[2024-01-24 10:57:37,956] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:37,961] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:37,961] [INFO] DQC Reference Directory: /var/lib/cwl/stgfed6c7c4-3a05-403e-8706-0b81fb450210/dqc_reference
[2024-01-24 10:57:39,327] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:39,328] [INFO] Task started: Prodigal
[2024-01-24 10:57:39,328] [INFO] Running command: gunzip -c /var/lib/cwl/stgf84c310f-7789-496a-8ae5-23da2dd227a5/GCF_001187435.1_ASM118743v1_genomic.fna.gz | prodigal -d GCF_001187435.1_ASM118743v1_genomic.fna/cds.fna -a GCF_001187435.1_ASM118743v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:00,658] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:00,659] [INFO] Task started: HMMsearch
[2024-01-24 10:58:00,659] [INFO] Running command: hmmsearch --tblout GCF_001187435.1_ASM118743v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfed6c7c4-3a05-403e-8706-0b81fb450210/dqc_reference/reference_markers.hmm GCF_001187435.1_ASM118743v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:01,028] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:01,030] [INFO] Found 6/6 markers.
[2024-01-24 10:58:01,084] [INFO] Query marker FASTA was written to GCF_001187435.1_ASM118743v1_genomic.fna/markers.fasta
[2024-01-24 10:58:01,085] [INFO] Task started: Blastn
[2024-01-24 10:58:01,085] [INFO] Running command: blastn -query GCF_001187435.1_ASM118743v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfed6c7c4-3a05-403e-8706-0b81fb450210/dqc_reference/reference_markers.fasta -out GCF_001187435.1_ASM118743v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:02,416] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:02,419] [INFO] Selected 16 target genomes.
[2024-01-24 10:58:02,420] [INFO] Target genome list was writen to GCF_001187435.1_ASM118743v1_genomic.fna/target_genomes.txt
[2024-01-24 10:58:02,439] [INFO] Task started: fastANI
[2024-01-24 10:58:02,439] [INFO] Running command: fastANI --query /var/lib/cwl/stgf84c310f-7789-496a-8ae5-23da2dd227a5/GCF_001187435.1_ASM118743v1_genomic.fna.gz --refList GCF_001187435.1_ASM118743v1_genomic.fna/target_genomes.txt --output GCF_001187435.1_ASM118743v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:34,001] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:34,001] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfed6c7c4-3a05-403e-8706-0b81fb450210/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:34,001] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfed6c7c4-3a05-403e-8706-0b81fb450210/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:34,014] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:34,014] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:34,014] [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 caatingaensis	strain=CMAA 1322	GCA_001187435.1	1678637	1678637	type	True	100.0	2335	2342	95	conclusive
Streptomyces mobaraensis	strain=DSM 40847	GCA_000342125.1	35621	35621	type	True	85.8933	1530	2342	95	below_threshold
Streptomyces mobaraensis	strain=DSM 40847	GCA_017916255.1	35621	35621	type	True	85.8843	1623	2342	95	below_threshold
Streptomyces huiliensis	strain=SCA2-4	GCA_020037025.1	2876027	2876027	type	True	85.7197	1471	2342	95	below_threshold
Streptomyces olivoverticillatus	strain=CECT 3266	GCA_014203555.1	66427	66427	type	True	84.683	1272	2342	95	below_threshold
Streptomyces abikoensis	strain=JCM 4002	GCA_014648775.1	97398	97398	type	True	84.4865	1429	2342	95	below_threshold
Streptomyces griseocarneus	strain=JCM 4580	GCA_014655595.1	51201	51201	type	True	84.4032	1415	2342	95	below_threshold
Streptomyces griseocarneus	strain=CGMCC4.1088	GCA_020093395.1	51201	51201	type	True	84.345	1407	2342	95	below_threshold
Streptomyces morookaense	strain=JCM 4793	GCA_014656115.1	1970	1970	type	True	84.1142	1425	2342	95	below_threshold
Streptomyces morookaense	strain=DSM 40503	GCA_013030945.1	1970	1970	type	True	83.9993	1398	2342	95	below_threshold
Streptomyces mashuensis	strain=JCM 4059	GCA_014654785.1	33904	33904	type	True	83.7315	1430	2342	95	below_threshold
Streptomyces hiroshimensis	strain=JCM 4586	GCA_014650335.1	66424	66424	type	True	83.7283	1439	2342	95	below_threshold
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	83.6909	1461	2342	95	below_threshold
