[2023-06-13 11:03:59,592] [INFO] DFAST_QC pipeline started.
[2023-06-13 11:03:59,595] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 11:03:59,595] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c188a5f-bf5d-42d6-b239-dc63b919cb94/dqc_reference
[2023-06-13 11:04:01,628] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 11:04:01,629] [INFO] Task started: Prodigal
[2023-06-13 11:04:01,629] [INFO] Running command: gunzip -c /var/lib/cwl/stg9d5b05eb-47f9-4205-b9b4-ba3ff1a96a31/GCA_022705185.1_ASM2270518v1_genomic.fna.gz | prodigal -d GCA_022705185.1_ASM2270518v1_genomic.fna/cds.fna -a GCA_022705185.1_ASM2270518v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 11:04:07,824] [INFO] Task succeeded: Prodigal
[2023-06-13 11:04:07,825] [INFO] Task started: HMMsearch
[2023-06-13 11:04:07,825] [INFO] Running command: hmmsearch --tblout GCA_022705185.1_ASM2270518v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c188a5f-bf5d-42d6-b239-dc63b919cb94/dqc_reference/reference_markers.hmm GCA_022705185.1_ASM2270518v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 11:04:08,061] [INFO] Task succeeded: HMMsearch
[2023-06-13 11:04:08,062] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg9d5b05eb-47f9-4205-b9b4-ba3ff1a96a31/GCA_022705185.1_ASM2270518v1_genomic.fna.gz]
[2023-06-13 11:04:08,093] [INFO] Query marker FASTA was written to GCA_022705185.1_ASM2270518v1_genomic.fna/markers.fasta
[2023-06-13 11:04:08,094] [INFO] Task started: Blastn
[2023-06-13 11:04:08,094] [INFO] Running command: blastn -query GCA_022705185.1_ASM2270518v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c188a5f-bf5d-42d6-b239-dc63b919cb94/dqc_reference/reference_markers.fasta -out GCA_022705185.1_ASM2270518v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 11:04:09,131] [INFO] Task succeeded: Blastn
[2023-06-13 11:04:09,136] [INFO] Selected 15 target genomes.
[2023-06-13 11:04:09,136] [INFO] Target genome list was writen to GCA_022705185.1_ASM2270518v1_genomic.fna/target_genomes.txt
[2023-06-13 11:04:09,139] [INFO] Task started: fastANI
[2023-06-13 11:04:09,140] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d5b05eb-47f9-4205-b9b4-ba3ff1a96a31/GCA_022705185.1_ASM2270518v1_genomic.fna.gz --refList GCA_022705185.1_ASM2270518v1_genomic.fna/target_genomes.txt --output GCA_022705185.1_ASM2270518v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 11:04:20,648] [INFO] Task succeeded: fastANI
[2023-06-13 11:04:20,648] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c188a5f-bf5d-42d6-b239-dc63b919cb94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 11:04:20,649] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c188a5f-bf5d-42d6-b239-dc63b919cb94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 11:04:20,665] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2023-06-13 11:04:20,665] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 11:04:20,665] [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
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	98.9901	604	667	95	conclusive
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	91.9436	526	667	95	below_threshold
Thauera propionica	strain=KNDSS-Mac4	GCA_002245655.1	2019431	2019431	type	True	84.5057	475	667	95	below_threshold
Thauera humireducens	strain=SgZ-1	GCA_001051995.2	1134435	1134435	type	True	84.493	485	667	95	below_threshold
Thauera chlorobenzoica	strain=3CB1	GCA_001922305.1	96773	96773	type	True	84.1664	439	667	95	below_threshold
Thauera aromatica	strain=K172	GCA_003030465.1	59405	59405	type	True	84.1022	431	667	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	84.0784	450	667	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	83.8402	446	667	95	below_threshold
Thauera linaloolentis	strain=47Lol = DSM 12138	GCA_000310205.1	76112	76112	type	True	83.2329	419	667	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	83.1869	430	667	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	80.7992	410	667	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	79.9575	327	667	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	79.8921	357	667	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	79.7534	316	667	95	below_threshold
