFO] Running command: hmmsearch --tblout GCF_002811705.1_ASM281170v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg593d0a33-ba2c-4bf2-9016-497f94986a53/dqc_reference/reference_markers.hmm GCF_002811705.1_ASM281170v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:15:37,229] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:15:37,230] [INFO] Found 6/6 markers.
[2024-01-25 18:15:37,281] [INFO] Query marker FASTA was written to GCF_002811705.1_ASM281170v2_genomic.fna/markers.fasta
[2024-01-25 18:15:37,281] [INFO] Task started: Blastn
[2024-01-25 18:15:37,281] [INFO] Running command: blastn -query GCF_002811705.1_ASM281170v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg593d0a33-ba2c-4bf2-9016-497f94986a53/dqc_reference/reference_markers.fasta -out GCF_002811705.1_ASM281170v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:15:38,561] [INFO] Task succeeded: Blastn
[2024-01-25 18:15:38,564] [INFO] Selected 15 target genomes.
[2024-01-25 18:15:38,564] [INFO] Target genome list was writen to GCF_002811705.1_ASM281170v2_genomic.fna/target_genomes.txt
[2024-01-25 18:15:38,580] [INFO] Task started: fastANI
[2024-01-25 18:15:38,580] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0454043-bfbd-4b48-99bb-f3ef23d23e61/GCF_002811705.1_ASM281170v2_genomic.fna.gz --refList GCF_002811705.1_ASM281170v2_genomic.fna/target_genomes.txt --output GCF_002811705.1_ASM281170v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:16:05,386] [INFO] Task succeeded: fastANI
[2024-01-25 18:16:05,386] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg593d0a33-ba2c-4bf2-9016-497f94986a53/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:16:05,387] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg593d0a33-ba2c-4bf2-9016-497f94986a53/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:16:05,398] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 18:16:05,398] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 18:16:05,398] [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 barkulensis	strain=RC 1831	GCA_002811705.2	1257026	1257026	type	True	100.0	2076	2079	95	inconclusive
Streptomyces barkulensis	strain=RC 1831	GCA_002843305.1	1257026	1257026	type	True	99.9203	2051	2079	95	inconclusive
Streptomyces pini	strain=PL19	GCA_900114215.1	1520580	1520580	type	True	96.7296	1814	2079	95	inconclusive
Streptomyces verrucosisporus	strain=CPB1-1	GCA_017114865.1	1695161	1695161	type	True	94.9854	1646	2079	95	below_threshold
Streptomyces radiopugnans	strain=CGMCC 4.3519	GCA_900110735.1	403935	403935	type	True	93.8018	1678	2079	95	below_threshold
Streptomyces taklimakanensis	strain=TRM43335	GCA_009709575.1	2569853	2569853	type	True	87.312	1470	2079	95	below_threshold
Streptomyces megasporus	strain=NRRL B-16372	GCA_000718985.1	44060	44060	type	True	87.2991	1363	2079	95	below_threshold
Streptomyces carminius	strain=TRM SA0054	GCA_002794255.1	2665496	2665496	type	True	86.7375	1454	2079	95	below_threshold
Streptomyces griseocarneus	strain=JCM 4580	GCA_014655595.1	51201	51201	type	True	81.361	1031	2079	95	below_threshold
Streptomyces gobiensis	strain=1_25	GCA_021216675.1	2875706	2875706	type	True	81.2223	959	2079	95	below_threshold
Streptomyces thermodiastaticus	strain=DSM 40573	GCA_021394575.1	44061	44061	type	True	81.0575	1023	2079	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	80.892	1133	2079	95	below_threshold
Streptomyces cacaoi	strain=NRRL B-1220	GCA_002154495.1	1898	1898	type	True	80.5575	927	2079	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	80.4727	1212	2079	95	below_threshold
Streptomyces ferrugineus	strain=CCTCC AA2014009	GCA_015160855.1	1413221	1413221	type	True	80.3835	1114	2079	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:16:05,404] [INFO] DFAST Taxonomy check result was written to GCF_002811705.1_ASM281170v2_genomic.fna/tc_result.tsv
[2024-01-25 18:16:05,405] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:16:05,405] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:16:05,405] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg593d0a33-ba2c-4bf2-9016-497f94986a53/dqc_reference/checkm_data
[2024-01-25 18:16:05,406] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:16:05,470] [INFO] Task started: CheckM
[2024-01-25 18:16:05,470] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002811705.1_ASM281170v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002811705.1_ASM281170v2_genomic.fna/checkm_input GCF_002811705.1_ASM281170v2_genomic.fna/checkm_result
[2024-01-25 18:17:14,934] [INFO] Task succeeded: CheckM
[2024-01-25 18:17:14,938] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:17:14,957] [INFO] ===== Completeness check finished =====
[2024-01-25 18:17:14,958] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:17:14,959] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002811705.1_ASM281170v2_genomic.fna/markers.fasta)
[2024-01-25 18:17:14,959] [INFO] Task started: Blastn
[2024-01-25 18:17:14,959] [INFO] Running command: blastn -query GCF_002811705.1_ASM281170v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg593d0a33-ba2c-4bf2-9016-497f94986a53/dqc_reference/reference_markers_gtdb.fasta -out GCF_002811705.1_ASM281170v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:17:17,049] [INFO] Task succeeded: Blastn
[2024-01-25 18:17:17,052] [INFO] Selected 11 target genomes.
[2024-01-25 18:17:17,052] [INFO] Target genome list was writen to GCF_002811705.1_ASM281170v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:17:17,079] [INFO] Task started: fastANI
[2024-01-25 18:17:17,079] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0454043-bfbd-4b48-99bb-f3ef23d23e61/GCF_002811705.1_ASM281170v2_genomic.fna.gz --refList GCF_002811705.1_ASM281170v2_genomic.fna/target_genomes_gtdb.txt --output GCF_002811705.1_ASM281170v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:17:38,545] [INFO] Task succeeded: fastANI
[2024-01-25 18:17:38,553] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:17:38,553] [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_002843305.1	s__Streptomyces barkulensis	99.9203	2051	2079	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.765	99.92	99.92	0.99	0.99	2	conclusive
GCF_900114215.1	s__Streptomyces pini	96.7296	1814	2079	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.765	N/A	N/A	N/A	N/A	1	-
GCF_017114865.1	s__Streptomyces verrucosisporus	94.9729	1647	2079	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.1585	N/A	N/A	N/A	N/A	1	-
GCF_900110735.1	s__Streptomyces radiopugnans	93.8314	1675	2079	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718985.1	s__Streptomyces megasporus	87.3412	1358	2079	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009709575.1	s__Streptomyces taklimakanensis	87.3147	1471	2079	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002794255.1	s__Streptomyces carminius	86.7551	1446	2079	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013302895.1	s__Streptomyces chlorinus	81.2017	1024	2079	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539165.1	s__Streptomyces cacaoi	80.4194	1073	2079	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.44	99.09	0.96	0.94	7	-
GCF_015160855.1	s__Streptomyces ferrugineus	80.3886	1114	2079	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013450295.1	s__Streptomyces sp013450295	80.2925	969	2079	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:17:38,554] [INFO] GTDB search result was written to GCF_002811705.1_ASM281170v2_genomic.fna/result_gtdb.tsv
[2024-01-25 18:17:38,555] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:17:38,559] [INFO] DFAST_QC result json was written to GCF_002811705.1_ASM281170v2_genomic.fna/dqc_result.json
[2024-01-25 18:17:38,559] [INFO] DFAST_QC completed!
[2024-01-25 18:17:38,559] [INFO] Total running time: 0h2m18s