[2024-01-24 12:40:07,132] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:07,134] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:07,134] [INFO] DQC Reference Directory: /var/lib/cwl/stg89ace275-2744-47bc-b7b9-701d0c8b6546/dqc_reference
[2024-01-24 12:40:08,541] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:08,542] [INFO] Task started: Prodigal
[2024-01-24 12:40:08,542] [INFO] Running command: gunzip -c /var/lib/cwl/stg9aea5bec-4509-414a-88fa-f6a60875ce33/GCF_000183545.2_ASM18354v3_genomic.fna.gz | prodigal -d GCF_000183545.2_ASM18354v3_genomic.fna/cds.fna -a GCF_000183545.2_ASM18354v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:16,888] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:16,889] [INFO] Task started: HMMsearch
[2024-01-24 12:40:16,889] [INFO] Running command: hmmsearch --tblout GCF_000183545.2_ASM18354v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg89ace275-2744-47bc-b7b9-701d0c8b6546/dqc_reference/reference_markers.hmm GCF_000183545.2_ASM18354v3_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:17,080] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:17,081] [INFO] Found 6/6 markers.
[2024-01-24 12:40:17,105] [INFO] Query marker FASTA was written to GCF_000183545.2_ASM18354v3_genomic.fna/markers.fasta
[2024-01-24 12:40:17,106] [INFO] Task started: Blastn
[2024-01-24 12:40:17,106] [INFO] Running command: blastn -query GCF_000183545.2_ASM18354v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg89ace275-2744-47bc-b7b9-701d0c8b6546/dqc_reference/reference_markers.fasta -out GCF_000183545.2_ASM18354v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:17,763] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:17,768] [INFO] Selected 17 target genomes.
[2024-01-24 12:40:17,768] [INFO] Target genome list was writen to GCF_000183545.2_ASM18354v3_genomic.fna/target_genomes.txt
[2024-01-24 12:40:17,779] [INFO] Task started: fastANI
[2024-01-24 12:40:17,779] [INFO] Running command: fastANI --query /var/lib/cwl/stg9aea5bec-4509-414a-88fa-f6a60875ce33/GCF_000183545.2_ASM18354v3_genomic.fna.gz --refList GCF_000183545.2_ASM18354v3_genomic.fna/target_genomes.txt --output GCF_000183545.2_ASM18354v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:30,289] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:30,290] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg89ace275-2744-47bc-b7b9-701d0c8b6546/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:30,290] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg89ace275-2744-47bc-b7b9-701d0c8b6546/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:30,301] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:40:30,301] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:30,301] [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
Thermaerobacter subterraneus	strain=DSM 13965	GCA_000183545.3	175696	175696	type	True	100.0	962	962	95	conclusive
Thermaerobacter marianensis	strain=DSM 12885	GCA_000184705.1	73919	73919	type	True	85.0046	734	962	95	below_threshold
Symbiobacterium thermophilum	strain=IAM14863	GCA_000009905.1	2734	2734	type	True	76.3365	145	962	95	below_threshold
Limnochorda pilosa	strain=HC45	GCA_001544015.1	1555112	1555112	type	True	76.0497	157	962	95	below_threshold
Geomonas paludis	strain=Red736	GCA_014193585.1	2740185	2740185	type	True	75.6384	60	962	95	below_threshold
Thiohalospira halophila	strain=HL 3	GCA_900112605.1	381300	381300	type	True	75.3559	81	962	95	below_threshold
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	75.267	72	962	95	below_threshold
Dissulfurirhabdus thermomarina	strain=DSM 100025	GCA_010499435.1	1765737	1765737	type	True	75.1997	75	962	95	below_threshold
Dissulfurirhabdus thermomarina	strain=SH388	GCA_012979235.1	1765737	1765737	type	True	75.1641	83	962	95	below_threshold
Acrocarpospora corrugata	strain=NBRC 13972	GCA_009687845.1	35763	35763	type	True	75.1197	137	962	95	below_threshold
Pseudomonas otitidis	strain=DSM 17224	GCA_900111835.1	319939	319939	suspected-type	True	75.0601	90	962	95	below_threshold
Dactylosporangium matsuzakiense	strain=NRRL B-16293	GCA_025264725.1	53360	53360	type	True	74.998	187	962	95	below_threshold
Streptomyces orinoci	strain=NRRL B-3379	GCA_003121295.1	67339	67339	type	True	74.9508	159	962	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:30,303] [INFO] DFAST Taxonomy check result was written to GCF_000183545.2_ASM18354v3_genomic.fna/tc_result.tsv