Nitrogeniibacter aestuarii	strain=H1-1-2A	GCA_017309585.1	2815343	2815343	type	True	78.5857	208	667	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 11:04:20,668] [INFO] DFAST Taxonomy check result was written to GCA_022705185.1_ASM2270518v1_genomic.fna/tc_result.tsv
[2023-06-13 11:04:20,668] [INFO] ===== Taxonomy check completed =====
[2023-06-13 11:04:20,668] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 11:04:20,669] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c188a5f-bf5d-42d6-b239-dc63b919cb94/dqc_reference/checkm_data
[2023-06-13 11:04:20,670] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 11:04:20,705] [INFO] Task started: CheckM
[2023-06-13 11:04:20,705] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022705185.1_ASM2270518v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022705185.1_ASM2270518v1_genomic.fna/checkm_input GCA_022705185.1_ASM2270518v1_genomic.fna/checkm_result
[2023-06-13 11:04:44,562] [INFO] Task succeeded: CheckM
[2023-06-13 11:04:44,563] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.29%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 11:04:44,587] [INFO] ===== Completeness check finished =====
[2023-06-13 11:04:44,587] [INFO] ===== Start GTDB Search =====
[2023-06-13 11:04:44,588] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022705185.1_ASM2270518v1_genomic.fna/markers.fasta)
[2023-06-13 11:04:44,588] [INFO] Task started: Blastn
[2023-06-13 11:04:44,588] [INFO] Running command: blastn -query GCA_022705185.1_ASM2270518v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c188a5f-bf5d-42d6-b239-dc63b919cb94/dqc_reference/reference_markers_gtdb.fasta -out GCA_022705185.1_ASM2270518v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 11:04:46,678] [INFO] Task succeeded: Blastn
[2023-06-13 11:04:46,685] [INFO] Selected 9 target genomes.
[2023-06-13 11:04:46,685] [INFO] Target genome list was writen to GCA_022705185.1_ASM2270518v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 11:04:46,693] [INFO] Task started: fastANI
[2023-06-13 11:04:46,693] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d5b05eb-47f9-4205-b9b4-ba3ff1a96a31/GCA_022705185.1_ASM2270518v1_genomic.fna.gz --refList GCA_022705185.1_ASM2270518v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022705185.1_ASM2270518v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 11:04:53,251] [INFO] Task succeeded: fastANI
[2023-06-13 11:04:53,262] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 11:04:53,262] [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_000310185.1	s__Thauera aminoaromatica	98.9901	604	667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	98.62	98.32	0.86	0.80	8	conclusive
GCA_003963015.1	s__Thauera sp003963015	92.2122	539	667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000310225.1	s__Thauera phenylacetica	91.8457	529	667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016790365.1	s__Thauera sp016790365	90.053	428	667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017997795.1	s__Thauera sp017997795	86.9893	395	667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002422685.1	s__Thauera sp002422685	86.736	454	667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003446655.1	s__Thauera sp003446655	85.7766	392	667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	99.50	99.50	0.90	0.90	2	-
GCF_009469595.1	s__Thauera sp009469595	83.0874	451	667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240785.1	s__Thauera sp018240785	83.0247	460	667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 11:04:53,265] [INFO] GTDB search result was written to GCA_022705185.1_ASM2270518v1_genomic.fna/result_gtdb.tsv
[2023-06-13 11:04:53,266] [INFO] ===== GTDB Search completed =====
[2023-06-13 11:04:53,270] [INFO] DFAST_QC result json was written to GCA_022705185.1_ASM2270518v1_genomic.fna/dqc_result.json
[2023-06-13 11:04:53,270] [INFO] DFAST_QC completed!
[2023-06-13 11:04:53,270] [INFO] Total running time: 0h0m54s