[2024-01-24 13:55:27,764] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:27,768] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:27,768] [INFO] DQC Reference Directory: /var/lib/cwl/stgbf44d5fb-20c9-4c6c-9556-87f4a8bad6aa/dqc_reference
[2024-01-24 13:55:28,939] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:28,940] [INFO] Task started: Prodigal
[2024-01-24 13:55:28,940] [INFO] Running command: gunzip -c /var/lib/cwl/stg77b848ab-ae80-4cd5-a174-3c9d1e79344d/GCF_000174435.1_ASM17443v1_genomic.fna.gz | prodigal -d GCF_000174435.1_ASM17443v1_genomic.fna/cds.fna -a GCF_000174435.1_ASM17443v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:39,915] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:39,916] [INFO] Task started: HMMsearch
[2024-01-24 13:55:39,916] [INFO] Running command: hmmsearch --tblout GCF_000174435.1_ASM17443v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbf44d5fb-20c9-4c6c-9556-87f4a8bad6aa/dqc_reference/reference_markers.hmm GCF_000174435.1_ASM17443v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:40,145] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:40,146] [INFO] Found 6/6 markers.
[2024-01-24 13:55:40,184] [INFO] Query marker FASTA was written to GCF_000174435.1_ASM17443v1_genomic.fna/markers.fasta
[2024-01-24 13:55:40,184] [INFO] Task started: Blastn
[2024-01-24 13:55:40,184] [INFO] Running command: blastn -query GCF_000174435.1_ASM17443v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf44d5fb-20c9-4c6c-9556-87f4a8bad6aa/dqc_reference/reference_markers.fasta -out GCF_000174435.1_ASM17443v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:40,743] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:40,746] [INFO] Selected 17 target genomes.
[2024-01-24 13:55:40,747] [INFO] Target genome list was writen to GCF_000174435.1_ASM17443v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:40,787] [INFO] Task started: fastANI
[2024-01-24 13:55:40,788] [INFO] Running command: fastANI --query /var/lib/cwl/stg77b848ab-ae80-4cd5-a174-3c9d1e79344d/GCF_000174435.1_ASM17443v1_genomic.fna.gz --refList GCF_000174435.1_ASM17443v1_genomic.fna/target_genomes.txt --output GCF_000174435.1_ASM17443v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:55:52,586] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:52,587] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbf44d5fb-20c9-4c6c-9556-87f4a8bad6aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:55:52,587] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbf44d5fb-20c9-4c6c-9556-87f4a8bad6aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:55:52,594] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:55:52,594] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:55:52,594] [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
Desulfonatronospira thiodismutans	strain=ASO3-1	GCA_000174435.1	488939	488939	type	True	100.0	1367	1367	95	conclusive
Desulfonatronovibrio hydrogenovorans	strain=DSM 9292	GCA_000686525.1	53245	53245	type	True	77.0319	138	1367	95	below_threshold
Solidesulfovibrio magneticus	strain=RS-1	GCA_000010665.1	184917	184917	type	True	76.9147	54	1367	95	below_threshold
Desulfovibrio sulfodismutans	strain=DSM 3696	GCA_013376455.1	63561	63561	type	True	76.6545	68	1367	95	below_threshold
Desulfovibrio sulfodismutans	strain=DSM 3696	GCA_010499425.1	63561	63561	type	True	76.3452	64	1367	95	below_threshold
Desulfomicrobium escambiense	strain=DSM 10707	GCA_000428825.1	29503	29503	type	True	76.2524	61	1367	95	below_threshold
Pseudodesulfovibrio hydrargyri	strain=BerOc1	GCA_001874525.1	2125990	2125990	type	True	76.1599	59	1367	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:55:52,596] [INFO] DFAST Taxonomy check result was written to GCF_000174435.1_ASM17443v1_genomic.fna/tc_result.tsv
[2024-01-24 13:55:52,597] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:55:52,597] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:55:52,597] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbf44d5fb-20c9-4c6c-9556-87f4a8bad6aa/dqc_reference/checkm_data
[2024-01-24 13:55:52,598] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:55:52,638] [INFO] Task started: CheckM
[2024-01-24 13:55:52,638] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000174435.1_ASM17443v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000174435.1_ASM17443v1_genomic.fna/checkm_input GCF_000174435.1_ASM17443v1_genomic.fna/checkm_result
[2024-01-24 13:56:27,313] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:27,314] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:27,336] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:27,336] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:27,337] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000174435.1_ASM17443v1_genomic.fna/markers.fasta)
[2024-01-24 13:56:27,337] [INFO] Task started: Blastn
[2024-01-24 13:56:27,337] [INFO] Running command: blastn -query GCF_000174435.1_ASM17443v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf44d5fb-20c9-4c6c-9556-87f4a8bad6aa/dqc_reference/reference_markers_gtdb.fasta -out GCF_000174435.1_ASM17443v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:28,046] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:28,049] [INFO] Selected 11 target genomes.
[2024-01-24 13:56:28,049] [INFO] Target genome list was writen to GCF_000174435.1_ASM17443v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:28,066] [INFO] Task started: fastANI
[2024-01-24 13:56:28,067] [INFO] Running command: fastANI --query /var/lib/cwl/stg77b848ab-ae80-4cd5-a174-3c9d1e79344d/GCF_000174435.1_ASM17443v1_genomic.fna.gz --refList GCF_000174435.1_ASM17443v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000174435.1_ASM17443v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:56:38,295] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:38,303] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:56:38,303] [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_000174435.1	s__Desulfonatronospira thiodismutans	100.0	1367	1367	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfonatronovibrionaceae;g__Desulfonatronospira	95.0	98.95	98.95	0.92	0.87	3	conclusive
GCA_003554505.1	s__Desulfonatronospira sp003554505	87.7781	331	1367	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfonatronovibrionaceae;g__Desulfonatronospira	95.0	98.55	98.34	0.64	0.62	3	-
GCA_003553695.1	s__Desulfonatronospira sp003553695	87.1412	512	1367	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfonatronovibrionaceae;g__Desulfonatronospira	95.0	99.25	99.02	0.85	0.82	4	-
GCA_003563255.1	s__Desulfonatronospira sp003563255	85.3747	551	1367	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfonatronovibrionaceae;g__Desulfonatronospira	95.0	98.64	98.64	0.80	0.80	2	-
GCA_003551155.1	s__Desulfonatronospira sp003551155	78.4288	213	1367	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfonatronovibrionaceae;g__Desulfonatronospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003566455.1	s__Desulfonatronovibrio sp003566455	77.4567	113	1367	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfonatronovibrionaceae;g__Desulfonatronovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007125075.1	s__Desulfonatronospira sp007125075	77.4361	161	1367	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfonatronovibrionaceae;g__Desulfonatronospira	95.0	99.79	99.69	0.89	0.83	4	-
GCA_007127015.1	s__Desulfonatronospira sp007127015	77.3462	92	1367	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfonatronovibrionaceae;g__Desulfonatronospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000428825.1	s__Desulfomicrobium escambiense	76.2571	61	1367	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfomicrobiaceae;g__Desulfomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:56:38,305] [INFO] GTDB search result was written to GCF_000174435.1_ASM17443v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:56:38,305] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:56:38,308] [INFO] DFAST_QC result json was written to GCF_000174435.1_ASM17443v1_genomic.fna/dqc_result.json
[2024-01-24 13:56:38,308] [INFO] DFAST_QC completed!
[2024-01-24 13:56:38,308] [INFO] Total running time: 0h1m11s