[2023-06-13 17:33:02,520] [INFO] DFAST_QC pipeline started.
[2023-06-13 17:33:02,523] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 17:33:02,523] [INFO] DQC Reference Directory: /var/lib/cwl/stg6fdaf70a-dcde-4d0a-ac03-4a82e6829cbc/dqc_reference
[2023-06-13 17:33:03,757] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 17:33:03,758] [INFO] Task started: Prodigal
[2023-06-13 17:33:03,758] [INFO] Running command: gunzip -c /var/lib/cwl/stg00b32149-0a52-40c0-8c0a-747d4b4a7cba/GCA_022614955.1_ASM2261495v1_genomic.fna.gz | prodigal -d GCA_022614955.1_ASM2261495v1_genomic.fna/cds.fna -a GCA_022614955.1_ASM2261495v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 17:33:09,453] [INFO] Task succeeded: Prodigal
[2023-06-13 17:33:09,453] [INFO] Task started: HMMsearch
[2023-06-13 17:33:09,453] [INFO] Running command: hmmsearch --tblout GCA_022614955.1_ASM2261495v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6fdaf70a-dcde-4d0a-ac03-4a82e6829cbc/dqc_reference/reference_markers.hmm GCA_022614955.1_ASM2261495v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 17:33:09,676] [INFO] Task succeeded: HMMsearch
[2023-06-13 17:33:09,677] [INFO] Found 6/6 markers.
[2023-06-13 17:33:09,706] [INFO] Query marker FASTA was written to GCA_022614955.1_ASM2261495v1_genomic.fna/markers.fasta
[2023-06-13 17:33:09,707] [INFO] Task started: Blastn
[2023-06-13 17:33:09,707] [INFO] Running command: blastn -query GCA_022614955.1_ASM2261495v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6fdaf70a-dcde-4d0a-ac03-4a82e6829cbc/dqc_reference/reference_markers.fasta -out GCA_022614955.1_ASM2261495v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 17:33:10,350] [INFO] Task succeeded: Blastn
[2023-06-13 17:33:10,353] [INFO] Selected 24 target genomes.
[2023-06-13 17:33:10,353] [INFO] Target genome list was writen to GCA_022614955.1_ASM2261495v1_genomic.fna/target_genomes.txt
[2023-06-13 17:33:10,356] [INFO] Task started: fastANI
[2023-06-13 17:33:10,356] [INFO] Running command: fastANI --query /var/lib/cwl/stg00b32149-0a52-40c0-8c0a-747d4b4a7cba/GCA_022614955.1_ASM2261495v1_genomic.fna.gz --refList GCA_022614955.1_ASM2261495v1_genomic.fna/target_genomes.txt --output GCA_022614955.1_ASM2261495v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 17:33:26,876] [INFO] Task succeeded: fastANI
[2023-06-13 17:33:26,876] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6fdaf70a-dcde-4d0a-ac03-4a82e6829cbc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 17:33:26,876] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6fdaf70a-dcde-4d0a-ac03-4a82e6829cbc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 17:33:26,882] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 17:33:26,882] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 17:33:26,882] [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
Dissulfurirhabdus thermomarina	strain=SH388	GCA_012979235.1	1765737	1765737	type	True	75.4536	55	641	95	below_threshold
Thermaerobacter marianensis	strain=DSM 12885	GCA_000184705.1	73919	73919	type	True	75.1114	55	641	95	below_threshold
Thermus filiformis	strain=ATCC 43280	GCA_000771745.2	276	276	type	True	75.0323	53	641	95	below_threshold
Myxococcus eversor	strain=AB053B	GCA_010894455.1	2709661	2709661	type	True	74.9424	54	641	95	below_threshold
Pyxidicoccus fallax	strain=DSM 14698	GCA_012933655.1	394095	394095	type	True	74.9358	69	641	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 17:33:26,885] [INFO] DFAST Taxonomy check result was written to GCA_022614955.1_ASM2261495v1_genomic.fna/tc_result.tsv
[2023-06-13 17:33:26,886] [INFO] ===== Taxonomy check completed =====
[2023-06-13 17:33:26,886] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 17:33:26,887] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6fdaf70a-dcde-4d0a-ac03-4a82e6829cbc/dqc_reference/checkm_data
[2023-06-13 17:33:26,888] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 17:33:26,918] [INFO] Task started: CheckM
[2023-06-13 17:33:26,918] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022614955.1_ASM2261495v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022614955.1_ASM2261495v1_genomic.fna/checkm_input GCA_022614955.1_ASM2261495v1_genomic.fna/checkm_result
[2023-06-13 17:33:47,397] [INFO] Task succeeded: CheckM
[2023-06-13 17:33:47,398] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.93%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 17:33:47,417] [INFO] ===== Completeness check finished =====
[2023-06-13 17:33:47,417] [INFO] ===== Start GTDB Search =====
[2023-06-13 17:33:47,418] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022614955.1_ASM2261495v1_genomic.fna/markers.fasta)
[2023-06-13 17:33:47,418] [INFO] Task started: Blastn
[2023-06-13 17:33:47,418] [INFO] Running command: blastn -query GCA_022614955.1_ASM2261495v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6fdaf70a-dcde-4d0a-ac03-4a82e6829cbc/dqc_reference/reference_markers_gtdb.fasta -out GCA_022614955.1_ASM2261495v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 17:33:48,284] [INFO] Task succeeded: Blastn
[2023-06-13 17:33:48,288] [INFO] Selected 21 target genomes.
