[2024-01-24 13:57:57,762] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:57,763] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:57,763] [INFO] DQC Reference Directory: /var/lib/cwl/stg17261f85-b3da-4676-aff9-77d66b8d9101/dqc_reference
[2024-01-24 13:57:59,098] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:59,099] [INFO] Task started: Prodigal
[2024-01-24 13:57:59,099] [INFO] Running command: gunzip -c /var/lib/cwl/stgc1103afb-3e87-4276-937b-7417f5802589/GCF_005048155.1_ASM504815v1_genomic.fna.gz | prodigal -d GCF_005048155.1_ASM504815v1_genomic.fna/cds.fna -a GCF_005048155.1_ASM504815v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:24,821] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:24,822] [INFO] Task started: HMMsearch
[2024-01-24 13:58:24,822] [INFO] Running command: hmmsearch --tblout GCF_005048155.1_ASM504815v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg17261f85-b3da-4676-aff9-77d66b8d9101/dqc_reference/reference_markers.hmm GCF_005048155.1_ASM504815v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:25,238] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:25,240] [INFO] Found 6/6 markers.
[2024-01-24 13:58:25,310] [INFO] Query marker FASTA was written to GCF_005048155.1_ASM504815v1_genomic.fna/markers.fasta
[2024-01-24 13:58:25,310] [INFO] Task started: Blastn
[2024-01-24 13:58:25,311] [INFO] Running command: blastn -query GCF_005048155.1_ASM504815v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg17261f85-b3da-4676-aff9-77d66b8d9101/dqc_reference/reference_markers.fasta -out GCF_005048155.1_ASM504815v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:26,733] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:26,737] [INFO] Selected 18 target genomes.
[2024-01-24 13:58:26,737] [INFO] Target genome list was writen to GCF_005048155.1_ASM504815v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:26,777] [INFO] Task started: fastANI
[2024-01-24 13:58:26,778] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1103afb-3e87-4276-937b-7417f5802589/GCF_005048155.1_ASM504815v1_genomic.fna.gz --refList GCF_005048155.1_ASM504815v1_genomic.fna/target_genomes.txt --output GCF_005048155.1_ASM504815v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:06,959] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:06,960] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg17261f85-b3da-4676-aff9-77d66b8d9101/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:06,961] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg17261f85-b3da-4676-aff9-77d66b8d9101/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:06,985] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:59:06,985] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:59:06,986] [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 piniterrae	strain=jys28	GCA_005048155.1	2571125	2571125	type	True	100.0	2817	2818	95	conclusive
Streptomyces inhibens	strain=NEAU-D10	GCA_003389455.1	2293571	2293571	type	True	87.5813	1846	2818	95	below_threshold
Streptomyces libani subsp. libani	strain=NBRC 13452	GCA_009811595.1	68044	68043	type	True	86.9873	1924	2818	95	below_threshold
Streptomyces decoyicus	strain=NRRL 2666	GCA_001270575.1	249567	249567	type	True	86.9599	1815	2818	95	below_threshold
Streptomyces decoyicus	strain=NRRL 2666	GCA_019880305.1	249567	249567	type	True	86.9438	1890	2818	95	below_threshold
Streptomyces libani subsp. libani	strain=JCM 4322	GCA_014649275.1	68044	68043	type	True	86.9125	1919	2818	95	below_threshold
Streptomyces chattanoogensis	strain=NRRL ISP-5002	GCA_001294335.1	66876	66876	type	True	86.8986	1978	2818	95	below_threshold
Streptomyces lydicamycinicus	strain=NBRC 110027	GCA_000829715.2	1546107	1546107	type	True	86.878	1884	2818	95	below_threshold
Streptomyces glebosus	strain=NBRC 13786	GCA_009811575.1	249580	249580	type	True	86.7925	1869	2818	95	below_threshold
Streptomyces caniferus	strain=NBRC 15389	GCA_009811555.1	285557	285557	type	True	86.7804	1869	2818	95	below_threshold
Streptomyces lydicus	strain=NRRL ISP-5461	GCA_000717345.1	47763	47763	suspected-type	True	86.6328	1829	2818	95	below_threshold
Streptomyces kronopolitis	strain=CGMCC 4.7323	GCA_014646275.1	1612435	1612435	type	True	86.5753	1703	2818	95	below_threshold
Streptomyces kasugaensis	strain=BCRC 12349	GCA_002261115.1	1946	1946	type	True	86.4519	1692	2818	95	below_threshold
Streptomyces pinistramenti	strain=SF28	GCA_020564935.1	2884812	2884812	type	True	85.8287	1568	2818	95	below_threshold
Streptomyces benahoarensis	strain=MZ03-37	GCA_007280575.1	2595054	2595054	type	True	84.4369	1253	2818	95	below_threshold
