[2024-01-24 14:12:34,772] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:34,774] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:34,774] [INFO] DQC Reference Directory: /var/lib/cwl/stg5525ead0-0bf0-4192-a125-5c2e896e5262/dqc_reference
[2024-01-24 14:12:36,221] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:36,222] [INFO] Task started: Prodigal
[2024-01-24 14:12:36,222] [INFO] Running command: gunzip -c /var/lib/cwl/stg7ccf5ad9-0ba1-4003-8498-8a14e65a3e81/GCF_000701705.1_ASM70170v1_genomic.fna.gz | prodigal -d GCF_000701705.1_ASM70170v1_genomic.fna/cds.fna -a GCF_000701705.1_ASM70170v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:50,087] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:50,088] [INFO] Task started: HMMsearch
[2024-01-24 14:12:50,088] [INFO] Running command: hmmsearch --tblout GCF_000701705.1_ASM70170v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5525ead0-0bf0-4192-a125-5c2e896e5262/dqc_reference/reference_markers.hmm GCF_000701705.1_ASM70170v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:50,402] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:50,403] [INFO] Found 6/6 markers.
[2024-01-24 14:12:50,442] [INFO] Query marker FASTA was written to GCF_000701705.1_ASM70170v1_genomic.fna/markers.fasta
[2024-01-24 14:12:50,443] [INFO] Task started: Blastn
[2024-01-24 14:12:50,443] [INFO] Running command: blastn -query GCF_000701705.1_ASM70170v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5525ead0-0bf0-4192-a125-5c2e896e5262/dqc_reference/reference_markers.fasta -out GCF_000701705.1_ASM70170v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:51,079] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:51,083] [INFO] Selected 19 target genomes.
[2024-01-24 14:12:51,083] [INFO] Target genome list was writen to GCF_000701705.1_ASM70170v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:51,089] [INFO] Task started: fastANI
[2024-01-24 14:12:51,089] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ccf5ad9-0ba1-4003-8498-8a14e65a3e81/GCF_000701705.1_ASM70170v1_genomic.fna.gz --refList GCF_000701705.1_ASM70170v1_genomic.fna/target_genomes.txt --output GCF_000701705.1_ASM70170v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:04,617] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:04,618] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5525ead0-0bf0-4192-a125-5c2e896e5262/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:04,619] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5525ead0-0bf0-4192-a125-5c2e896e5262/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:04,631] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:13:04,632] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:13:04,632] [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
Bilophila wadsworthia	strain=ATCC 49260	GCA_000701705.1	35833	35833	type	True	100.0	1433	1448	95	conclusive
Mailhella massiliensis	strain=Marseille-P3199	GCA_900155525.1	1903261	1903261	type	True	78.1636	170	1448	95	below_threshold
Cupidesulfovibrio liaohensis	strain=XJ01	GCA_011682075.1	2604158	2604158	type	True	77.5699	144	1448	95	below_threshold
Cupidesulfovibrio oxamicus	strain=NCIMB 9442	GCA_015731765.1	32016	32016	type	True	77.453	144	1448	95	below_threshold
Desulfovibrio piger	strain=ATCC 29098	GCA_000156375.1	901	901	suspected-type	True	77.4067	180	1448	95	below_threshold
Cupidesulfovibrio termitidis	strain=HI1	GCA_000504305.1	42252	42252	type	True	77.4044	170	1448	95	below_threshold
Desulfovibrio vulgaris	strain=Hildenborough	GCA_902167245.1	881	881	type	True	77.1902	138	1448	95	below_threshold
Desulfovibrio vulgaris	strain=Hildenborough	GCA_000195755.1	881	881	type	True	77.0354	144	1448	95	below_threshold
Desulfovibrio subterraneus	strain=HN2	GCA_013340285.1	2718620	2718620	type	True	76.7023	92	1448	95	below_threshold
Desulfomicrobium escambiense	strain=DSM 10707	GCA_000428825.1	29503	29503	type	True	76.5136	84	1448	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:04,633] [INFO] DFAST Taxonomy check result was written to GCF_000701705.1_ASM70170v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:04,634] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:04,634] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:04,635] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5525ead0-0bf0-4192-a125-5c2e896e5262/dqc_reference/checkm_data
[2024-01-24 14:13:04,636] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:04,684] [INFO] Task started: CheckM
[2024-01-24 14:13:04,684] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000701705.1_ASM70170v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000701705.1_ASM70170v1_genomic.fna/checkm_input GCF_000701705.1_ASM70170v1_genomic.fna/checkm_result
[2024-01-24 14:13:46,204] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:46,205] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:46,225] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:46,226] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:46,226] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000701705.1_ASM70170v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:46,227] [INFO] Task started: Blastn
[2024-01-24 14:13:46,227] [INFO] Running command: blastn -query GCF_000701705.1_ASM70170v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5525ead0-0bf0-4192-a125-5c2e896e5262/dqc_reference/reference_markers_gtdb.fasta -out GCF_000701705.1_ASM70170v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:47,167] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:47,170] [INFO] Selected 8 target genomes.
[2024-01-24 14:13:47,170] [INFO] Target genome list was writen to GCF_000701705.1_ASM70170v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:47,207] [INFO] Task started: fastANI
[2024-01-24 14:13:47,208] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ccf5ad9-0ba1-4003-8498-8a14e65a3e81/GCF_000701705.1_ASM70170v1_genomic.fna.gz --refList GCF_000701705.1_ASM70170v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000701705.1_ASM70170v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:53,032] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:53,038] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:53,038] [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_000701705.1	s__Bilophila wadsworthia	100.0	1433	1448	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Bilophila	95.0	98.41	97.08	0.87	0.83	9	conclusive
GCA_900550745.1	s__Bilophila sp900550745	92.5907	512	1448	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Bilophila	95.0	97.48	97.27	0.74	0.71	3	-
GCA_900553145.1	s__Bilophila sp900553145	90.0154	827	1448	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_902373525.1	s__Bilophila sp902373525	84.8323	714	1448	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Bilophila	95.0	98.79	98.79	0.94	0.94	2	-
GCA_019114025.1	s__Bilophila faecipullorum	82.2827	446	1448	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Bilophila	95.0	99.16	98.64	0.81	0.70	3	-
GCA_900555975.1	s__Mailhella sp900555975	77.8545	50	1448	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Mailhella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:13:53,040] [INFO] GTDB search result was written to GCF_000701705.1_ASM70170v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:53,041] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:53,044] [INFO] DFAST_QC result json was written to GCF_000701705.1_ASM70170v1_genomic.fna/dqc_result.json
[2024-01-24 14:13:53,044] [INFO] DFAST_QC completed!
[2024-01-24 14:13:53,044] [INFO] Total running time: 0h1m18s