[2023-06-30 14:17:30,567] [INFO] DFAST_QC pipeline started.
[2023-06-30 14:17:30,570] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 14:17:30,570] [INFO] DQC Reference Directory: /var/lib/cwl/stg448b5def-8be4-42e1-b515-358bbcf997a9/dqc_reference
[2023-06-30 14:17:32,796] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 14:17:32,798] [INFO] Task started: Prodigal
[2023-06-30 14:17:32,798] [INFO] Running command: gunzip -c /var/lib/cwl/stg56c92a99-9d8c-474b-a267-c6832cf929ab/GCA_024644635.1_ASM2464463v1_genomic.fna.gz | prodigal -d GCA_024644635.1_ASM2464463v1_genomic.fna/cds.fna -a GCA_024644635.1_ASM2464463v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 14:17:39,745] [INFO] Task succeeded: Prodigal
[2023-06-30 14:17:39,746] [INFO] Task started: HMMsearch
[2023-06-30 14:17:39,746] [INFO] Running command: hmmsearch --tblout GCA_024644635.1_ASM2464463v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg448b5def-8be4-42e1-b515-358bbcf997a9/dqc_reference/reference_markers.hmm GCA_024644635.1_ASM2464463v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 14:17:40,005] [INFO] Task succeeded: HMMsearch
[2023-06-30 14:17:40,007] [INFO] Found 6/6 markers.
[2023-06-30 14:17:40,042] [INFO] Query marker FASTA was written to GCA_024644635.1_ASM2464463v1_genomic.fna/markers.fasta
[2023-06-30 14:17:40,043] [INFO] Task started: Blastn
[2023-06-30 14:17:40,043] [INFO] Running command: blastn -query GCA_024644635.1_ASM2464463v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg448b5def-8be4-42e1-b515-358bbcf997a9/dqc_reference/reference_markers.fasta -out GCA_024644635.1_ASM2464463v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:17:40,702] [INFO] Task succeeded: Blastn
[2023-06-30 14:17:40,707] [INFO] Selected 29 target genomes.
[2023-06-30 14:17:40,708] [INFO] Target genome list was writen to GCA_024644635.1_ASM2464463v1_genomic.fna/target_genomes.txt
[2023-06-30 14:17:40,709] [INFO] Task started: fastANI
[2023-06-30 14:17:40,709] [INFO] Running command: fastANI --query /var/lib/cwl/stg56c92a99-9d8c-474b-a267-c6832cf929ab/GCA_024644635.1_ASM2464463v1_genomic.fna.gz --refList GCA_024644635.1_ASM2464463v1_genomic.fna/target_genomes.txt --output GCA_024644635.1_ASM2464463v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 14:17:56,319] [INFO] Task succeeded: fastANI
[2023-06-30 14:17:56,319] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg448b5def-8be4-42e1-b515-358bbcf997a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 14:17:56,320] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg448b5def-8be4-42e1-b515-358bbcf997a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 14:17:56,329] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 14:17:56,329] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 14:17:56,330] [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
Desulfuromonas acetexigens	strain=2873	GCA_007051125.1	38815	38815	type	True	77.3298	64	731	95	below_threshold
Desulfuromonas acetexigens		GCA_900111775.1	38815	38815	type	True	77.2622	62	731	95	below_threshold
Geothermobacter ehrlichii	strain=SS015	GCA_008124615.1	213224	213224	type	True	77.2268	85	731	95	below_threshold
Desulfuromonas versatilis	strain=NIT-T3	GCA_019704135.1	2802975	2802975	type	True	77.1435	121	731	95	below_threshold
Geoalkalibacter halelectricus	strain=SAP-1	GCA_025263685.1	2847045	2847045	type	True	76.7741	55	731	95	below_threshold
Geothermobacter hydrogeniphilus	strain=EPR-M	GCA_002093115.1	1969733	1969733	type	True	76.6248	91	731	95	below_threshold
Malonomonas rubra	strain=DSM 5091	GCA_900142125.1	57040	57040	type	True	76.5354	72	731	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 14:17:56,332] [INFO] DFAST Taxonomy check result was written to GCA_024644635.1_ASM2464463v1_genomic.fna/tc_result.tsv
[2023-06-30 14:17:56,332] [INFO] ===== Taxonomy check completed =====
[2023-06-30 14:17:56,332] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 14:17:56,332] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg448b5def-8be4-42e1-b515-358bbcf997a9/dqc_reference/checkm_data
[2023-06-30 14:17:56,333] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 14:17:56,368] [INFO] Task started: CheckM
