[2024-01-24 12:46:49,364] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:46:49,366] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:46:49,366] [INFO] DQC Reference Directory: /var/lib/cwl/stge6ee06f8-64a1-4230-a497-e87e882522f3/dqc_reference
[2024-01-24 12:46:50,567] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:46:50,568] [INFO] Task started: Prodigal
[2024-01-24 12:46:50,568] [INFO] Running command: gunzip -c /var/lib/cwl/stg8739c578-ff34-4094-99e4-62312490560a/GCF_009834665.1_ASM983466v1_genomic.fna.gz | prodigal -d GCF_009834665.1_ASM983466v1_genomic.fna/cds.fna -a GCF_009834665.1_ASM983466v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:08,601] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:08,602] [INFO] Task started: HMMsearch
[2024-01-24 12:47:08,602] [INFO] Running command: hmmsearch --tblout GCF_009834665.1_ASM983466v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge6ee06f8-64a1-4230-a497-e87e882522f3/dqc_reference/reference_markers.hmm GCF_009834665.1_ASM983466v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:08,880] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:08,883] [INFO] Found 6/6 markers.
[2024-01-24 12:47:08,937] [INFO] Query marker FASTA was written to GCF_009834665.1_ASM983466v1_genomic.fna/markers.fasta
[2024-01-24 12:47:08,938] [INFO] Task started: Blastn
[2024-01-24 12:47:08,938] [INFO] Running command: blastn -query GCF_009834665.1_ASM983466v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6ee06f8-64a1-4230-a497-e87e882522f3/dqc_reference/reference_markers.fasta -out GCF_009834665.1_ASM983466v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:10,265] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:10,270] [INFO] Selected 20 target genomes.
[2024-01-24 12:47:10,270] [INFO] Target genome list was writen to GCF_009834665.1_ASM983466v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:10,278] [INFO] Task started: fastANI
[2024-01-24 12:47:10,278] [INFO] Running command: fastANI --query /var/lib/cwl/stg8739c578-ff34-4094-99e4-62312490560a/GCF_009834665.1_ASM983466v1_genomic.fna.gz --refList GCF_009834665.1_ASM983466v1_genomic.fna/target_genomes.txt --output GCF_009834665.1_ASM983466v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:44,348] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:44,349] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge6ee06f8-64a1-4230-a497-e87e882522f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:44,349] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge6ee06f8-64a1-4230-a497-e87e882522f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:44,364] [INFO] Found 20 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 12:47:44,364] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:44,364] [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=ATCC 10745	GCA_009834665.1	1906	1906	suspected-type	True	100.0	2224	2290	95	conclusive
Streptomyces fradiae	strain=ATCC 10745	GCA_008704425.1	1906	1906	suspected-type	True	99.975	2176	2290	95	conclusive
Streptomyces fradiae	strain=DSM 40063	GCA_002119225.1	1906	1906	suspected-type	True	99.8194	1976	2290	95	conclusive
Streptomyces fradiae	strain=NRRL B-1195	GCA_002154445.1	1906	1906	suspected-type	True	99.3682	1279	2290	95	conclusive
Streptomyces roseolilacinus	strain=JCM 4335	GCA_014649335.1	66904	66904	type	True	89.0417	1656	2290	95	below_threshold
Streptomyces somaliensis	strain=DSM 40738	GCA_024349285.1	78355	78355	type	True	88.1027	1318	2290	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	87.9869	1358	2290	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	82.9723	1328	2290	95	below_threshold
Streptomyces nymphaeiformis	strain=SFB5A	GCA_014203895.1	2663842	2663842	type	True	82.6075	1341	2290	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	82.4655	1271	2290	95	below_threshold
Streptomyces bobili	strain=NRRL B-1338	GCA_002154575.1	67280	67280	type	True	81.2784	1027	2290	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	81.237	1312	2290	95	below_threshold
Streptomyces galilaeus	strain=ATCC 14969	GCA_008704575.1	33899	33899	type	True	81.2168	1231	2290	95	below_threshold
Streptomyces galilaeus	strain=JCM 4757	GCA_014650835.1	33899	33899	type	True	81.1307	1257	2290	95	below_threshold
Actinacidiphila guanduensis	strain=CGMCC 4.2022	GCA_900103985.1	310781	310781	type	True	79.8374	1070	2290	95	below_threshold
Actinacidiphila paucisporea	strain=CGMCC 4.2025	GCA_900142575.1	310782	310782	type	True	79.706	1060	2290	95	below_threshold
