[2024-01-25 17:43:50,487] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:43:50,488] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:43:50,488] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c8f2008-e3e2-491a-b317-ed18fc09ccda/dqc_reference
[2024-01-25 17:43:51,604] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:43:51,605] [INFO] Task started: Prodigal
[2024-01-25 17:43:51,605] [INFO] Running command: gunzip -c /var/lib/cwl/stga76be673-ef15-4f90-a498-9c057a555ca1/GCF_014649415.1_ASM1464941v1_genomic.fna.gz | prodigal -d GCF_014649415.1_ASM1464941v1_genomic.fna/cds.fna -a GCF_014649415.1_ASM1464941v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:44:09,922] [INFO] Task succeeded: Prodigal
[2024-01-25 17:44:09,923] [INFO] Task started: HMMsearch
[2024-01-25 17:44:09,923] [INFO] Running command: hmmsearch --tblout GCF_014649415.1_ASM1464941v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c8f2008-e3e2-491a-b317-ed18fc09ccda/dqc_reference/reference_markers.hmm GCF_014649415.1_ASM1464941v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:44:10,416] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:44:10,417] [INFO] Found 6/6 markers.
[2024-01-25 17:44:10,472] [INFO] Query marker FASTA was written to GCF_014649415.1_ASM1464941v1_genomic.fna/markers.fasta
[2024-01-25 17:44:10,472] [INFO] Task started: Blastn
[2024-01-25 17:44:10,473] [INFO] Running command: blastn -query GCF_014649415.1_ASM1464941v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c8f2008-e3e2-491a-b317-ed18fc09ccda/dqc_reference/reference_markers.fasta -out GCF_014649415.1_ASM1464941v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:44:11,722] [INFO] Task succeeded: Blastn
[2024-01-25 17:44:11,725] [INFO] Selected 17 target genomes.
[2024-01-25 17:44:11,725] [INFO] Target genome list was writen to GCF_014649415.1_ASM1464941v1_genomic.fna/target_genomes.txt
[2024-01-25 17:44:11,735] [INFO] Task started: fastANI
[2024-01-25 17:44:11,735] [INFO] Running command: fastANI --query /var/lib/cwl/stga76be673-ef15-4f90-a498-9c057a555ca1/GCF_014649415.1_ASM1464941v1_genomic.fna.gz --refList GCF_014649415.1_ASM1464941v1_genomic.fna/target_genomes.txt --output GCF_014649415.1_ASM1464941v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:44:44,261] [INFO] Task succeeded: fastANI
[2024-01-25 17:44:44,261] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c8f2008-e3e2-491a-b317-ed18fc09ccda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:44:44,262] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c8f2008-e3e2-491a-b317-ed18fc09ccda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:44:44,272] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:44:44,273] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 17:44:44,273] [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 badius	strain=JCM 4350	GCA_014649415.1	1941	1941	type	True	99.9998	2465	2473	95	inconclusive
Streptomyces sindenensis	strain=JCM 4164	GCA_014649035.1	67363	67363	type	True	95.8212	2100	2473	95	inconclusive
Streptomyces parvus	strain=JCM 4069	GCA_014648875.1	66428	66428	type	True	94.6657	2097	2473	95	below_threshold
Streptomyces parvus	strain=NRRL B-1455	GCA_008632535.1	66428	66428	type	True	94.5452	1892	2473	95	below_threshold
Streptomyces anulatus	strain=JCM 4721	GCA_014650675.1	1892	1892	type	True	91.7678	2033	2473	95	below_threshold
Streptomyces griseus	strain=DSM 40236	GCA_900105705.1	1911	1911	type	True	91.2989	2012	2473	95	below_threshold
Streptomyces californicus	strain=FDAARGOS_1209	GCA_016906185.1	67351	67351	type	True	90.2854	1936	2473	95	below_threshold
Streptomyces rhizosphaericola	strain=1AS2c	GCA_004794175.1	2564098	2564098	type	True	88.6887	1524	2473	95	below_threshold
[Kitasatospora] papulosa	strain=NRRL B-16504	GCA_000717245.1	1464011	1464011	type	True	84.573	1587	2473	95	below_threshold
Streptomyces nymphaeiformis	strain=SFB5A	GCA_014203895.1	2663842	2663842	type	True	82.7003	1385	2473	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	82.5857	1333	2473	95	below_threshold
Streptomyces genisteinicus	strain=CRPJ-33	GCA_014489615.1	2768068	2768068	type	True	82.369	1461	2473	95	below_threshold
Streptomyces spiralis	strain=JCM 3302	GCA_014654675.1	66376	66376	type	True	81.4504	1268	2473	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	81.1769	1190	2473	95	below_threshold
Actinacidiphila oryziradicis	strain=NEAU-C40	GCA_005047355.1	2571141	2571141	type	True	79.7536	1009	2473	95	below_threshold
Streptomyces xiaopingdaonensis	strain=DUT 180	GCA_000262345.1	1565415	1565415	type	True	79.3347	868	2473	95	below_threshold
