[2023-06-30 15:09:13,745] [INFO] DFAST_QC pipeline started.
[2023-06-30 15:09:13,749] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 15:09:13,749] [INFO] DQC Reference Directory: /var/lib/cwl/stg84d828ca-1ae1-4827-8667-608d882443db/dqc_reference
[2023-06-30 15:09:15,063] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 15:09:15,066] [INFO] Task started: Prodigal
[2023-06-30 15:09:15,066] [INFO] Running command: gunzip -c /var/lib/cwl/stgbfc327b1-141d-472a-bf59-b1d700f033b0/GCA_024230975.1_ASM2423097v1_genomic.fna.gz | prodigal -d GCA_024230975.1_ASM2423097v1_genomic.fna/cds.fna -a GCA_024230975.1_ASM2423097v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 15:09:26,135] [INFO] Task succeeded: Prodigal
[2023-06-30 15:09:26,136] [INFO] Task started: HMMsearch
[2023-06-30 15:09:26,136] [INFO] Running command: hmmsearch --tblout GCA_024230975.1_ASM2423097v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84d828ca-1ae1-4827-8667-608d882443db/dqc_reference/reference_markers.hmm GCA_024230975.1_ASM2423097v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 15:09:26,489] [INFO] Task succeeded: HMMsearch
[2023-06-30 15:09:26,490] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgbfc327b1-141d-472a-bf59-b1d700f033b0/GCA_024230975.1_ASM2423097v1_genomic.fna.gz]
[2023-06-30 15:09:26,542] [INFO] Query marker FASTA was written to GCA_024230975.1_ASM2423097v1_genomic.fna/markers.fasta
[2023-06-30 15:09:26,543] [INFO] Task started: Blastn
[2023-06-30 15:09:26,543] [INFO] Running command: blastn -query GCA_024230975.1_ASM2423097v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84d828ca-1ae1-4827-8667-608d882443db/dqc_reference/reference_markers.fasta -out GCA_024230975.1_ASM2423097v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 15:09:27,230] [INFO] Task succeeded: Blastn
[2023-06-30 15:09:27,235] [INFO] Selected 18 target genomes.
[2023-06-30 15:09:27,235] [INFO] Target genome list was writen to GCA_024230975.1_ASM2423097v1_genomic.fna/target_genomes.txt
[2023-06-30 15:09:27,241] [INFO] Task started: fastANI
[2023-06-30 15:09:27,241] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfc327b1-141d-472a-bf59-b1d700f033b0/GCA_024230975.1_ASM2423097v1_genomic.fna.gz --refList GCA_024230975.1_ASM2423097v1_genomic.fna/target_genomes.txt --output GCA_024230975.1_ASM2423097v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 15:09:42,833] [INFO] Task succeeded: fastANI
[2023-06-30 15:09:42,834] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84d828ca-1ae1-4827-8667-608d882443db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 15:09:42,834] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84d828ca-1ae1-4827-8667-608d882443db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 15:09:42,848] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 15:09:42,848] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 15:09:42,849] [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
Desulfobacula phenolica	strain=DSM 3384	GCA_900105645.1	90732	90732	type	True	77.3487	123	721	95	below_threshold
Desulfobacula toluolica	strain=Tol2	GCA_000307105.1	28223	28223	type	True	76.9427	127	721	95	below_threshold
Desulfospira joergensenii	strain=DSM 10085	GCA_000420085.1	53329	53329	type	True	76.8198	144	721	95	below_threshold
Desulfocicer vacuolatum	strain=DSM 3385	GCA_900176365.1	2298	2298	type	True	76.4608	58	721	95	below_threshold
Desulfobacter hydrogenophilus	strain=AcRS1	GCA_004319545.1	2291	2291	type	True	76.3916	75	721	95	below_threshold
Desulfotignum balticum	strain=DSM 7044	GCA_000421285.1	115781	115781	type	True	76.3378	89	721	95	below_threshold
Desulfobacter latus	strain=AcRS2	GCA_013389365.1	2292	2292	type	True	76.3187	54	721	95	below_threshold
Desulfotignum phosphitoxidans	strain=DSM 13687	GCA_000350545.1	190898	190898	type	True	76.1919	84	721	95	below_threshold
Desulfobacter hydrogenophilus	strain=DSM 3380	GCA_003261095.1	2291	2291	type	True	76.168	72	721	95	below_threshold
Desulfobacter hydrogenophilus	strain=DSM 3380	GCA_010499545.1	2291	2291	type	True	76.168	72	721	95	below_threshold
Desulfobacter postgatei	strain=2ac9	GCA_000233695.3	2293	2293	type	True	76.0803	57	721	95	below_threshold
Desulfobacter curvatus	strain=DSM 3379	GCA_000373985.1	2290	2290	type	True	75.9828	61	721	95	below_threshold
