[2023-06-30 00:38:44,771] [INFO] DFAST_QC pipeline started.
[2023-06-30 00:38:44,776] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 00:38:44,776] [INFO] DQC Reference Directory: /var/lib/cwl/stgbdcade8e-a4b3-4eed-886e-d656c822a1e8/dqc_reference
[2023-06-30 00:38:45,983] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 00:38:45,984] [INFO] Task started: Prodigal
[2023-06-30 00:38:45,984] [INFO] Running command: gunzip -c /var/lib/cwl/stgb516a257-cd28-4b9c-a5bd-3faee4eb19af/GCA_024709915.1_ASM2470991v1_genomic.fna.gz | prodigal -d GCA_024709915.1_ASM2470991v1_genomic.fna/cds.fna -a GCA_024709915.1_ASM2470991v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 00:38:52,778] [INFO] Task succeeded: Prodigal
[2023-06-30 00:38:52,779] [INFO] Task started: HMMsearch
[2023-06-30 00:38:52,779] [INFO] Running command: hmmsearch --tblout GCA_024709915.1_ASM2470991v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbdcade8e-a4b3-4eed-886e-d656c822a1e8/dqc_reference/reference_markers.hmm GCA_024709915.1_ASM2470991v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 00:38:52,943] [INFO] Task succeeded: HMMsearch
[2023-06-30 00:38:52,944] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb516a257-cd28-4b9c-a5bd-3faee4eb19af/GCA_024709915.1_ASM2470991v1_genomic.fna.gz]
[2023-06-30 00:38:52,970] [INFO] Query marker FASTA was written to GCA_024709915.1_ASM2470991v1_genomic.fna/markers.fasta
[2023-06-30 00:38:52,970] [INFO] Task started: Blastn
[2023-06-30 00:38:52,971] [INFO] Running command: blastn -query GCA_024709915.1_ASM2470991v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbdcade8e-a4b3-4eed-886e-d656c822a1e8/dqc_reference/reference_markers.fasta -out GCA_024709915.1_ASM2470991v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:38:53,585] [INFO] Task succeeded: Blastn
[2023-06-30 00:38:53,588] [INFO] Selected 9 target genomes.
[2023-06-30 00:38:53,588] [INFO] Target genome list was writen to GCA_024709915.1_ASM2470991v1_genomic.fna/target_genomes.txt
[2023-06-30 00:38:53,589] [INFO] Task started: fastANI
[2023-06-30 00:38:53,589] [INFO] Running command: fastANI --query /var/lib/cwl/stgb516a257-cd28-4b9c-a5bd-3faee4eb19af/GCA_024709915.1_ASM2470991v1_genomic.fna.gz --refList GCA_024709915.1_ASM2470991v1_genomic.fna/target_genomes.txt --output GCA_024709915.1_ASM2470991v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 00:39:00,862] [INFO] Task succeeded: fastANI
[2023-06-30 00:39:00,863] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbdcade8e-a4b3-4eed-886e-d656c822a1e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 00:39:00,863] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbdcade8e-a4b3-4eed-886e-d656c822a1e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 00:39:00,872] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2023-06-30 00:39:00,872] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-30 00:39:00,872] [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 aromatica	strain=K172	GCA_003030465.1	59405	59405	type	True	95.6507	701	792	95	conclusive
Thauera chlorobenzoica	strain=3CB1	GCA_001922305.1	96773	96773	type	True	93.8348	701	792	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	93.8282	704	792	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	84.0201	474	792	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	83.5639	488	792	95	below_threshold
Thauera propionica	strain=KNDSS-Mac4	GCA_002245655.1	2019431	2019431	type	True	82.5373	460	792	95	below_threshold
Thauera humireducens	strain=SgZ-1	GCA_001051995.2	1134435	1134435	type	True	82.402	478	792	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	82.3395	456	792	95	below_threshold
Thauera phenolivorans	strain=ZV1C	GCA_001696715.1	1792543	1792543	type	True	82.2356	458	792	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 00:39:00,875] [INFO] DFAST Taxonomy check result was written to GCA_024709915.1_ASM2470991v1_genomic.fna/tc_result.tsv
