[2024-01-24 14:46:35,373] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:35,375] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:35,376] [INFO] DQC Reference Directory: /var/lib/cwl/stge22a3eb1-eda2-4158-bddd-840c9109bd56/dqc_reference
[2024-01-24 14:46:36,567] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:36,567] [INFO] Task started: Prodigal
[2024-01-24 14:46:36,568] [INFO] Running command: gunzip -c /var/lib/cwl/stg558db9fe-2a77-4b96-9629-dd05fd24a4db/GCF_002154445.1_ASM215444v1_genomic.fna.gz | prodigal -d GCF_002154445.1_ASM215444v1_genomic.fna/cds.fna -a GCF_002154445.1_ASM215444v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:46:50,206] [INFO] Task succeeded: Prodigal
[2024-01-24 14:46:50,207] [INFO] Task started: HMMsearch
[2024-01-24 14:46:50,207] [INFO] Running command: hmmsearch --tblout GCF_002154445.1_ASM215444v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge22a3eb1-eda2-4158-bddd-840c9109bd56/dqc_reference/reference_markers.hmm GCF_002154445.1_ASM215444v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:46:50,568] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:46:50,570] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg558db9fe-2a77-4b96-9629-dd05fd24a4db/GCF_002154445.1_ASM215444v1_genomic.fna.gz]
[2024-01-24 14:46:50,627] [INFO] Query marker FASTA was written to GCF_002154445.1_ASM215444v1_genomic.fna/markers.fasta
[2024-01-24 14:46:50,628] [INFO] Task started: Blastn
[2024-01-24 14:46:50,628] [INFO] Running command: blastn -query GCF_002154445.1_ASM215444v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge22a3eb1-eda2-4158-bddd-840c9109bd56/dqc_reference/reference_markers.fasta -out GCF_002154445.1_ASM215444v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:46:52,043] [INFO] Task succeeded: Blastn
[2024-01-24 14:46:52,046] [INFO] Selected 20 target genomes.
[2024-01-24 14:46:52,047] [INFO] Target genome list was writen to GCF_002154445.1_ASM215444v1_genomic.fna/target_genomes.txt
[2024-01-24 14:46:52,056] [INFO] Task started: fastANI
[2024-01-24 14:46:52,057] [INFO] Running command: fastANI --query /var/lib/cwl/stg558db9fe-2a77-4b96-9629-dd05fd24a4db/GCF_002154445.1_ASM215444v1_genomic.fna.gz --refList GCF_002154445.1_ASM215444v1_genomic.fna/target_genomes.txt --output GCF_002154445.1_ASM215444v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:19,198] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:19,198] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge22a3eb1-eda2-4158-bddd-840c9109bd56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:19,199] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge22a3eb1-eda2-4158-bddd-840c9109bd56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:19,219] [INFO] Found 20 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 14:47:19,219] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:19,220] [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 fradiae	strain=NRRL B-1195	GCA_002154445.1	1906	1906	suspected-type	True	100.0	1290	1315	95	conclusive
Streptomyces fradiae	strain=ATCC 10745	GCA_008704425.1	1906	1906	suspected-type	True	99.912	1301	1315	95	conclusive
Streptomyces fradiae	strain=DSM 40063	GCA_002119225.1	1906	1906	suspected-type	True	99.9052	1302	1315	95	conclusive
Streptomyces fradiae	strain=ATCC 10745	GCA_009834665.1	1906	1906	suspected-type	True	99.8835	1299	1315	95	conclusive
Streptomyces roseolilacinus	strain=JCM 4335	GCA_014649335.1	66904	66904	type	True	89.3648	1020	1315	95	below_threshold
Streptomyces somaliensis	strain=DSM 40738	GCA_024349285.1	78355	78355	type	True	88.0366	893	1315	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	87.8399	913	1315	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	83.3894	857	1315	95	below_threshold
Streptomyces nymphaeiformis	strain=SFB5A	GCA_014203895.1	2663842	2663842	type	True	83.2159	853	1315	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	83.0502	820	1315	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	81.8929	836	1315	95	below_threshold
Streptomyces galilaeus	strain=ATCC 14969	GCA_008704575.1	33899	33899	type	True	81.6806	795	1315	95	below_threshold
Streptomyces bobili	strain=NRRL B-1338	GCA_002154575.1	67280	67280	type	True	81.6585	725	1315	95	below_threshold
Streptomyces galilaeus	strain=JCM 4757	GCA_014650835.1	33899	33899	type	True	81.4939	825	1315	95	below_threshold
Actinacidiphila guanduensis	strain=CGMCC 4.2022	GCA_900103985.1	310781	310781	type	True	80.1703	721	1315	95	below_threshold
Actinacidiphila paucisporea	strain=CGMCC 4.2025	GCA_900142575.1	310782	310782	type	True	80.0116	729	1315	95	below_threshold
Streptomyces sedi	strain=JCM 16909	GCA_006335015.1	555059	555059	type	True	79.1714	581	1315	95	below_threshold
Wenjunlia vitaminophila	strain=ATCC 31673	GCA_001445835.1	76728	76728	type	True	78.9766	578	1315	95	below_threshold
Wenjunlia vitaminophila	strain=DSM 41686	GCA_000380165.1	76728	76728	type	True	78.9476	570	1315	95	below_threshold
