[2024-01-25 18:20:35,741] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:20:35,743] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:20:35,743] [INFO] DQC Reference Directory: /var/lib/cwl/stg008b3a50-c6b3-4673-adf6-0e899dd31009/dqc_reference
[2024-01-25 18:20:36,879] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:20:36,879] [INFO] Task started: Prodigal
[2024-01-25 18:20:36,880] [INFO] Running command: gunzip -c /var/lib/cwl/stg5b7af6e7-2d5a-4800-8f77-589aa0ed166b/GCF_009811635.1_ASM981163v1_genomic.fna.gz | prodigal -d GCF_009811635.1_ASM981163v1_genomic.fna/cds.fna -a GCF_009811635.1_ASM981163v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:20:57,364] [INFO] Task succeeded: Prodigal
[2024-01-25 18:20:57,365] [INFO] Task started: HMMsearch
[2024-01-25 18:20:57,365] [INFO] Running command: hmmsearch --tblout GCF_009811635.1_ASM981163v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg008b3a50-c6b3-4673-adf6-0e899dd31009/dqc_reference/reference_markers.hmm GCF_009811635.1_ASM981163v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:20:57,656] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:20:57,658] [INFO] Found 6/6 markers.
[2024-01-25 18:20:57,717] [INFO] Query marker FASTA was written to GCF_009811635.1_ASM981163v1_genomic.fna/markers.fasta
[2024-01-25 18:20:57,717] [INFO] Task started: Blastn
[2024-01-25 18:20:57,717] [INFO] Running command: blastn -query GCF_009811635.1_ASM981163v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg008b3a50-c6b3-4673-adf6-0e899dd31009/dqc_reference/reference_markers.fasta -out GCF_009811635.1_ASM981163v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:20:58,945] [INFO] Task succeeded: Blastn
[2024-01-25 18:20:58,948] [INFO] Selected 17 target genomes.
[2024-01-25 18:20:58,948] [INFO] Target genome list was writen to GCF_009811635.1_ASM981163v1_genomic.fna/target_genomes.txt
[2024-01-25 18:20:58,960] [INFO] Task started: fastANI
[2024-01-25 18:20:58,960] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b7af6e7-2d5a-4800-8f77-589aa0ed166b/GCF_009811635.1_ASM981163v1_genomic.fna.gz --refList GCF_009811635.1_ASM981163v1_genomic.fna/target_genomes.txt --output GCF_009811635.1_ASM981163v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:21:34,795] [INFO] Task succeeded: fastANI
[2024-01-25 18:21:34,796] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg008b3a50-c6b3-4673-adf6-0e899dd31009/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:21:34,796] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg008b3a50-c6b3-4673-adf6-0e899dd31009/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:21:34,806] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:21:34,806] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:21:34,807] [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 tubercidicus	strain=NBRC 13090	GCA_009811635.1	47759	47759	type	True	100.0	2638	2641	95	conclusive
Streptomyces lydicamycinicus	strain=NBRC 110027	GCA_000829715.2	1546107	1546107	type	True	92.6745	2095	2641	95	below_threshold
Streptomyces glebosus	strain=NBRC 13786	GCA_009811575.1	249580	249580	type	True	92.4627	2099	2641	95	below_threshold
Streptomyces platensis	strain=ATCC 23948	GCA_008704855.1	58346	58346	type	True	92.3588	2109	2641	95	below_threshold
Streptomyces libani subsp. libani	strain=NBRC 13452	GCA_009811595.1	68044	68043	type	True	92.3532	2174	2641	95	below_threshold
Streptomyces platensis	strain=DSM 40041	GCA_002119195.1	58346	58346	type	True	92.3512	2058	2641	95	below_threshold
Streptomyces libani subsp. libani	strain=JCM 4322	GCA_014649275.1	68044	68043	type	True	92.3452	2153	2641	95	below_threshold
Streptomyces decoyicus	strain=NRRL 2666	GCA_019880305.1	249567	249567	type	True	89.8969	1991	2641	95	below_threshold
Streptomyces decoyicus	strain=NRRL 2666	GCA_001270575.1	249567	249567	type	True	89.8614	1911	2641	95	below_threshold
Streptomyces caniferus	strain=NBRC 15389	GCA_009811555.1	285557	285557	type	True	89.6069	2027	2641	95	below_threshold
Streptomyces angustmyceticus	strain=JCM 4053	GCA_019933235.1	285578	285578	type	True	89.4003	2036	2641	95	below_threshold
