[2024-01-24 14:47:55,929] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:55,932] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:55,932] [INFO] DQC Reference Directory: /var/lib/cwl/stgc486697c-1e08-4a77-9645-d74a3441ff0c/dqc_reference
[2024-01-24 14:47:58,524] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:58,527] [INFO] Task started: Prodigal
[2024-01-24 14:47:58,527] [INFO] Running command: gunzip -c /var/lib/cwl/stg824daea0-0a37-486e-9114-121dd3d84494/GCF_002563855.1_ASM256385v1_genomic.fna.gz | prodigal -d GCF_002563855.1_ASM256385v1_genomic.fna/cds.fna -a GCF_002563855.1_ASM256385v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:48:06,152] [INFO] Task succeeded: Prodigal
[2024-01-24 14:48:06,153] [INFO] Task started: HMMsearch
[2024-01-24 14:48:06,153] [INFO] Running command: hmmsearch --tblout GCF_002563855.1_ASM256385v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc486697c-1e08-4a77-9645-d74a3441ff0c/dqc_reference/reference_markers.hmm GCF_002563855.1_ASM256385v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:48:06,422] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:48:06,424] [INFO] Found 6/6 markers.
[2024-01-24 14:48:06,454] [INFO] Query marker FASTA was written to GCF_002563855.1_ASM256385v1_genomic.fna/markers.fasta
[2024-01-24 14:48:06,454] [INFO] Task started: Blastn
[2024-01-24 14:48:06,454] [INFO] Running command: blastn -query GCF_002563855.1_ASM256385v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc486697c-1e08-4a77-9645-d74a3441ff0c/dqc_reference/reference_markers.fasta -out GCF_002563855.1_ASM256385v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:07,176] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:07,179] [INFO] Selected 17 target genomes.
[2024-01-24 14:48:07,179] [INFO] Target genome list was writen to GCF_002563855.1_ASM256385v1_genomic.fna/target_genomes.txt
[2024-01-24 14:48:07,202] [INFO] Task started: fastANI
[2024-01-24 14:48:07,203] [INFO] Running command: fastANI --query /var/lib/cwl/stg824daea0-0a37-486e-9114-121dd3d84494/GCF_002563855.1_ASM256385v1_genomic.fna.gz --refList GCF_002563855.1_ASM256385v1_genomic.fna/target_genomes.txt --output GCF_002563855.1_ASM256385v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:48:17,881] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:17,882] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc486697c-1e08-4a77-9645-d74a3441ff0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:48:17,883] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc486697c-1e08-4a77-9645-d74a3441ff0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:48:17,894] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:48:17,894] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:48:17,894] [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
Tepidiforma bonchosmolovskayae	strain=3753O	GCA_008838325.1	2601677	2601677	type	True	91.994	857	914	95	below_threshold
Agrococcus pavilionensis	strain=RW1	GCA_000400485.1	1346502	1346502	type	True	75.2185	58	914	95	below_threshold
Actinomyces haliotis	strain=JCM 18848	GCA_015355765.1	1280843	1280843	type	True	75.1974	66	914	95	below_threshold
Arenimonas metalli	strain=CF5-1	GCA_000747155.1	948077	948077	type	True	74.9623	60	914	95	below_threshold
Aminobacter aganoensis	strain=DSM 7051	GCA_014206975.1	83264	83264	type	True	74.955	63	914	95	below_threshold
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	74.9338	63	914	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	74.8554	144	914	95	below_threshold
Gemmatirosa kalamazoonensis	strain=KBS708	GCA_000522985.1	861299	861299	type	True	74.8483	98	914	95	below_threshold
Paroceanicella profunda	strain=D4M1	GCA_005887635.2	2579971	2579971	type	True	74.7799	66	914	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:48:17,896] [INFO] DFAST Taxonomy check result was written to GCF_002563855.1_ASM256385v1_genomic.fna/tc_result.tsv
[2024-01-24 14:48:17,897] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:48:17,897] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:48:17,897] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc486697c-1e08-4a77-9645-d74a3441ff0c/dqc_reference/checkm_data
[2024-01-24 14:48:17,898] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:48:17,948] [INFO] Task started: CheckM
[2024-01-24 14:48:17,948] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002563855.1_ASM256385v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002563855.1_ASM256385v1_genomic.fna/checkm_input GCF_002563855.1_ASM256385v1_genomic.fna/checkm_result
[2024-01-24 14:48:45,881] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:45,882] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:45,910] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:45,910] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:45,911] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002563855.1_ASM256385v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:45,911] [INFO] Task started: Blastn
[2024-01-24 14:48:45,911] [INFO] Running command: blastn -query GCF_002563855.1_ASM256385v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc486697c-1e08-4a77-9645-d74a3441ff0c/dqc_reference/reference_markers_gtdb.fasta -out GCF_002563855.1_ASM256385v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:46,922] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:46,927] [INFO] Selected 11 target genomes.
[2024-01-24 14:48:46,927] [INFO] Target genome list was writen to GCF_002563855.1_ASM256385v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:46,956] [INFO] Task started: fastANI
[2024-01-24 14:48:46,956] [INFO] Running command: fastANI --query /var/lib/cwl/stg824daea0-0a37-486e-9114-121dd3d84494/GCF_002563855.1_ASM256385v1_genomic.fna.gz --refList GCF_002563855.1_ASM256385v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002563855.1_ASM256385v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:54,269] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:54,284] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:54,284] [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
GCA_002563855.1	s__Tepidiforma sp002563855	100.0	914	914	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__Tepidiforma	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008838325.1	s__Tepidiforma bonchosmolovskayae	91.994	857	914	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__Tepidiforma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003104995.1	s__FeB-14 sp003104995	78.4342	327	914	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__FeB-14	95.0	99.84	99.84	0.86	0.86	2	-
GCA_016234445.1	s__JACRBT01 sp016234445	77.9829	312	914	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__JACRBT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016703545.1	s__JACPOQ01 sp016703545	77.7624	263	914	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__JACPOQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015075555.1	s__UCB2 sp015075555	77.6113	212	914	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__UCB2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003577245.1	s__UCB2 sp003577245	77.5361	152	914	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__UCB2	95.0	99.02	98.75	0.69	0.69	3	-
GCA_011048275.1	s__HRBIN29 sp011048275	77.5084	196	914	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__HRBIN29	95.0	99.99	99.99	0.99	0.99	3	-
GCA_016719395.1	s__FeB-14 sp016719395	77.4995	267	914	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__FeB-14	95.0	98.39	98.17	0.95	0.93	9	-
GCA_013822275.1	s__PNKC01 sp013822275	77.1204	186	914	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__PNKC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009840945.1	s__VXMT01 sp009840945	75.4335	92	914	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__VXMT01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:54,286] [INFO] GTDB search result was written to GCF_002563855.1_ASM256385v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:54,287] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:54,290] [INFO] DFAST_QC result json was written to GCF_002563855.1_ASM256385v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:54,290] [INFO] DFAST_QC completed!
[2024-01-24 14:48:54,291] [INFO] Total running time: 0h0m58s