[2024-01-24 13:13:12,342] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:12,344] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:12,344] [INFO] DQC Reference Directory: /var/lib/cwl/stg297c0033-bb48-4f6f-bc0c-68530c003206/dqc_reference
[2024-01-24 13:13:13,860] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:13,861] [INFO] Task started: Prodigal
[2024-01-24 13:13:13,861] [INFO] Running command: gunzip -c /var/lib/cwl/stg1732300d-810d-47f3-83c9-948a0fd9f4dc/GCF_004212445.1_ASM421244v1_genomic.fna.gz | prodigal -d GCF_004212445.1_ASM421244v1_genomic.fna/cds.fna -a GCF_004212445.1_ASM421244v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:36,182] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:36,182] [INFO] Task started: HMMsearch
[2024-01-24 13:13:36,182] [INFO] Running command: hmmsearch --tblout GCF_004212445.1_ASM421244v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg297c0033-bb48-4f6f-bc0c-68530c003206/dqc_reference/reference_markers.hmm GCF_004212445.1_ASM421244v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:36,603] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:36,605] [INFO] Found 6/6 markers.
[2024-01-24 13:13:36,675] [INFO] Query marker FASTA was written to GCF_004212445.1_ASM421244v1_genomic.fna/markers.fasta
[2024-01-24 13:13:36,676] [INFO] Task started: Blastn
[2024-01-24 13:13:36,676] [INFO] Running command: blastn -query GCF_004212445.1_ASM421244v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg297c0033-bb48-4f6f-bc0c-68530c003206/dqc_reference/reference_markers.fasta -out GCF_004212445.1_ASM421244v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:38,009] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:38,012] [INFO] Selected 13 target genomes.
[2024-01-24 13:13:38,013] [INFO] Target genome list was writen to GCF_004212445.1_ASM421244v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:38,083] [INFO] Task started: fastANI
[2024-01-24 13:13:38,083] [INFO] Running command: fastANI --query /var/lib/cwl/stg1732300d-810d-47f3-83c9-948a0fd9f4dc/GCF_004212445.1_ASM421244v1_genomic.fna.gz --refList GCF_004212445.1_ASM421244v1_genomic.fna/target_genomes.txt --output GCF_004212445.1_ASM421244v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:07,127] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:07,128] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg297c0033-bb48-4f6f-bc0c-68530c003206/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:07,128] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg297c0033-bb48-4f6f-bc0c-68530c003206/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:07,143] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:14:07,143] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:14:07,143] [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 alfalfae	strain=XY25	GCA_004212445.1	1642299	1642299	type	True	100.0	2545	2552	95	conclusive
Streptomyces alfalfae	strain=XY25	GCA_004127445.1	1642299	1642299	type	True	99.9999	2552	2552	95	conclusive
Streptomyces alboniger	strain=NRRL B-1832	GCA_001418385.1	132473	132473	type	True	88.3039	1544	2552	95	below_threshold
Streptomyces alboniger	strain=ATCC 12461	GCA_008704395.1	132473	132473	type	True	88.2041	1825	2552	95	below_threshold
Streptomyces atriruber	strain=NRRL B-24165	GCA_001418325.1	545121	545121	type	True	87.5279	1634	2552	95	below_threshold
Streptomyces silaceus	strain=NRRL B-24166	GCA_001419745.1	545123	545123	type	True	87.4691	1631	2552	95	below_threshold
Streptomyces kanamyceticus	strain=ATCC 12853	GCA_008704495.1	1967	1967	type	True	86.9607	1853	2552	95	below_threshold
Streptomyces kanamyceticus	strain=NRRL B-2535	GCA_001418465.1	1967	1967	type	True	86.9051	1640	2552	95	below_threshold
Streptomyces durmitorensis	strain=MS405	GCA_023498005.1	319947	319947	type	True	85.3374	1797	2552	95	below_threshold
Streptomyces spectabilis	strain=KCTC9218	GCA_022698305.1	68270	68270	type	True	84.2079	1724	2552	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	82.4266	1497	2552	95	below_threshold
Streptomyces aurantiacus	strain=NRRL ISP-5412	GCA_001418335.1	47760	47760	type	True	82.4001	1333	2552	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	81.9473	1530	2552	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:07,144] [INFO] DFAST Taxonomy check result was written to GCF_004212445.1_ASM421244v1_genomic.fna/tc_result.tsv
