[2024-01-24 12:53:55,947] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:55,948] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:55,949] [INFO] DQC Reference Directory: /var/lib/cwl/stg3058cab7-d4d6-4983-b4ff-4d4782dca1e1/dqc_reference
[2024-01-24 12:53:57,227] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:57,228] [INFO] Task started: Prodigal
[2024-01-24 12:53:57,228] [INFO] Running command: gunzip -c /var/lib/cwl/stg4576cf37-9b7c-4ad7-b7c3-a5e3e2615afa/GCF_000725565.1_Doro.v1.0_genomic.fna.gz | prodigal -d GCF_000725565.1_Doro.v1.0_genomic.fna/cds.fna -a GCF_000725565.1_Doro.v1.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:26,597] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:26,597] [INFO] Task started: HMMsearch
[2024-01-24 12:54:26,597] [INFO] Running command: hmmsearch --tblout GCF_000725565.1_Doro.v1.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3058cab7-d4d6-4983-b4ff-4d4782dca1e1/dqc_reference/reference_markers.hmm GCF_000725565.1_Doro.v1.0_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:27,008] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:27,010] [INFO] Found 6/6 markers.
[2024-01-24 12:54:27,079] [INFO] Query marker FASTA was written to GCF_000725565.1_Doro.v1.0_genomic.fna/markers.fasta
[2024-01-24 12:54:27,080] [INFO] Task started: Blastn
[2024-01-24 12:54:27,080] [INFO] Running command: blastn -query GCF_000725565.1_Doro.v1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg3058cab7-d4d6-4983-b4ff-4d4782dca1e1/dqc_reference/reference_markers.fasta -out GCF_000725565.1_Doro.v1.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:28,472] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:28,476] [INFO] Selected 14 target genomes.
[2024-01-24 12:54:28,476] [INFO] Target genome list was writen to GCF_000725565.1_Doro.v1.0_genomic.fna/target_genomes.txt
[2024-01-24 12:54:28,485] [INFO] Task started: fastANI
[2024-01-24 12:54:28,485] [INFO] Running command: fastANI --query /var/lib/cwl/stg4576cf37-9b7c-4ad7-b7c3-a5e3e2615afa/GCF_000725565.1_Doro.v1.0_genomic.fna.gz --refList GCF_000725565.1_Doro.v1.0_genomic.fna/target_genomes.txt --output GCF_000725565.1_Doro.v1.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:55:00,127] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:00,127] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3058cab7-d4d6-4983-b4ff-4d4782dca1e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:55:00,128] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3058cab7-d4d6-4983-b4ff-4d4782dca1e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:55:00,139] [INFO] Found 14 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 12:55:00,139] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:55:00,139] [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 rimosus	strain=ATCC 10970	GCA_008704655.1	1927	1927	type	True	97.8288	2830	3134	95	conclusive
Streptomyces rimosus subsp. rimosus	strain=NRRL ISP-5260	GCA_000717285.1	132474	1927	type	True	97.8121	2807	3134	95	conclusive
Streptomyces rimosus subsp. rimosus	strain=ATCC 10970	GCA_000331185.2	132474	1927	type	True	97.8097	2829	3134	95	conclusive
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	97.7968	2836	3134	95	conclusive
Streptomyces albofaciens	strain=ATCC 23873	GCA_008634025.1	66866	66866	type	True	94.1407	2612	3134	95	below_threshold
Streptomyces paromomycinus	strain=NBRC 15454	GCA_003865155.1	92743	92743	type	True	89.7146	2401	3134	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	89.7085	2324	3134	95	below_threshold
Streptomyces pinistramenti	strain=SF28	GCA_020564935.1	2884812	2884812	type	True	83.9636	1540	3134	95	below_threshold
Streptomyces thermoviolaceus subsp. thermoviolaceus	strain=JCM 4843	GCA_014650975.1	66860	1952	type	True	80.9857	1127	3134	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	80.9218	1559	3134	95	below_threshold
Streptomyces thermoviolaceus subsp. thermoviolaceus	strain=NBRC 13905	GCA_012034235.1	66860	1952	type	True	80.8568	1138	3134	95	below_threshold
Streptomyces thermoviolaceus subsp. apingens	strain=JCM 4312	GCA_014649255.1	66859	1952	type	True	80.7804	1151	3134	95	below_threshold