Streptomyces paromomycinus	strain=NBRC 15454	GCA_003865155.1	92743	92743	type	True	83.9752	1632	2818	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	83.8246	1586	2818	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	83.7989	1670	2818	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:06,988] [INFO] DFAST Taxonomy check result was written to GCF_005048155.1_ASM504815v1_genomic.fna/tc_result.tsv
[2024-01-24 13:59:06,989] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:06,989] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:06,989] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg17261f85-b3da-4676-aff9-77d66b8d9101/dqc_reference/checkm_data
[2024-01-24 13:59:06,991] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:07,075] [INFO] Task started: CheckM
[2024-01-24 13:59:07,076] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005048155.1_ASM504815v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005048155.1_ASM504815v1_genomic.fna/checkm_input GCF_005048155.1_ASM504815v1_genomic.fna/checkm_result
[2024-01-24 14:00:30,297] [INFO] Task succeeded: CheckM
[2024-01-24 14:00:30,298] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:00:30,321] [INFO] ===== Completeness check finished =====
[2024-01-24 14:00:30,321] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:00:30,322] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005048155.1_ASM504815v1_genomic.fna/markers.fasta)
[2024-01-24 14:00:30,322] [INFO] Task started: Blastn
[2024-01-24 14:00:30,322] [INFO] Running command: blastn -query GCF_005048155.1_ASM504815v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg17261f85-b3da-4676-aff9-77d66b8d9101/dqc_reference/reference_markers_gtdb.fasta -out GCF_005048155.1_ASM504815v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:00:32,542] [INFO] Task succeeded: Blastn
[2024-01-24 14:00:32,546] [INFO] Selected 14 target genomes.
[2024-01-24 14:00:32,547] [INFO] Target genome list was writen to GCF_005048155.1_ASM504815v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:00:32,615] [INFO] Task started: fastANI
[2024-01-24 14:00:32,615] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1103afb-3e87-4276-937b-7417f5802589/GCF_005048155.1_ASM504815v1_genomic.fna.gz --refList GCF_005048155.1_ASM504815v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005048155.1_ASM504815v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:01:03,402] [INFO] Task succeeded: fastANI
[2024-01-24 14:01:03,418] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:01:03,418] [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_005048155.1	s__Streptomyces piniterrae	100.0	2817	2818	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003389455.1	s__Streptomyces inhibens	87.6108	1840	2818	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009811595.1	s__Streptomyces libani	86.9887	1924	2818	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.04	96.45	0.91	0.86	12	-
GCF_001270575.1	s__Streptomyces decoyicus	86.9631	1815	2818	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.25	96.25	0.87	0.87	2	-
GCF_001294335.1	s__Streptomyces chattanoogensis	86.8744	1981	2818	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.46	97.46	0.90	0.90	2	-
GCF_009811555.1	s__Streptomyces caniferus	86.7477	1875	2818	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004122735.1	s__Streptomyces sioyaensis	86.7027	1709	2818	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.26	95.36	0.89	0.84	9	-
GCF_000717345.1	s__Streptomyces lydicus	86.6013	1834	2818	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.39	95.38	0.95	0.89	6	-
GCA_000720995.1	s__Streptomyces celluloflavus	86.5911	1643	2818	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.24	98.62	0.95	0.89	4	-
GCF_900187385.1	s__Streptomyces sp900187385	86.571	1779	2818	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.81	99.51	0.98	0.96	9	-
GCF_004125265.1	s__Streptomyces lydicus_C	86.5539	1765	2818	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646275.1	s__Streptomyces kronopolitis	86.527	1710	2818	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002082195.1	s__Streptomyces gilvosporeus	86.1876	1831	2818	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0251	N/A	N/A	N/A	N/A	1	-
GCF_000935125.1	s__Streptomyces natalensis	86.1408	1825	2818	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0251	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:01:03,420] [INFO] GTDB search result was written to GCF_005048155.1_ASM504815v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:01:03,420] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:01:03,424] [INFO] DFAST_QC result json was written to GCF_005048155.1_ASM504815v1_genomic.fna/dqc_result.json
[2024-01-24 14:01:03,424] [INFO] DFAST_QC completed!
[2024-01-24 14:01:03,424] [INFO] Total running time: 0h3m6s