Desulfobacter vibrioformis	strain=DSM 8776	GCA_000745975.1	34031	34031	type	True	75.852	71	721	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 15:09:42,852] [INFO] DFAST Taxonomy check result was written to GCA_024230975.1_ASM2423097v1_genomic.fna/tc_result.tsv
[2023-06-30 15:09:42,852] [INFO] ===== Taxonomy check completed =====
[2023-06-30 15:09:42,853] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 15:09:42,853] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84d828ca-1ae1-4827-8667-608d882443db/dqc_reference/checkm_data
[2023-06-30 15:09:42,855] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 15:09:42,915] [INFO] Task started: CheckM
[2023-06-30 15:09:42,915] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024230975.1_ASM2423097v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024230975.1_ASM2423097v1_genomic.fna/checkm_input GCA_024230975.1_ASM2423097v1_genomic.fna/checkm_result
[2023-06-30 15:10:20,951] [INFO] Task succeeded: CheckM
[2023-06-30 15:10:20,953] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.27%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 15:10:20,978] [INFO] ===== Completeness check finished =====
[2023-06-30 15:10:20,978] [INFO] ===== Start GTDB Search =====
[2023-06-30 15:10:20,979] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024230975.1_ASM2423097v1_genomic.fna/markers.fasta)
[2023-06-30 15:10:20,979] [INFO] Task started: Blastn
[2023-06-30 15:10:20,979] [INFO] Running command: blastn -query GCA_024230975.1_ASM2423097v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84d828ca-1ae1-4827-8667-608d882443db/dqc_reference/reference_markers_gtdb.fasta -out GCA_024230975.1_ASM2423097v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 15:10:21,854] [INFO] Task succeeded: Blastn
[2023-06-30 15:10:21,859] [INFO] Selected 11 target genomes.
[2023-06-30 15:10:21,860] [INFO] Target genome list was writen to GCA_024230975.1_ASM2423097v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 15:10:21,901] [INFO] Task started: fastANI
[2023-06-30 15:10:21,902] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfc327b1-141d-472a-bf59-b1d700f033b0/GCA_024230975.1_ASM2423097v1_genomic.fna.gz --refList GCA_024230975.1_ASM2423097v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024230975.1_ASM2423097v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 15:10:29,872] [INFO] Task succeeded: fastANI
[2023-06-30 15:10:29,884] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 15:10:29,884] [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_016744295.1	s__NBML01 sp016744295	82.5963	434	721	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__NBML01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016743945.1	s__NBML01 sp016743945	82.4231	416	721	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__NBML01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013792075.1	s__NBML01 sp013792075	80.9087	366	721	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__NBML01	95.0	99.85	99.75	0.95	0.94	3	-
GCA_018816605.1	s__NBML01 sp018816605	80.6216	309	721	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__NBML01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014237455.1	s__Desulfobacula sp014237455	78.6101	125	721	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfobacula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002085465.1	s__NBML01 sp002085465	78.3957	123	721	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__NBML01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011389575.1	s__Desulfotignum sp011389575	76.8389	93	721	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011389555.1	s__Desulfotignum sp011389555	76.3979	73	721	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000421285.1	s__Desulfotignum balticum	76.3378	89	721	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum	96.875	N/A	N/A	N/A	N/A	1	-
GCF_000745975.1	s__Desulfobacter vibrioformis	75.852	71	721	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 15:10:29,886] [INFO] GTDB search result was written to GCA_024230975.1_ASM2423097v1_genomic.fna/result_gtdb.tsv
[2023-06-30 15:10:29,887] [INFO] ===== GTDB Search completed =====
[2023-06-30 15:10:29,891] [INFO] DFAST_QC result json was written to GCA_024230975.1_ASM2423097v1_genomic.fna/dqc_result.json
[2023-06-30 15:10:29,891] [INFO] DFAST_QC completed!
[2023-06-30 15:10:29,891] [INFO] Total running time: 0h1m16s