[2023-06-30 14:17:56,368] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024644635.1_ASM2464463v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024644635.1_ASM2464463v1_genomic.fna/checkm_input GCA_024644635.1_ASM2464463v1_genomic.fna/checkm_result
[2023-06-30 14:18:24,396] [INFO] Task succeeded: CheckM
[2023-06-30 14:18:24,397] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 25.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 14:18:24,428] [INFO] ===== Completeness check finished =====
[2023-06-30 14:18:24,429] [INFO] ===== Start GTDB Search =====
[2023-06-30 14:18:24,429] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024644635.1_ASM2464463v1_genomic.fna/markers.fasta)
[2023-06-30 14:18:24,429] [INFO] Task started: Blastn
[2023-06-30 14:18:24,430] [INFO] Running command: blastn -query GCA_024644635.1_ASM2464463v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg448b5def-8be4-42e1-b515-358bbcf997a9/dqc_reference/reference_markers_gtdb.fasta -out GCA_024644635.1_ASM2464463v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:18:25,475] [INFO] Task succeeded: Blastn
[2023-06-30 14:18:25,480] [INFO] Selected 36 target genomes.
[2023-06-30 14:18:25,481] [INFO] Target genome list was writen to GCA_024644635.1_ASM2464463v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 14:18:25,518] [INFO] Task started: fastANI
[2023-06-30 14:18:25,518] [INFO] Running command: fastANI --query /var/lib/cwl/stg56c92a99-9d8c-474b-a267-c6832cf929ab/GCA_024644635.1_ASM2464463v1_genomic.fna.gz --refList GCA_024644635.1_ASM2464463v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024644635.1_ASM2464463v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 14:18:43,216] [INFO] Task succeeded: fastANI
[2023-06-30 14:18:43,230] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 14:18:43,230] [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_006226895.1	s__M0040 sp006226895	78.0044	94	731	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__BM103;g__M0040	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012974435.1	s__M0040 sp012974435	77.6861	161	731	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__BM103;g__M0040	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014860225.1	s__M0040 sp014860225	77.5435	185	731	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__BM103;g__M0040	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111775.1	s__Trichloromonas acetexigens	77.3702	63	731	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Trichloromonadaceae;g__Trichloromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008124615.1	s__Geothermobacter ehrlichii	77.2604	84	731	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geothermobacteraceae;g__Geothermobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009731355.2	s__SZUA-540 sp009731355	76.9357	56	731	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__SZUA-540;g__SZUA-540	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002869615.1	s__BM707 sp002869615	76.9271	69	731	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__UBA2294;g__BM707	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002868845.1	s__BM501 sp002868845	76.8064	64	731	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__BM501;g__BM501	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002868905.1	s__BM304 sp002868905	76.7472	79	731	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geothermobacteraceae;g__BM304	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002093115.1	s__PPFX01 sp002093115	76.7429	91	731	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geothermobacteraceae;g__PPFX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014860175.1	s__JACZKF01 sp014860175	76.3751	57	731	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__JACZKF01;g__JACZKF01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 14:18:43,232] [INFO] GTDB search result was written to GCA_024644635.1_ASM2464463v1_genomic.fna/result_gtdb.tsv
[2023-06-30 14:18:43,233] [INFO] ===== GTDB Search completed =====
[2023-06-30 14:18:43,249] [INFO] DFAST_QC result json was written to GCA_024644635.1_ASM2464463v1_genomic.fna/dqc_result.json
[2023-06-30 14:18:43,249] [INFO] DFAST_QC completed!
[2023-06-30 14:18:43,249] [INFO] Total running time: 0h1m13s