[2023-06-16 20:19:59,060] [INFO] DFAST_QC pipeline started.
[2023-06-16 20:19:59,062] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 20:19:59,062] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c411c96-7473-44bb-872c-bf62ef70501c/dqc_reference
[2023-06-16 20:20:00,283] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 20:20:00,284] [INFO] Task started: Prodigal
[2023-06-16 20:20:00,284] [INFO] Running command: gunzip -c /var/lib/cwl/stgd7840e57-78aa-4362-b63d-0900c75b5feb/GCA_013824525.1_ASM1382452v1_genomic.fna.gz | prodigal -d GCA_013824525.1_ASM1382452v1_genomic.fna/cds.fna -a GCA_013824525.1_ASM1382452v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 20:20:06,033] [INFO] Task succeeded: Prodigal
[2023-06-16 20:20:06,033] [INFO] Task started: HMMsearch
[2023-06-16 20:20:06,033] [INFO] Running command: hmmsearch --tblout GCA_013824525.1_ASM1382452v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c411c96-7473-44bb-872c-bf62ef70501c/dqc_reference/reference_markers.hmm GCA_013824525.1_ASM1382452v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 20:20:06,212] [INFO] Task succeeded: HMMsearch
[2023-06-16 20:20:06,213] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgd7840e57-78aa-4362-b63d-0900c75b5feb/GCA_013824525.1_ASM1382452v1_genomic.fna.gz]
[2023-06-16 20:20:06,237] [INFO] Query marker FASTA was written to GCA_013824525.1_ASM1382452v1_genomic.fna/markers.fasta
[2023-06-16 20:20:06,237] [INFO] Task started: Blastn
[2023-06-16 20:20:06,237] [INFO] Running command: blastn -query GCA_013824525.1_ASM1382452v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c411c96-7473-44bb-872c-bf62ef70501c/dqc_reference/reference_markers.fasta -out GCA_013824525.1_ASM1382452v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 20:20:06,890] [INFO] Task succeeded: Blastn
[2023-06-16 20:20:06,894] [INFO] Selected 15 target genomes.
[2023-06-16 20:20:06,894] [INFO] Target genome list was writen to GCA_013824525.1_ASM1382452v1_genomic.fna/target_genomes.txt
[2023-06-16 20:20:06,901] [INFO] Task started: fastANI
[2023-06-16 20:20:06,901] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7840e57-78aa-4362-b63d-0900c75b5feb/GCA_013824525.1_ASM1382452v1_genomic.fna.gz --refList GCA_013824525.1_ASM1382452v1_genomic.fna/target_genomes.txt --output GCA_013824525.1_ASM1382452v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 20:20:15,968] [INFO] Task succeeded: fastANI
[2023-06-16 20:20:15,969] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c411c96-7473-44bb-872c-bf62ef70501c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 20:20:15,969] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c411c96-7473-44bb-872c-bf62ef70501c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 20:20:15,979] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 20:20:15,979] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-16 20:20:15,979] [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
Pseudodesulfovibrio indicus	strain=DSM 101483	GCA_004365595.1	1716143	1716143	type	True	78.4294	118	324	95	below_threshold
Paucidesulfovibrio longus	strain=DSM 6739	GCA_000420485.1	889	889	type	True	78.3834	102	324	95	below_threshold
Pseudodesulfovibrio indicus	strain=J2	GCA_001563225.1	1716143	1716143	type	True	78.3671	120	324	95	below_threshold
Pseudodesulfovibrio mercurii	strain=ND132	GCA_000189295.2	641491	641491	type	True	78.2635	129	324	95	below_threshold
Fundidesulfovibrio magnetotacticus	strain=FSS-1	GCA_013019105.1	2730080	2730080	type	True	77.9709	122	324	95	below_threshold
Pseudodesulfovibrio hydrargyri	strain=BerOc1	GCA_001874525.1	2125990	2125990	type	True	77.9532	128	324	95	below_threshold
Pseudodesulfovibrio aespoeensis	strain=Aspo-2	GCA_000176915.2	182210	182210	type	True	77.9456	119	324	95	below_threshold
Desulfomicrobium escambiense	strain=DSM 10707	GCA_000428825.1	29503	29503	type	True	77.4986	87	324	95	below_threshold
Fundidesulfovibrio putealis	strain=DSM 16056	GCA_000429325.1	270496	270496	type	True	77.4589	109	324	95	below_threshold
Cupidesulfovibrio termitidis	strain=HI1	GCA_000504305.1	42252	42252	type	True	77.411	97	324	95	below_threshold
Solidesulfovibrio carbinolicus	strain=DSM 3852	GCA_004135975.1	296842	296842	type	True	77.2866	98	324	95	below_threshold
Pseudodesulfovibrio alkaliphilus	strain=F-1	GCA_009729555.1	2661613	2661613	type	True	77.2327	89	324	95	below_threshold
Solidesulfovibrio fructosivorans	strain=JJ	GCA_000179555.1	878	878	type	True	77.2183	86	324	95	below_threshold
Desulfohalovibrio reitneri	strain=L21-Syr-AB	GCA_000711295.1	1307759	1307759	type	True	77.1261	94	324	95	below_threshold