[2024-01-24 13:14:07,145] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:07,145] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:07,145] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg297c0033-bb48-4f6f-bc0c-68530c003206/dqc_reference/checkm_data
[2024-01-24 13:14:07,146] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:07,219] [INFO] Task started: CheckM
[2024-01-24 13:14:07,219] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004212445.1_ASM421244v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004212445.1_ASM421244v1_genomic.fna/checkm_input GCF_004212445.1_ASM421244v1_genomic.fna/checkm_result
[2024-01-24 13:15:53,557] [INFO] Task succeeded: CheckM
[2024-01-24 13:15:53,559] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:15:53,581] [INFO] ===== Completeness check finished =====
[2024-01-24 13:15:53,581] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:15:53,581] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004212445.1_ASM421244v1_genomic.fna/markers.fasta)
[2024-01-24 13:15:53,582] [INFO] Task started: Blastn
[2024-01-24 13:15:53,582] [INFO] Running command: blastn -query GCF_004212445.1_ASM421244v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg297c0033-bb48-4f6f-bc0c-68530c003206/dqc_reference/reference_markers_gtdb.fasta -out GCF_004212445.1_ASM421244v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:15:55,645] [INFO] Task succeeded: Blastn
[2024-01-24 13:15:55,649] [INFO] Selected 12 target genomes.
[2024-01-24 13:15:55,649] [INFO] Target genome list was writen to GCF_004212445.1_ASM421244v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:15:55,670] [INFO] Task started: fastANI
[2024-01-24 13:15:55,670] [INFO] Running command: fastANI --query /var/lib/cwl/stg1732300d-810d-47f3-83c9-948a0fd9f4dc/GCF_004212445.1_ASM421244v1_genomic.fna.gz --refList GCF_004212445.1_ASM421244v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004212445.1_ASM421244v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:16:21,449] [INFO] Task succeeded: fastANI
[2024-01-24 13:16:21,468] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:16:21,468] [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_004127445.1	s__Streptomyces alfalfae	99.9999	2552	2552	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.46	98.55	0.94	0.88	8	conclusive
GCF_003945545.1	s__Streptomyces sp003945545	88.4136	1831	2552	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008704395.1	s__Streptomyces alboniger	88.2327	1821	2552	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.40	96.83	0.93	0.87	3	-
GCF_016905445.1	s__Streptomyces sp016905445	88.0807	1746	2552	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004010275.1	s__Streptomyces huasconensis	87.9669	1802	2552	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418325.1	s__Streptomyces atriruber	87.5471	1632	2552	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001419745.1	s__Streptomyces silaceus	87.494	1628	2552	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.58	99.58	0.96	0.96	2	-
GCF_008642335.1	s__Streptomyces venezuelae_F	87.3287	1817	2552	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008642355.1	s__Streptomyces venezuelae_B	87.1973	1843	2552	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.58	99.56	0.88	0.87	4	-
GCF_008642315.1	s__Streptomyces venezuelae_D	87.141	1843	2552	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002556545.1	s__Streptomyces formicae	87.0187	1860	2552	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008704495.1	s__Streptomyces kanamyceticus	86.936	1859	2552	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:16:21,470] [INFO] GTDB search result was written to GCF_004212445.1_ASM421244v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:16:21,470] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:16:21,475] [INFO] DFAST_QC result json was written to GCF_004212445.1_ASM421244v1_genomic.fna/dqc_result.json
[2024-01-24 13:16:21,475] [INFO] DFAST_QC completed!
[2024-01-24 13:16:21,475] [INFO] Total running time: 0h3m9s