Microbacterium cremeum	strain=NY27	GCA_015277855.1	2782169	2782169	type	True	76.3814	185	1315	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:19,221] [INFO] DFAST Taxonomy check result was written to GCF_002154445.1_ASM215444v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:19,222] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:19,222] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:19,223] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge22a3eb1-eda2-4158-bddd-840c9109bd56/dqc_reference/checkm_data
[2024-01-24 14:47:19,224] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:19,290] [INFO] Task started: CheckM
[2024-01-24 14:47:19,291] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002154445.1_ASM215444v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002154445.1_ASM215444v1_genomic.fna/checkm_input GCF_002154445.1_ASM215444v1_genomic.fna/checkm_result
[2024-01-24 14:48:01,082] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:01,084] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:01,108] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:01,108] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:01,109] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002154445.1_ASM215444v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:01,109] [INFO] Task started: Blastn
[2024-01-24 14:48:01,109] [INFO] Running command: blastn -query GCF_002154445.1_ASM215444v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge22a3eb1-eda2-4158-bddd-840c9109bd56/dqc_reference/reference_markers_gtdb.fasta -out GCF_002154445.1_ASM215444v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:03,482] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:03,486] [INFO] Selected 17 target genomes.
[2024-01-24 14:48:03,487] [INFO] Target genome list was writen to GCF_002154445.1_ASM215444v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:03,501] [INFO] Task started: fastANI
[2024-01-24 14:48:03,501] [INFO] Running command: fastANI --query /var/lib/cwl/stg558db9fe-2a77-4b96-9629-dd05fd24a4db/GCF_002154445.1_ASM215444v1_genomic.fna.gz --refList GCF_002154445.1_ASM215444v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002154445.1_ASM215444v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:27,147] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:27,166] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:27,166] [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_008704425.1	s__Streptomyces fradiae	99.912	1301	1315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.82	99.37	0.98	0.97	5	conclusive
GCF_000478605.2	s__Streptomyces thermolilacinus	89.9774	1036	1315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649335.1	s__Streptomyces roseolilacinus	89.3358	1022	1315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012396115.1	s__Streptomyces somaliensis	88.1976	774	1315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000258595.1	s__Streptomyces somaliensis_A	87.8944	871	1315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001484625.1	s__Streptomyces kanasensis	86.7535	974	1315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927245.1	s__Streptomyces sp012927245	83.362	875	1315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014656075.1	s__Streptomyces hydrogenans	83.0077	882	1315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.17	97.53	0.88	0.87	3	-
GCF_013387495.1	s__Streptomyces sp013387495	82.9793	802	1315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103455.1	s__Streptomyces wuyuanensis	82.9462	824	1315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011694815.1	s__Streptomyces liangshanensis	81.9799	787	1315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008042275.1	s__Streptomyces sp008042275	81.8739	810	1315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002154575.1	s__Streptomyces bobili	81.6956	721	1315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.61	97.61	0.88	0.85	3	-
GCF_007595705.1	s__Streptomyces sp007595705	81.3704	762	1315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006335015.1	s__Streptomyces sedi	79.1403	587	1315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015277855.1	s__Microbacterium sp015277855	76.3536	188	1315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001476285.1	s__Microbacterium testaceum_B	76.1683	159	1315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.43	98.38	0.88	0.88	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:27,168] [INFO] GTDB search result was written to GCF_002154445.1_ASM215444v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:27,169] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:27,176] [INFO] DFAST_QC result json was written to GCF_002154445.1_ASM215444v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:27,176] [INFO] DFAST_QC completed!
[2024-01-24 14:48:27,176] [INFO] Total running time: 0h1m52s