[2024-01-24 11:51:37,288] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:37,290] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:37,290] [INFO] DQC Reference Directory: /var/lib/cwl/stg719d435e-e84a-4307-ada9-e3414875d5c2/dqc_reference
[2024-01-24 11:51:38,566] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:38,567] [INFO] Task started: Prodigal
[2024-01-24 11:51:38,567] [INFO] Running command: gunzip -c /var/lib/cwl/stgce3e675e-7eba-4e31-b64b-9091b791baa9/GCF_026230175.1_ASM2623017v1_genomic.fna.gz | prodigal -d GCF_026230175.1_ASM2623017v1_genomic.fna/cds.fna -a GCF_026230175.1_ASM2623017v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:51,510] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:51,510] [INFO] Task started: HMMsearch
[2024-01-24 11:51:51,510] [INFO] Running command: hmmsearch --tblout GCF_026230175.1_ASM2623017v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg719d435e-e84a-4307-ada9-e3414875d5c2/dqc_reference/reference_markers.hmm GCF_026230175.1_ASM2623017v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:51,774] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:51,776] [INFO] Found 6/6 markers.
[2024-01-24 11:51:51,814] [INFO] Query marker FASTA was written to GCF_026230175.1_ASM2623017v1_genomic.fna/markers.fasta
[2024-01-24 11:51:51,815] [INFO] Task started: Blastn
[2024-01-24 11:51:51,815] [INFO] Running command: blastn -query GCF_026230175.1_ASM2623017v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg719d435e-e84a-4307-ada9-e3414875d5c2/dqc_reference/reference_markers.fasta -out GCF_026230175.1_ASM2623017v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:52,432] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:52,436] [INFO] Selected 16 target genomes.
[2024-01-24 11:51:52,436] [INFO] Target genome list was writen to GCF_026230175.1_ASM2623017v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:52,444] [INFO] Task started: fastANI
[2024-01-24 11:51:52,444] [INFO] Running command: fastANI --query /var/lib/cwl/stgce3e675e-7eba-4e31-b64b-9091b791baa9/GCF_026230175.1_ASM2623017v1_genomic.fna.gz --refList GCF_026230175.1_ASM2623017v1_genomic.fna/target_genomes.txt --output GCF_026230175.1_ASM2623017v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:03,053] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:03,053] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg719d435e-e84a-4307-ada9-e3414875d5c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:03,054] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg719d435e-e84a-4307-ada9-e3414875d5c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:03,067] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:52:03,067] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:52:03,067] [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 subterraneus	strain=HN2	GCA_013340285.1	2718620	2718620	type	True	84.0173	959	1315	95	below_threshold
Desulfovibrio psychrotolerans	strain=JS1	GCA_013340305.1	415242	415242	type	True	79.6778	572	1315	95	below_threshold
Cupidesulfovibrio termitidis	strain=HI1	GCA_000504305.1	42252	42252	type	True	78.086	265	1315	95	below_threshold
Cupidesulfovibrio liaohensis	strain=XJ01	GCA_011682075.1	2604158	2604158	type	True	78.007	240	1315	95	below_threshold
Cupidesulfovibrio oxamicus	strain=NCIMB 9442	GCA_015731765.1	32016	32016	type	True	77.9392	223	1315	95	below_threshold
Desulfovibrio vulgaris	strain=Hildenborough	GCA_000195755.1	881	881	type	True	77.822	211	1315	95	below_threshold
Desulfovibrio vulgaris	strain=Hildenborough	GCA_902167245.1	881	881	type	True	77.8194	217	1315	95	below_threshold
Oleidesulfovibrio alaskensis	strain=DSM 16109	GCA_000482745.1	58180	58180	type	True	77.5615	199	1315	95	below_threshold
Desulfovibrio piger	strain=ATCC 29098	GCA_000156375.1	901	901	suspected-type	True	77.4474	126	1315	95	below_threshold
Bilophila wadsworthia	strain=ATCC 49260	GCA_000701705.1	35833	35833	type	True	76.8536	101	1315	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:03,069] [INFO] DFAST Taxonomy check result was written to GCF_026230175.1_ASM2623017v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:03,070] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:03,070] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:03,071] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg719d435e-e84a-4307-ada9-e3414875d5c2/dqc_reference/checkm_data
[2024-01-24 11:52:03,071] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:03,113] [INFO] Task started: CheckM