Streptomyces sulphureus	strain=DSM 40104	GCA_000381025.1	47758	47758	type	True	79.2607	893	2473	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:44:44,274] [INFO] DFAST Taxonomy check result was written to GCF_014649415.1_ASM1464941v1_genomic.fna/tc_result.tsv
[2024-01-25 17:44:44,275] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:44:44,275] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:44:44,275] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c8f2008-e3e2-491a-b317-ed18fc09ccda/dqc_reference/checkm_data
[2024-01-25 17:44:44,276] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:44:44,347] [INFO] Task started: CheckM
[2024-01-25 17:44:44,348] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014649415.1_ASM1464941v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014649415.1_ASM1464941v1_genomic.fna/checkm_input GCF_014649415.1_ASM1464941v1_genomic.fna/checkm_result
[2024-01-25 17:46:09,788] [INFO] Task succeeded: CheckM
[2024-01-25 17:46:09,789] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:46:09,826] [INFO] ===== Completeness check finished =====
[2024-01-25 17:46:09,826] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:46:09,827] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014649415.1_ASM1464941v1_genomic.fna/markers.fasta)
[2024-01-25 17:46:09,827] [INFO] Task started: Blastn
[2024-01-25 17:46:09,827] [INFO] Running command: blastn -query GCF_014649415.1_ASM1464941v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c8f2008-e3e2-491a-b317-ed18fc09ccda/dqc_reference/reference_markers_gtdb.fasta -out GCF_014649415.1_ASM1464941v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:46:11,955] [INFO] Task succeeded: Blastn
[2024-01-25 17:46:11,959] [INFO] Selected 14 target genomes.
[2024-01-25 17:46:11,959] [INFO] Target genome list was writen to GCF_014649415.1_ASM1464941v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:46:11,968] [INFO] Task started: fastANI
[2024-01-25 17:46:11,968] [INFO] Running command: fastANI --query /var/lib/cwl/stga76be673-ef15-4f90-a498-9c057a555ca1/GCF_014649415.1_ASM1464941v1_genomic.fna.gz --refList GCF_014649415.1_ASM1464941v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014649415.1_ASM1464941v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:46:40,280] [INFO] Task succeeded: fastANI
[2024-01-25 17:46:40,293] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:46:40,293] [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_014649035.1	s__Streptomyces sindenensis	95.8112	2101	2473	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0775	95.83	95.78	0.85	0.84	5	conclusive
GCF_014648875.1	s__Streptomyces parvus	94.6663	2097	2473	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2347	97.39	96.11	0.86	0.79	24	-
GCF_001687325.1	s__Streptomyces sp001687325	94.4831	1993	2473	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649875.1	s__Streptomyces rubiginosohelvolus	94.3703	2047	2473	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.2941	98.09	96.67	0.91	0.87	22	-
GCF_003501885.1	s__Streptomyces globisporus_D	94.3509	1869	2473	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.6693	N/A	N/A	N/A	N/A	1	-
GCA_014649555.1	s__Streptomyces globisporus	94.2016	2030	2473	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.2941	98.88	97.57	0.92	0.86	14	-
GCF_000718455.1	s__Streptomyces globisporus_A	94.1356	1986	2473	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2621	N/A	N/A	N/A	N/A	1	-
GCA_002551355.1	s__Streptomyces sp002551355	92.6413	1960	2473	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001008345.1	s__Streptomyces showdoensis	82.6648	1351	2473	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418135.1	s__Streptomyces aureus_A	82.6253	1251	2473	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.5951	N/A	N/A	N/A	N/A	1	-
GCF_014650455.1	s__Streptomyces xanthochromogenes	82.6131	1335	2473	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.56	97.90	0.92	0.90	3	-
GCF_008704425.1	s__Streptomyces fradiae	81.9544	1281	2473	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.82	99.37	0.98	0.97	5	-
GCF_001279725.1	s__Streptomyces sp001279725	81.6751	1187	2473	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016598615.1	s__Streptomyces sp016598615	81.2964	1399	2473	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 17:46:40,295] [INFO] GTDB search result was written to GCF_014649415.1_ASM1464941v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:46:40,296] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:46:40,300] [INFO] DFAST_QC result json was written to GCF_014649415.1_ASM1464941v1_genomic.fna/dqc_result.json
[2024-01-25 17:46:40,300] [INFO] DFAST_QC completed!
[2024-01-25 17:46:40,300] [INFO] Total running time: 0h2m50s