[2024-01-24 14:03:03,214] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:03:03,216] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:03:03,216] [INFO] DQC Reference Directory: /var/lib/cwl/stg7dea0214-ad06-4c3f-a162-ae5346696d3f/dqc_reference
[2024-01-24 14:03:04,567] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:03:04,568] [INFO] Task started: Prodigal
[2024-01-24 14:03:04,568] [INFO] Running command: gunzip -c /var/lib/cwl/stg1ae5ba4f-e00e-409a-936d-770573dfcd85/GCF_014202345.1_ASM1420234v1_genomic.fna.gz | prodigal -d GCF_014202345.1_ASM1420234v1_genomic.fna/cds.fna -a GCF_014202345.1_ASM1420234v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:03:16,232] [INFO] Task succeeded: Prodigal
[2024-01-24 14:03:16,233] [INFO] Task started: HMMsearch
[2024-01-24 14:03:16,233] [INFO] Running command: hmmsearch --tblout GCF_014202345.1_ASM1420234v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7dea0214-ad06-4c3f-a162-ae5346696d3f/dqc_reference/reference_markers.hmm GCF_014202345.1_ASM1420234v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:03:16,531] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:03:16,533] [INFO] Found 6/6 markers.
[2024-01-24 14:03:16,630] [INFO] Query marker FASTA was written to GCF_014202345.1_ASM1420234v1_genomic.fna/markers.fasta
[2024-01-24 14:03:16,630] [INFO] Task started: Blastn
[2024-01-24 14:03:16,630] [INFO] Running command: blastn -query GCF_014202345.1_ASM1420234v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7dea0214-ad06-4c3f-a162-ae5346696d3f/dqc_reference/reference_markers.fasta -out GCF_014202345.1_ASM1420234v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:17,254] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:17,258] [INFO] Selected 10 target genomes.
[2024-01-24 14:03:17,258] [INFO] Target genome list was writen to GCF_014202345.1_ASM1420234v1_genomic.fna/target_genomes.txt
[2024-01-24 14:03:17,266] [INFO] Task started: fastANI
[2024-01-24 14:03:17,266] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ae5ba4f-e00e-409a-936d-770573dfcd85/GCF_014202345.1_ASM1420234v1_genomic.fna.gz --refList GCF_014202345.1_ASM1420234v1_genomic.fna/target_genomes.txt --output GCF_014202345.1_ASM1420234v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:03:23,304] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:23,305] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7dea0214-ad06-4c3f-a162-ae5346696d3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:03:23,305] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7dea0214-ad06-4c3f-a162-ae5346696d3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:03:23,323] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:03:23,323] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:03:23,323] [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
Desulfovibrio intestinalis	strain=DSM 11275	GCA_014202345.1	58621	58621	type	True	100.0	1137	1138	95	conclusive
Desulfovibrio porci	strain=PG-178-WT-4	GCA_009696265.1	2605782	2605782	type	True	78.7811	343	1138	95	below_threshold
Desulfovibrio legallii	strain=H1T	GCA_004309735.1	571438	571438	type	True	78.7716	360	1138	95	below_threshold
Desulfovibrio piger	strain=ATCC 29098	GCA_000156375.1	901	901	suspected-type	True	78.206	241	1138	95	below_threshold
Cupidesulfovibrio liaohensis	strain=XJ01	GCA_011682075.1	2604158	2604158	type	True	77.4098	115	1138	95	below_threshold
Megalodesulfovibrio gigas	strain=DSM 1382	GCA_000429285.1	879	879	type	True	77.2973	67	1138	95	below_threshold
Megalodesulfovibrio gigas	strain=ATCC 19364	GCA_000468495.1	879	879	type	True	77.166	69	1138	95	below_threshold
Cupidesulfovibrio termitidis	strain=HI1	GCA_000504305.1	42252	42252	type	True	77.1508	145	1138	95	below_threshold
Desulfovibrio sulfodismutans	strain=DSM 3696	GCA_013376455.1	63561	63561	type	True	76.3416	55	1138	95	below_threshold
Desulfovibrio sulfodismutans	strain=DSM 3696	GCA_010499425.1	63561	63561	type	True	76.3246	54	1138	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:03:23,325] [INFO] DFAST Taxonomy check result was written to GCF_014202345.1_ASM1420234v1_genomic.fna/tc_result.tsv
[2024-01-24 14:03:23,326] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:03:23,327] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:03:23,327] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7dea0214-ad06-4c3f-a162-ae5346696d3f/dqc_reference/checkm_data
[2024-01-24 14:03:23,328] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:03:23,363] [INFO] Task started: CheckM
[2024-01-24 14:03:23,363] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014202345.1_ASM1420234v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014202345.1_ASM1420234v1_genomic.fna/checkm_input GCF_014202345.1_ASM1420234v1_genomic.fna/checkm_result
[2024-01-24 14:04:02,053] [INFO] Task succeeded: CheckM
[2024-01-24 14:04:02,056] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:04:02,078] [INFO] ===== Completeness check finished =====
[2024-01-24 14:04:02,079] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:04:02,079] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014202345.1_ASM1420234v1_genomic.fna/markers.fasta)
[2024-01-24 14:04:02,080] [INFO] Task started: Blastn
[2024-01-24 14:04:02,080] [INFO] Running command: blastn -query GCF_014202345.1_ASM1420234v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7dea0214-ad06-4c3f-a162-ae5346696d3f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014202345.1_ASM1420234v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:04:03,063] [INFO] Task succeeded: Blastn
[2024-01-24 14:04:03,066] [INFO] Selected 7 target genomes.
[2024-01-24 14:04:03,066] [INFO] Target genome list was writen to GCF_014202345.1_ASM1420234v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:04:03,076] [INFO] Task started: fastANI
[2024-01-24 14:04:03,077] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ae5ba4f-e00e-409a-936d-770573dfcd85/GCF_014202345.1_ASM1420234v1_genomic.fna.gz --refList GCF_014202345.1_ASM1420234v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014202345.1_ASM1420234v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:04:08,472] [INFO] Task succeeded: fastANI
[2024-01-24 14:04:08,483] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:04:08,484] [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_014202345.1	s__Desulfovibrio intestinalis	100.0	1137	1138	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002237645.1	s__Desulfovibrio sp002237645	83.9576	799	1138	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902702915.1	s__Desulfovibrio sp900095395	83.9179	776	1138	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	99.97	99.97	0.99	0.99	2	-
GCA_905214305.1	s__Desulfovibrio sp905214305	81.5164	577	1138	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000022125.1	s__Desulfovibrio desulfuricans_A	81.3615	593	1138	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	99.36	99.22	0.93	0.89	5	-
GCA_003251995.1	s__Desulfovibrio desulfuricans_B	79.1535	223	1138	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910575755.1	s__Desulfovibrio sp910575755	78.6332	288	1138	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:04:08,485] [INFO] GTDB search result was written to GCF_014202345.1_ASM1420234v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:04:08,486] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:04:08,489] [INFO] DFAST_QC result json was written to GCF_014202345.1_ASM1420234v1_genomic.fna/dqc_result.json
[2024-01-24 14:04:08,490] [INFO] DFAST_QC completed!
[2024-01-24 14:04:08,490] [INFO] Total running time: 0h1m5s