[2024-01-24 12:22:28,368] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:28,371] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:28,372] [INFO] DQC Reference Directory: /var/lib/cwl/stgcfa9eb00-7b0a-4610-87b0-b1b47def3d14/dqc_reference
[2024-01-24 12:22:29,834] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:29,835] [INFO] Task started: Prodigal
[2024-01-24 12:22:29,835] [INFO] Running command: gunzip -c /var/lib/cwl/stg579d0c22-06b3-4da1-b9ab-a2d3748d6321/GCF_003122365.1_ASM312236v1_genomic.fna.gz | prodigal -d GCF_003122365.1_ASM312236v1_genomic.fna/cds.fna -a GCF_003122365.1_ASM312236v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:50,767] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:50,767] [INFO] Task started: HMMsearch
[2024-01-24 12:22:50,767] [INFO] Running command: hmmsearch --tblout GCF_003122365.1_ASM312236v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcfa9eb00-7b0a-4610-87b0-b1b47def3d14/dqc_reference/reference_markers.hmm GCF_003122365.1_ASM312236v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:51,194] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:51,195] [INFO] Found 6/6 markers.
[2024-01-24 12:22:51,253] [INFO] Query marker FASTA was written to GCF_003122365.1_ASM312236v1_genomic.fna/markers.fasta
[2024-01-24 12:22:51,254] [INFO] Task started: Blastn
[2024-01-24 12:22:51,254] [INFO] Running command: blastn -query GCF_003122365.1_ASM312236v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfa9eb00-7b0a-4610-87b0-b1b47def3d14/dqc_reference/reference_markers.fasta -out GCF_003122365.1_ASM312236v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:52,650] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:52,654] [INFO] Selected 11 target genomes.
[2024-01-24 12:22:52,654] [INFO] Target genome list was writen to GCF_003122365.1_ASM312236v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:52,658] [INFO] Task started: fastANI
[2024-01-24 12:22:52,658] [INFO] Running command: fastANI --query /var/lib/cwl/stg579d0c22-06b3-4da1-b9ab-a2d3748d6321/GCF_003122365.1_ASM312236v1_genomic.fna.gz --refList GCF_003122365.1_ASM312236v1_genomic.fna/target_genomes.txt --output GCF_003122365.1_ASM312236v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:15,052] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:15,053] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcfa9eb00-7b0a-4610-87b0-b1b47def3d14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:15,053] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcfa9eb00-7b0a-4610-87b0-b1b47def3d14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:15,066] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:15,067] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:15,067] [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 spongiicola	strain=HNM0071	GCA_003122365.1	1690221	1690221	type	True	100.0	2392	2393	95	conclusive
Streptomyces tirandamycinicus	strain=HNM0039	GCA_003097515.1	2174846	2174846	type	True	92.3857	1841	2393	95	below_threshold
Streptomyces wuyuanensis	strain=CGMCC 4.7042	GCA_900103455.1	1196353	1196353	type	True	89.1115	1704	2393	95	below_threshold
Streptomyces marianii	strain=ICN19	GCA_005795905.1	1817406	1817406	type	True	89.0098	1777	2393	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	84.3904	1498	2393	95	below_threshold
Streptomyces genisteinicus	strain=CRPJ-33	GCA_014489615.1	2768068	2768068	type	True	82.2574	1348	2393	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	82.1221	1103	2393	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	81.9163	1308	2393	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	81.236	1200	2393	95	below_threshold
Streptomyces longispororuber	strain=JCM 4784	GCA_014656095.1	68230	68230	type	True	81.1261	1252	2393	95	below_threshold
Streptomyces cyaneochromogenes	strain=MK-45	GCA_003963535.1	2496836	2496836	type	True	80.9583	1310	2393	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:15,069] [INFO] DFAST Taxonomy check result was written to GCF_003122365.1_ASM312236v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:15,070] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:15,070] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:15,070] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcfa9eb00-7b0a-4610-87b0-b1b47def3d14/dqc_reference/checkm_data
[2024-01-24 12:23:15,072] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:15,141] [INFO] Task started: CheckM
[2024-01-24 12:23:15,142] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003122365.1_ASM312236v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003122365.1_ASM312236v1_genomic.fna/checkm_input GCF_003122365.1_ASM312236v1_genomic.fna/checkm_result
[2024-01-24 12:25:12,523] [INFO] Task succeeded: CheckM
[2024-01-24 12:25:12,524] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:25:12,551] [INFO] ===== Completeness check finished =====
[2024-01-24 12:25:12,551] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:25:12,552] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003122365.1_ASM312236v1_genomic.fna/markers.fasta)
[2024-01-24 12:25:12,552] [INFO] Task started: Blastn
[2024-01-24 12:25:12,552] [INFO] Running command: blastn -query GCF_003122365.1_ASM312236v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfa9eb00-7b0a-4610-87b0-b1b47def3d14/dqc_reference/reference_markers_gtdb.fasta -out GCF_003122365.1_ASM312236v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:25:14,598] [INFO] Task succeeded: Blastn
[2024-01-24 12:25:14,602] [INFO] Selected 6 target genomes.
[2024-01-24 12:25:14,602] [INFO] Target genome list was writen to GCF_003122365.1_ASM312236v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:25:14,612] [INFO] Task started: fastANI
[2024-01-24 12:25:14,613] [INFO] Running command: fastANI --query /var/lib/cwl/stg579d0c22-06b3-4da1-b9ab-a2d3748d6321/GCF_003122365.1_ASM312236v1_genomic.fna.gz --refList GCF_003122365.1_ASM312236v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003122365.1_ASM312236v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:25:27,462] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:27,472] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:25:27,473] [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_003122365.1	s__Streptomyces spongiicola	100.0	2391	2393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.39	99.39	0.96	0.96	2	conclusive
GCA_003725745.1	s__Streptomyces sp003725745	94.639	1983	2393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003097515.1	s__Streptomyces tirandamycinicus	92.3747	1844	2393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.65	98.27	0.90	0.88	6	-
GCF_011766325.1	s__Streptomyces sp011766325	92.2029	1796	2393	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	89.1074	1705	2393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005795905.1	s__Streptomyces marianii	89.0207	1779	2393	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 12:25:27,474] [INFO] GTDB search result was written to GCF_003122365.1_ASM312236v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:25:27,475] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:25:27,477] [INFO] DFAST_QC result json was written to GCF_003122365.1_ASM312236v1_genomic.fna/dqc_result.json
[2024-01-24 12:25:27,478] [INFO] DFAST_QC completed!
[2024-01-24 12:25:27,478] [INFO] Total running time: 0h2m59s