Actinacidiphila paucisporea	strain=CGMCC 4.2025	GCA_900142575.1	310782	310782	type	True	79.9872	1163	3134	95	below_threshold
Actinacidiphila epipremni	strain=PRB2-1	GCA_012034175.1	2053013	2053013	type	True	79.6475	1277	3134	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:55:00,141] [INFO] DFAST Taxonomy check result was written to GCF_000725565.1_Doro.v1.0_genomic.fna/tc_result.tsv
[2024-01-24 12:55:00,142] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:55:00,142] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:55:00,142] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3058cab7-d4d6-4983-b4ff-4d4782dca1e1/dqc_reference/checkm_data
[2024-01-24 12:55:00,143] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:55:00,229] [INFO] Task started: CheckM
[2024-01-24 12:55:00,229] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000725565.1_Doro.v1.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000725565.1_Doro.v1.0_genomic.fna/checkm_input GCF_000725565.1_Doro.v1.0_genomic.fna/checkm_result
[2024-01-24 12:56:37,956] [INFO] Task succeeded: CheckM
[2024-01-24 12:56:37,957] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:56:37,982] [INFO] ===== Completeness check finished =====
[2024-01-24 12:56:37,982] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:56:37,983] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000725565.1_Doro.v1.0_genomic.fna/markers.fasta)
[2024-01-24 12:56:37,983] [INFO] Task started: Blastn
[2024-01-24 12:56:37,983] [INFO] Running command: blastn -query GCF_000725565.1_Doro.v1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg3058cab7-d4d6-4983-b4ff-4d4782dca1e1/dqc_reference/reference_markers_gtdb.fasta -out GCF_000725565.1_Doro.v1.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:56:40,058] [INFO] Task succeeded: Blastn
[2024-01-24 12:56:40,061] [INFO] Selected 11 target genomes.
[2024-01-24 12:56:40,061] [INFO] Target genome list was writen to GCF_000725565.1_Doro.v1.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:56:40,080] [INFO] Task started: fastANI
[2024-01-24 12:56:40,081] [INFO] Running command: fastANI --query /var/lib/cwl/stg4576cf37-9b7c-4ad7-b7c3-a5e3e2615afa/GCF_000725565.1_Doro.v1.0_genomic.fna.gz --refList GCF_000725565.1_Doro.v1.0_genomic.fna/target_genomes_gtdb.txt --output GCF_000725565.1_Doro.v1.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:57:06,772] [INFO] Task succeeded: fastANI
[2024-01-24 12:57:06,782] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:57:06,782] [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_008704655.1	s__Streptomyces rimosus	97.8221	2831	3134	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.17	96.53	0.95	0.89	49	conclusive
GCF_008634025.1	s__Streptomyces albofaciens	94.1249	2614	3134	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720725.1	s__Streptomyces rimosus_A	94.0002	2554	3134	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905005.1	s__Streptomyces sp001905005	90.0452	2402	3134	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003865135.1	s__Streptomyces chrestomyceticus	89.8683	2395	3134	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.95	95.89	0.90	0.88	4	-
GCF_000715845.1	s__Streptomyces monomycini	89.8423	2232	3134	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013387495.1	s__Streptomyces sp013387495	81.0731	1226	3134	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019049245.1	s__Streptomyces sp019049245	80.2965	1377	3134	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142575.1	s__Streptomyces paucisporeus	79.942	1172	3134	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000701325.1	s__Streptomyces sp000701325	79.7991	1158	3134	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012034175.1	s__Streptomyces sp012034175	79.6228	1282	3134	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 12:57:06,784] [INFO] GTDB search result was written to GCF_000725565.1_Doro.v1.0_genomic.fna/result_gtdb.tsv
[2024-01-24 12:57:06,784] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:57:06,787] [INFO] DFAST_QC result json was written to GCF_000725565.1_Doro.v1.0_genomic.fna/dqc_result.json
[2024-01-24 12:57:06,788] [INFO] DFAST_QC completed!
[2024-01-24 12:57:06,788] [INFO] Total running time: 0h3m11s