Streptomyces kronopolitis	strain=CGMCC 4.7323	GCA_014646275.1	1612435	1612435	type	True	88.8119	1865	2641	95	below_threshold
Streptomyces pinistramenti	strain=SF28	GCA_020564935.1	2884812	2884812	type	True	85.5291	1522	2641	95	below_threshold
Streptomyces benahoarensis	strain=MZ03-37	GCA_007280575.1	2595054	2595054	type	True	84.5431	1255	2641	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	83.8332	1595	2641	95	below_threshold
Streptomyces paromomycinus	strain=NBRC 15454	GCA_003865155.1	92743	92743	type	True	83.7268	1596	2641	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	83.7215	1547	2641	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:21:34,808] [INFO] DFAST Taxonomy check result was written to GCF_009811635.1_ASM981163v1_genomic.fna/tc_result.tsv
[2024-01-25 18:21:34,809] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:21:34,809] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:21:34,809] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg008b3a50-c6b3-4673-adf6-0e899dd31009/dqc_reference/checkm_data
[2024-01-25 18:21:34,810] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:21:34,882] [INFO] Task started: CheckM
[2024-01-25 18:21:34,882] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009811635.1_ASM981163v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009811635.1_ASM981163v1_genomic.fna/checkm_input GCF_009811635.1_ASM981163v1_genomic.fna/checkm_result
[2024-01-25 18:23:10,167] [INFO] Task succeeded: CheckM
[2024-01-25 18:23:10,169] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:23:10,190] [INFO] ===== Completeness check finished =====
[2024-01-25 18:23:10,190] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:23:10,191] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009811635.1_ASM981163v1_genomic.fna/markers.fasta)
[2024-01-25 18:23:10,191] [INFO] Task started: Blastn
[2024-01-25 18:23:10,191] [INFO] Running command: blastn -query GCF_009811635.1_ASM981163v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg008b3a50-c6b3-4673-adf6-0e899dd31009/dqc_reference/reference_markers_gtdb.fasta -out GCF_009811635.1_ASM981163v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:23:12,250] [INFO] Task succeeded: Blastn
[2024-01-25 18:23:12,252] [INFO] Selected 8 target genomes.
[2024-01-25 18:23:12,252] [INFO] Target genome list was writen to GCF_009811635.1_ASM981163v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:23:12,257] [INFO] Task started: fastANI
[2024-01-25 18:23:12,258] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b7af6e7-2d5a-4800-8f77-589aa0ed166b/GCF_009811635.1_ASM981163v1_genomic.fna.gz --refList GCF_009811635.1_ASM981163v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009811635.1_ASM981163v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:23:30,701] [INFO] Task succeeded: fastANI
[2024-01-25 18:23:30,708] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:23:30,708] [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_009811635.1	s__Streptomyces tubercidicus	100.0	2637	2641	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_008704855.1	s__Streptomyces platensis	92.3703	2109	2641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.55	95.21	0.91	0.87	7	-
GCF_009811595.1	s__Streptomyces libani	92.3188	2179	2641	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	89.8486	1913	2641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.25	96.25	0.87	0.87	2	-
GCF_009811555.1	s__Streptomyces caniferus	89.6346	2023	2641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187385.1	s__Streptomyces sp900187385	89.543	1979	2641	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	89.5127	1979	2641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009176265.1	s__Streptomyces angustmyceticus	89.4593	1999	2641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:23:30,709] [INFO] GTDB search result was written to GCF_009811635.1_ASM981163v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:23:30,710] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:23:30,713] [INFO] DFAST_QC result json was written to GCF_009811635.1_ASM981163v1_genomic.fna/dqc_result.json
[2024-01-25 18:23:30,713] [INFO] DFAST_QC completed!
[2024-01-25 18:23:30,713] [INFO] Total running time: 0h2m55s