[2023-06-13 17:33:48,288] [INFO] Target genome list was writen to GCA_022614955.1_ASM2261495v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 17:33:48,311] [INFO] Task started: fastANI
[2023-06-13 17:33:48,311] [INFO] Running command: fastANI --query /var/lib/cwl/stg00b32149-0a52-40c0-8c0a-747d4b4a7cba/GCA_022614955.1_ASM2261495v1_genomic.fna.gz --refList GCA_022614955.1_ASM2261495v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022614955.1_ASM2261495v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 17:33:59,593] [INFO] Task succeeded: fastANI
[2023-06-13 17:33:59,601] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 17:33:59,602] [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_016180705.1	s__JACPAU01 sp016180705	83.04	274	641	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Methylomirabilales;f__JACPAU01;g__JACPAU01	95.0	96.92	96.92	0.61	0.61	2	-
GCA_001443495.1	s__CSP1-5 sp001443495	77.3223	80	641	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Methylomirabilales;f__CSP1-5;g__CSP1-5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016209735.1	s__2-02-FULL-66-22 sp016209735	77.0333	51	641	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Methylomirabilales;f__2-02-FULL-66-22;g__2-02-FULL-66-22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011054645.1	s__2-02-FULL-66-22 sp011054645	77.0236	132	641	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Methylomirabilales;f__2-02-FULL-66-22;g__2-02-FULL-66-22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016180655.1	s__2-02-FULL-66-22 sp016180655	76.9699	128	641	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Methylomirabilales;f__2-02-FULL-66-22;g__2-02-FULL-66-22	95.0	98.77	98.64	0.80	0.76	5	-
GCA_001771285.1	s__2-02-FULL-66-22 sp001771285	76.9435	115	641	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Methylomirabilales;f__2-02-FULL-66-22;g__2-02-FULL-66-22	95.0	99.46	99.46	0.82	0.82	2	-
GCA_016208645.1	s__2-02-FULL-66-22 sp016208645	76.8343	110	641	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Methylomirabilales;f__2-02-FULL-66-22;g__2-02-FULL-66-22	95.0	98.75	98.75	0.78	0.78	2	-
GCA_001788415.1	s__UBA12499 sp001788415	75.6983	68	641	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Rokubacteriales;f__CSP1-6;g__UBA12499	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003220315.1	s__20CM-2-70-11 sp003220315	75.5457	50	641	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Rokubacteriales;f__CSP1-6;g__20CM-2-70-11	95.0	99.38	99.31	0.92	0.87	7	-
GCA_001788495.1	s__GWA2-73-35 sp001788495	75.2508	59	641	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Rokubacteriales;f__CSP1-6;g__GWA2-73-35	95.0	99.58	99.46	0.87	0.84	4	-
GCF_000184705.1	s__Thermaerobacter marianensis	75.1234	54	641	d__Bacteria;p__Firmicutes_E;c__Thermaerobacteria;o__Thermaerobacterales;f__Thermaerobacteraceae;g__Thermaerobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 17:33:59,603] [INFO] GTDB search result was written to GCA_022614955.1_ASM2261495v1_genomic.fna/result_gtdb.tsv
[2023-06-13 17:33:59,603] [INFO] ===== GTDB Search completed =====
[2023-06-13 17:33:59,607] [INFO] DFAST_QC result json was written to GCA_022614955.1_ASM2261495v1_genomic.fna/dqc_result.json
[2023-06-13 17:33:59,607] [INFO] DFAST_QC completed!
[2023-06-13 17:33:59,607] [INFO] Total running time: 0h0m57s