[2023-06-30 00:39:00,875] [INFO] ===== Taxonomy check completed =====
[2023-06-30 00:39:00,875] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 00:39:00,876] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbdcade8e-a4b3-4eed-886e-d656c822a1e8/dqc_reference/checkm_data
[2023-06-30 00:39:00,877] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 00:39:00,905] [INFO] Task started: CheckM
[2023-06-30 00:39:00,905] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024709915.1_ASM2470991v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024709915.1_ASM2470991v1_genomic.fna/checkm_input GCA_024709915.1_ASM2470991v1_genomic.fna/checkm_result
[2023-06-30 00:39:25,600] [INFO] Task succeeded: CheckM
[2023-06-30 00:39:25,602] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.77%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 00:39:25,620] [INFO] ===== Completeness check finished =====
[2023-06-30 00:39:25,620] [INFO] ===== Start GTDB Search =====
[2023-06-30 00:39:25,620] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024709915.1_ASM2470991v1_genomic.fna/markers.fasta)
[2023-06-30 00:39:25,621] [INFO] Task started: Blastn
[2023-06-30 00:39:25,621] [INFO] Running command: blastn -query GCA_024709915.1_ASM2470991v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbdcade8e-a4b3-4eed-886e-d656c822a1e8/dqc_reference/reference_markers_gtdb.fasta -out GCA_024709915.1_ASM2470991v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:39:26,492] [INFO] Task succeeded: Blastn
[2023-06-30 00:39:26,496] [INFO] Selected 11 target genomes.
[2023-06-30 00:39:26,496] [INFO] Target genome list was writen to GCA_024709915.1_ASM2470991v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 00:39:26,503] [INFO] Task started: fastANI
[2023-06-30 00:39:26,503] [INFO] Running command: fastANI --query /var/lib/cwl/stgb516a257-cd28-4b9c-a5bd-3faee4eb19af/GCA_024709915.1_ASM2470991v1_genomic.fna.gz --refList GCA_024709915.1_ASM2470991v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024709915.1_ASM2470991v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 00:39:34,538] [INFO] Task succeeded: fastANI
[2023-06-30 00:39:34,548] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 00:39:34,548] [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_003030465.1	s__Thauera aromatica	95.6507	701	792	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001922305.1	s__Thauera chlorobenzoica	93.8073	702	792	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	97.93	95.88	0.91	0.86	3	-
GCF_000310225.1	s__Thauera phenylacetica	83.9813	475	792	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963015.1	s__Thauera sp003963015	83.9183	479	792	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000310185.1	s__Thauera aminoaromatica	83.5775	487	792	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	98.62	98.32	0.86	0.80	8	-
GCA_017997795.1	s__Thauera sp017997795	83.4203	373	792	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	83.1693	439	792	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	82.6912	364	792	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	99.50	99.50	0.90	0.90	2	-
GCF_001591165.1	s__Thauera butanivorans	82.3171	456	792	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001696715.1	s__Thauera phenolivorans	82.2385	458	792	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	99.27	99.27	0.98	0.98	2	-
GCA_018240785.1	s__Thauera sp018240785	81.3709	443	792	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 00:39:34,550] [INFO] GTDB search result was written to GCA_024709915.1_ASM2470991v1_genomic.fna/result_gtdb.tsv
[2023-06-30 00:39:34,550] [INFO] ===== GTDB Search completed =====
[2023-06-30 00:39:34,554] [INFO] DFAST_QC result json was written to GCA_024709915.1_ASM2470991v1_genomic.fna/dqc_result.json
[2023-06-30 00:39:34,554] [INFO] DFAST_QC completed!
[2023-06-30 00:39:34,554] [INFO] Total running time: 0h0m50s