[2024-01-24 13:17:32,215] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:32,217] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:32,218] [INFO] DQC Reference Directory: /var/lib/cwl/stgdaef7d29-6e32-43be-bd32-2d482bf3b572/dqc_reference
[2024-01-24 13:17:33,503] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:33,504] [INFO] Task started: Prodigal
[2024-01-24 13:17:33,504] [INFO] Running command: gunzip -c /var/lib/cwl/stg5cfa1203-308d-4c7c-8048-7cf714b87831/GCF_004794175.1_ASM479417v1_genomic.fna.gz | prodigal -d GCF_004794175.1_ASM479417v1_genomic.fna/cds.fna -a GCF_004794175.1_ASM479417v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:50,120] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:50,120] [INFO] Task started: HMMsearch
[2024-01-24 13:17:50,120] [INFO] Running command: hmmsearch --tblout GCF_004794175.1_ASM479417v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdaef7d29-6e32-43be-bd32-2d482bf3b572/dqc_reference/reference_markers.hmm GCF_004794175.1_ASM479417v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:50,480] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:50,481] [INFO] Found 6/6 markers.
[2024-01-24 13:17:50,537] [INFO] Query marker FASTA was written to GCF_004794175.1_ASM479417v1_genomic.fna/markers.fasta
[2024-01-24 13:17:50,537] [INFO] Task started: Blastn
[2024-01-24 13:17:50,537] [INFO] Running command: blastn -query GCF_004794175.1_ASM479417v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdaef7d29-6e32-43be-bd32-2d482bf3b572/dqc_reference/reference_markers.fasta -out GCF_004794175.1_ASM479417v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:51,851] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:51,855] [INFO] Selected 14 target genomes.
[2024-01-24 13:17:51,856] [INFO] Target genome list was writen to GCF_004794175.1_ASM479417v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:51,862] [INFO] Task started: fastANI
[2024-01-24 13:17:51,863] [INFO] Running command: fastANI --query /var/lib/cwl/stg5cfa1203-308d-4c7c-8048-7cf714b87831/GCF_004794175.1_ASM479417v1_genomic.fna.gz --refList GCF_004794175.1_ASM479417v1_genomic.fna/target_genomes.txt --output GCF_004794175.1_ASM479417v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:17,027] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:17,027] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdaef7d29-6e32-43be-bd32-2d482bf3b572/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:17,028] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdaef7d29-6e32-43be-bd32-2d482bf3b572/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:17,044] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:18:17,044] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:18:17,044] [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 rhizosphaericola	strain=1AS2c	GCA_004794175.1	2564098	2564098	type	True	100.0	1983	2003	95	inconclusive
Streptomyces cavourensis	strain=DSM 41795	GCA_006788935.1	67258	67258	type	True	95.7294	1851	2003	95	inconclusive
Streptomyces cavourensis	strain=JCM 4298	GCA_014649215.1	67258	67258	type	True	95.7274	1823	2003	95	inconclusive
Streptomyces microflavus	strain=JCM 4496	GCA_014650075.1	1919	1919	type	True	91.5042	1726	2003	95	below_threshold
Streptomyces sindenensis	strain=JCM 4164	GCA_014649035.1	67363	67363	type	True	88.9657	1545	2003	95	below_threshold
Streptomyces parvus	strain=NRRL B-1455	GCA_008632535.1	66428	66428	type	True	88.9546	1492	2003	95	below_threshold
Streptomyces parvus	strain=JCM 4069	GCA_014648875.1	66428	66428	type	True	88.9393	1608	2003	95	below_threshold
Streptomyces anulatus	strain=JCM 4721	GCA_014650675.1	1892	1892	type	True	88.851	1602	2003	95	below_threshold
Streptomyces californicus	strain=FDAARGOS_1209	GCA_016906185.1	67351	67351	type	True	88.339	1580	2003	95	below_threshold
Streptomyces californicus	strain=NRRL B-2098	GCA_000717645.1	67351	67351	type	True	88.29	1569	2003	95	below_threshold
[Kitasatospora] papulosa	strain=NRRL B-16504	GCA_000717245.1	1464011	1464011	type	True	84.6085	1337	2003	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	82.799	1199	2003	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	82.3426	927	2003	95	below_threshold