Streptomyces orinoci	strain=NRRL B-3379	GCA_003121295.1	67339	67339	type	True	83.2725	1407	2342	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	81.1761	1071	2342	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	80.8121	1203	2342	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:34,016] [INFO] DFAST Taxonomy check result was written to GCF_001187435.1_ASM118743v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:34,017] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:34,017] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:34,017] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfed6c7c4-3a05-403e-8706-0b81fb450210/dqc_reference/checkm_data
[2024-01-24 10:58:34,020] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:34,087] [INFO] Task started: CheckM
[2024-01-24 10:58:34,087] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001187435.1_ASM118743v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001187435.1_ASM118743v1_genomic.fna/checkm_input GCF_001187435.1_ASM118743v1_genomic.fna/checkm_result
[2024-01-24 11:00:10,077] [INFO] Task succeeded: CheckM
[2024-01-24 11:00:10,078] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 13.54%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:00:10,104] [INFO] ===== Completeness check finished =====
[2024-01-24 11:00:10,104] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:00:10,105] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001187435.1_ASM118743v1_genomic.fna/markers.fasta)
[2024-01-24 11:00:10,105] [INFO] Task started: Blastn
[2024-01-24 11:00:10,105] [INFO] Running command: blastn -query GCF_001187435.1_ASM118743v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfed6c7c4-3a05-403e-8706-0b81fb450210/dqc_reference/reference_markers_gtdb.fasta -out GCF_001187435.1_ASM118743v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:00:12,280] [INFO] Task succeeded: Blastn
[2024-01-24 11:00:12,284] [INFO] Selected 12 target genomes.
[2024-01-24 11:00:12,284] [INFO] Target genome list was writen to GCF_001187435.1_ASM118743v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:00:12,304] [INFO] Task started: fastANI
[2024-01-24 11:00:12,305] [INFO] Running command: fastANI --query /var/lib/cwl/stgf84c310f-7789-496a-8ae5-23da2dd227a5/GCF_001187435.1_ASM118743v1_genomic.fna.gz --refList GCF_001187435.1_ASM118743v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001187435.1_ASM118743v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:00:36,441] [INFO] Task succeeded: fastANI
[2024-01-24 11:00:36,459] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:00:36,459] [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_001187435.1	s__Streptomyces caatingaensis	100.0	2338	2342	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_015999245.1	s__Streptomyces sp015999245	90.467	1765	2342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013055795.1	s__Streptomyces sp013055795	86.1456	1540	2342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017916255.1	s__Streptomyces mobaraensis	85.8565	1625	2342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.59	99.19	0.96	0.92	3	-
GCF_014253015.1	s__Streptomyces sp014253015	85.852	1593	2342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203555.1	s__Streptomyces olivoverticillatus	84.7002	1270	2342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648775.1	s__Streptomyces abikoensis	84.5278	1424	2342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.57	96.57	0.89	0.89	2	-
GCF_014655595.1	s__Streptomyces griseocarneus	84.3714	1422	2342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650495.1	s__Streptomyces cinnamoneus	84.3488	1389	2342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014654785.1	s__Streptomyces mashuensis	83.7548	1427	2342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003674045.1	s__Streptomyces griseocarneus_A	83.6509	1441	2342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003121295.1	s__Streptomyces orinoci	83.3243	1400	2342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:00:36,461] [INFO] GTDB search result was written to GCF_001187435.1_ASM118743v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:00:36,461] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:00:36,465] [INFO] DFAST_QC result json was written to GCF_001187435.1_ASM118743v1_genomic.fna/dqc_result.json
[2024-01-24 11:00:36,465] [INFO] DFAST_QC completed!
[2024-01-24 11:00:36,465] [INFO] Total running time: 0h2m59s