[2024-01-24 12:40:30,304] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:30,304] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:30,304] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg89ace275-2744-47bc-b7b9-701d0c8b6546/dqc_reference/checkm_data
[2024-01-24 12:40:30,305] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:30,332] [INFO] Task started: CheckM
[2024-01-24 12:40:30,333] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000183545.2_ASM18354v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000183545.2_ASM18354v3_genomic.fna/checkm_input GCF_000183545.2_ASM18354v3_genomic.fna/checkm_result
[2024-01-24 12:41:00,733] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:00,734] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:00,755] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:00,755] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:00,756] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000183545.2_ASM18354v3_genomic.fna/markers.fasta)
[2024-01-24 12:41:00,756] [INFO] Task started: Blastn
[2024-01-24 12:41:00,756] [INFO] Running command: blastn -query GCF_000183545.2_ASM18354v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg89ace275-2744-47bc-b7b9-701d0c8b6546/dqc_reference/reference_markers_gtdb.fasta -out GCF_000183545.2_ASM18354v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:01,708] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:01,712] [INFO] Selected 10 target genomes.
[2024-01-24 12:41:01,712] [INFO] Target genome list was writen to GCF_000183545.2_ASM18354v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:01,720] [INFO] Task started: fastANI
[2024-01-24 12:41:01,720] [INFO] Running command: fastANI --query /var/lib/cwl/stg9aea5bec-4509-414a-88fa-f6a60875ce33/GCF_000183545.2_ASM18354v3_genomic.fna.gz --refList GCF_000183545.2_ASM18354v3_genomic.fna/target_genomes_gtdb.txt --output GCF_000183545.2_ASM18354v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:07,277] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:07,285] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:07,286] [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_000183545.2	s__Thermaerobacter subterraneus	100.0	962	962	d__Bacteria;p__Firmicutes_E;c__Thermaerobacteria;o__Thermaerobacterales;f__Thermaerobacteraceae;g__Thermaerobacter	95.0	95.08	95.08	0.91	0.91	2	conclusive
GCF_000184705.1	s__Thermaerobacter marianensis	85.0546	730	962	d__Bacteria;p__Firmicutes_E;c__Thermaerobacteria;o__Thermaerobacterales;f__Thermaerobacteraceae;g__Thermaerobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004634385.1	s__Thermaerobacter sp004634385	84.3592	729	962	d__Bacteria;p__Firmicutes_E;c__Thermaerobacteria;o__Thermaerobacterales;f__Thermaerobacteraceae;g__Thermaerobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242195.1	s__Thermaerobacter sp003242195	79.8306	328	962	d__Bacteria;p__Firmicutes_E;c__Thermaerobacteria;o__Thermaerobacterales;f__Thermaerobacteraceae;g__Thermaerobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017577485.1	s__RSA17 sp002919105	77.1873	221	962	d__Bacteria;p__Firmicutes_E;c__Thermaerobacteria;o__Thermaerobacterales;f__RSA17;g__RSA17	95.0	99.68	99.68	0.97	0.97	2	-
GCA_018729555.1	s__RBS10-35 sp018729555	76.6835	72	962	d__Bacteria;p__Firmicutes_E;c__RBS10-35;o__RBS10-35;f__RBS10-35;g__RBS10-35	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242505.1	s__ZC4RG38 sp003242505	76.167	139	962	d__Bacteria;p__Firmicutes_E;c__Symbiobacteriia;o__Symbiobacteriales;f__ZC4RG38;g__ZC4RG38	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001544015.1	s__Limnochorda pilosa	76.0218	160	962	d__Bacteria;p__Firmicutes_G;c__Limnochordia;o__Limnochordales;f__Limnochordaceae;g__Limnochorda	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:07,287] [INFO] GTDB search result was written to GCF_000183545.2_ASM18354v3_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:07,288] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:07,291] [INFO] DFAST_QC result json was written to GCF_000183545.2_ASM18354v3_genomic.fna/dqc_result.json
[2024-01-24 12:41:07,291] [INFO] DFAST_QC completed!
[2024-01-24 12:41:07,292] [INFO] Total running time: 0h1m0s