[2024-01-24 11:52:03,114] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026230175.1_ASM2623017v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026230175.1_ASM2623017v1_genomic.fna/checkm_input GCF_026230175.1_ASM2623017v1_genomic.fna/checkm_result
[2024-01-24 11:52:43,188] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:43,192] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:43,210] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:43,211] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:43,211] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026230175.1_ASM2623017v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:43,211] [INFO] Task started: Blastn
[2024-01-24 11:52:43,212] [INFO] Running command: blastn -query GCF_026230175.1_ASM2623017v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg719d435e-e84a-4307-ada9-e3414875d5c2/dqc_reference/reference_markers_gtdb.fasta -out GCF_026230175.1_ASM2623017v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:44,121] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:44,125] [INFO] Selected 17 target genomes.
[2024-01-24 11:52:44,125] [INFO] Target genome list was writen to GCF_026230175.1_ASM2623017v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:44,140] [INFO] Task started: fastANI
[2024-01-24 11:52:44,141] [INFO] Running command: fastANI --query /var/lib/cwl/stgce3e675e-7eba-4e31-b64b-9091b791baa9/GCF_026230175.1_ASM2623017v1_genomic.fna.gz --refList GCF_026230175.1_ASM2623017v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026230175.1_ASM2623017v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:55,363] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:55,379] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:52:55,380] [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_013340285.1	s__Halodesulfovibrio subterraneus	84.0032	961	1315	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Halodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003252375.1	s__Halodesulfovibrio sp003252375	81.2014	610	1315	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Halodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013340305.1	s__Halodesulfovibrio psychrotolerans	79.6862	571	1315	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Halodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000504305.1	s__Cupidesulfovibrio termitidis	78.0991	266	1315	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Cupidesulfovibrio	95.0	98.21	98.21	0.92	0.92	2	-
GCF_000021385.1	s__Cupidesulfovibrio vulgaris_A	77.9796	273	1315	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Cupidesulfovibrio	95.0	97.08	97.08	0.92	0.92	2	-
GCF_015731765.1	s__Cupidesulfovibrio oxamicus	77.9706	221	1315	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Cupidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000482745.1	s__Oleidesulfovibrio alaskensis	77.5688	199	1315	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Oleidesulfovibrio	95.0	99.29	99.19	0.96	0.95	4	-
GCA_902373525.1	s__Bilophila sp902373525	76.9938	117	1315	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Bilophila	95.0	98.79	98.79	0.94	0.94	2	-
GCF_000701705.1	s__Bilophila wadsworthia	76.8536	101	1315	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Bilophila	95.0	98.41	97.08	0.87	0.83	9	-
GCF_000519125.1	s__Desulfocurvus vexinensis	76.8469	131	1315	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfocurvus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900553145.1	s__Bilophila sp900553145	76.7069	97	1315	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Bilophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015709205.1	s__JACCQO01 sp015709205	76.4921	151	1315	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__JACCQO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905215675.1	s__Desulfovibrio sp905215675	76.4783	79	1315	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_018816865.1	s__Desulfovibrio_Q sp018816865	76.3265	115	1315	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio_Q	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:55,392] [INFO] GTDB search result was written to GCF_026230175.1_ASM2623017v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:55,393] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:55,399] [INFO] DFAST_QC result json was written to GCF_026230175.1_ASM2623017v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:55,400] [INFO] DFAST_QC completed!
[2024-01-24 11:52:55,400] [INFO] Total running time: 0h1m18s