Streptomyces somaliensis	strain=DSM 40738	GCA_024349285.1	78355	78355	type	True	82.1892	916	2003	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:17,046] [INFO] DFAST Taxonomy check result was written to GCF_004794175.1_ASM479417v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:17,047] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:17,047] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:17,047] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdaef7d29-6e32-43be-bd32-2d482bf3b572/dqc_reference/checkm_data
[2024-01-24 13:18:17,048] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:17,234] [INFO] Task started: CheckM
[2024-01-24 13:18:17,234] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004794175.1_ASM479417v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004794175.1_ASM479417v1_genomic.fna/checkm_input GCF_004794175.1_ASM479417v1_genomic.fna/checkm_result
[2024-01-24 13:19:12,903] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:12,905] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:12,928] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:12,929] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:12,929] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004794175.1_ASM479417v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:12,929] [INFO] Task started: Blastn
[2024-01-24 13:19:12,930] [INFO] Running command: blastn -query GCF_004794175.1_ASM479417v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdaef7d29-6e32-43be-bd32-2d482bf3b572/dqc_reference/reference_markers_gtdb.fasta -out GCF_004794175.1_ASM479417v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:15,007] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:15,012] [INFO] Selected 13 target genomes.
[2024-01-24 13:19:15,012] [INFO] Target genome list was writen to GCF_004794175.1_ASM479417v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:15,023] [INFO] Task started: fastANI
[2024-01-24 13:19:15,023] [INFO] Running command: fastANI --query /var/lib/cwl/stg5cfa1203-308d-4c7c-8048-7cf714b87831/GCF_004794175.1_ASM479417v1_genomic.fna.gz --refList GCF_004794175.1_ASM479417v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004794175.1_ASM479417v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:38,561] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:38,572] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:38,573] [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
GCA_003268675.1	s__Streptomyces bacillaris	95.854	1805	2003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.84	95.80	0.88	0.83	37	conclusive
GCF_002082585.1	s__Streptomyces albolongus	91.8355	1659	2003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718135.1	s__Streptomyces cyaneofuscatus	91.6739	1711	2003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.78	95.81	0.91	0.85	12	-
GCF_003610995.1	s__Streptomyces sp003116725	91.607	1672	2003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.40	95.27	0.92	0.85	7	-
GCF_014650075.1	s__Streptomyces microflavus	91.494	1726	2003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.25	97.27	0.91	0.85	13	-
GCF_001905595.1	s__Streptomyces sp001905595	91.0711	1590	2003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.40	99.32	0.92	0.90	4	-
GCF_001687325.1	s__Streptomyces sp001687325	89.3542	1579	2003	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	89.2428	1596	2003	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	88.9786	1462	2003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.6693	N/A	N/A	N/A	N/A	1	-
GCF_014649035.1	s__Streptomyces sindenensis	88.9763	1544	2003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0775	95.83	95.78	0.85	0.84	5	-
GCF_014648875.1	s__Streptomyces parvus	88.9646	1605	2003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2347	97.39	96.11	0.86	0.79	24	-
GCA_002551355.1	s__Streptomyces sp002551355	88.9322	1565	2003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002382885.1	s__Streptomyces sp002382885	88.8895	1487	2003	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 13:19:38,574] [INFO] GTDB search result was written to GCF_004794175.1_ASM479417v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:38,575] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:38,578] [INFO] DFAST_QC result json was written to GCF_004794175.1_ASM479417v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:38,578] [INFO] DFAST_QC completed!
[2024-01-24 13:19:38,578] [INFO] Total running time: 0h2m6s