Desulfocurvibacter africanus subsp. africanus	strain=DSM 2603	GCA_000422545.1	1511600	873	type	True	77.0641	80	324	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 20:20:15,981] [INFO] DFAST Taxonomy check result was written to GCA_013824525.1_ASM1382452v1_genomic.fna/tc_result.tsv
[2023-06-16 20:20:15,982] [INFO] ===== Taxonomy check completed =====
[2023-06-16 20:20:15,982] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 20:20:15,982] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c411c96-7473-44bb-872c-bf62ef70501c/dqc_reference/checkm_data
[2023-06-16 20:20:15,983] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 20:20:16,012] [INFO] Task started: CheckM
[2023-06-16 20:20:16,012] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013824525.1_ASM1382452v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013824525.1_ASM1382452v1_genomic.fna/checkm_input GCA_013824525.1_ASM1382452v1_genomic.fna/checkm_result
[2023-06-16 20:20:36,641] [INFO] Task succeeded: CheckM
[2023-06-16 20:20:36,642] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.54%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-16 20:20:36,659] [INFO] ===== Completeness check finished =====
[2023-06-16 20:20:36,659] [INFO] ===== Start GTDB Search =====
[2023-06-16 20:20:36,660] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013824525.1_ASM1382452v1_genomic.fna/markers.fasta)
[2023-06-16 20:20:36,660] [INFO] Task started: Blastn
[2023-06-16 20:20:36,660] [INFO] Running command: blastn -query GCA_013824525.1_ASM1382452v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c411c96-7473-44bb-872c-bf62ef70501c/dqc_reference/reference_markers_gtdb.fasta -out GCA_013824525.1_ASM1382452v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 20:20:37,718] [INFO] Task succeeded: Blastn
[2023-06-16 20:20:37,721] [INFO] Selected 9 target genomes.
[2023-06-16 20:20:37,721] [INFO] Target genome list was writen to GCA_013824525.1_ASM1382452v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 20:20:37,727] [INFO] Task started: fastANI
[2023-06-16 20:20:37,727] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7840e57-78aa-4362-b63d-0900c75b5feb/GCA_013824525.1_ASM1382452v1_genomic.fna.gz --refList GCA_013824525.1_ASM1382452v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013824525.1_ASM1382452v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 20:20:42,758] [INFO] Task succeeded: fastANI
[2023-06-16 20:20:42,767] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-16 20:20:42,767] [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_018822105.1	s__Humidesulfovibrio sp018822105	87.6767	288	324	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Humidesulfovibrio	95.0	99.99	99.99	0.99	0.99	2	-
GCA_001799475.1	s__Humidesulfovibrio sp001799475	86.957	264	324	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Humidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002840405.1	s__Humidesulfovibrio sp002840405	86.5078	285	324	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Humidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903843965.1	s__Humidesulfovibrio sp903843965	86.4972	287	324	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Humidesulfovibrio	95.0	99.96	99.89	0.96	0.94	12	-
GCA_018817515.1	s__Humidesulfovibrio sp018817515	85.7374	281	324	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Humidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016218665.1	s__Humidesulfovibrio sp016218665	83.3189	230	324	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Humidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188225.1	s__Humidesulfovibrio mexicanus	81.3875	225	324	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Humidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002422505.1	s__Humidesulfovibrio sp002422505	81.3641	227	324	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Humidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001871085.1	s__Humidesulfovibrio sp001871085	80.6111	195	324	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Humidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 20:20:42,769] [INFO] GTDB search result was written to GCA_013824525.1_ASM1382452v1_genomic.fna/result_gtdb.tsv
[2023-06-16 20:20:42,771] [INFO] ===== GTDB Search completed =====
[2023-06-16 20:20:42,774] [INFO] DFAST_QC result json was written to GCA_013824525.1_ASM1382452v1_genomic.fna/dqc_result.json
[2023-06-16 20:20:42,774] [INFO] DFAST_QC completed!
[2023-06-16 20:20:42,774] [INFO] Total running time: 0h0m44s