Streptomyces sedi	strain=JCM 16909	GCA_006335015.1	555059	555059	type	True	78.8016	889	2290	95	below_threshold
Wenjunlia vitaminophila	strain=DSM 41686	GCA_000380165.1	76728	76728	type	True	78.5928	850	2290	95	below_threshold
Wenjunlia vitaminophila	strain=ATCC 31673	GCA_001445835.1	76728	76728	type	True	78.5901	848	2290	95	below_threshold
Microbacterium cremeum	strain=NY27	GCA_015277855.1	2782169	2782169	type	True	75.8572	297	2290	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:44,366] [INFO] DFAST Taxonomy check result was written to GCF_009834665.1_ASM983466v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:44,368] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:44,368] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:44,368] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge6ee06f8-64a1-4230-a497-e87e882522f3/dqc_reference/checkm_data
[2024-01-24 12:47:44,369] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:44,442] [INFO] Task started: CheckM
[2024-01-24 12:47:44,442] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009834665.1_ASM983466v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009834665.1_ASM983466v1_genomic.fna/checkm_input GCF_009834665.1_ASM983466v1_genomic.fna/checkm_result
[2024-01-24 12:49:12,513] [INFO] Task succeeded: CheckM
[2024-01-24 12:49:12,514] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:49:12,535] [INFO] ===== Completeness check finished =====
[2024-01-24 12:49:12,536] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:49:12,536] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009834665.1_ASM983466v1_genomic.fna/markers.fasta)
[2024-01-24 12:49:12,536] [INFO] Task started: Blastn
[2024-01-24 12:49:12,537] [INFO] Running command: blastn -query GCF_009834665.1_ASM983466v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6ee06f8-64a1-4230-a497-e87e882522f3/dqc_reference/reference_markers_gtdb.fasta -out GCF_009834665.1_ASM983466v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:49:14,668] [INFO] Task succeeded: Blastn
[2024-01-24 12:49:14,671] [INFO] Selected 17 target genomes.
[2024-01-24 12:49:14,671] [INFO] Target genome list was writen to GCF_009834665.1_ASM983466v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:49:14,682] [INFO] Task started: fastANI
[2024-01-24 12:49:14,683] [INFO] Running command: fastANI --query /var/lib/cwl/stg8739c578-ff34-4094-99e4-62312490560a/GCF_009834665.1_ASM983466v1_genomic.fna.gz --refList GCF_009834665.1_ASM983466v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009834665.1_ASM983466v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:49:42,435] [INFO] Task succeeded: fastANI
[2024-01-24 12:49:42,448] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:49:42,449] [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	99.975	2176	2290	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	89.7181	1683	2290	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	89.0487	1656	2290	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	88.4168	1031	2290	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	88.0235	1248	2290	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	86.2846	1511	2290	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	82.718	1370	2290	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	82.7024	1322	2290	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	82.4925	1252	2290	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	82.2504	1294	2290	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	81.423	1236	2290	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	81.3847	1247	2290	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	81.2753	1028	2290	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	80.8853	1177	2290	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	78.7871	892	2290	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	75.8764	293	2290	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	75.8117	237	2290	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 12:49:42,450] [INFO] GTDB search result was written to GCF_009834665.1_ASM983466v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:49:42,451] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:49:42,455] [INFO] DFAST_QC result json was written to GCF_009834665.1_ASM983466v1_genomic.fna/dqc_result.json
[2024-01-24 12:49:42,455] [INFO] DFAST_QC completed!
[2024-01-24 12:49:42,455] [INFO] Total running time: 0h2m53s