[2024-01-24 13:09:49,070] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:49,072] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:49,072] [INFO] DQC Reference Directory: /var/lib/cwl/stg8e186d31-42b6-4034-b14b-1e19f35198bf/dqc_reference
[2024-01-24 13:09:50,425] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:50,426] [INFO] Task started: Prodigal
[2024-01-24 13:09:50,426] [INFO] Running command: gunzip -c /var/lib/cwl/stg637bb33e-6bc8-498a-a894-955b8ace89e3/GCF_004309735.1_ASM430973v1_genomic.fna.gz | prodigal -d GCF_004309735.1_ASM430973v1_genomic.fna/cds.fna -a GCF_004309735.1_ASM430973v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:58,941] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:58,942] [INFO] Task started: HMMsearch
[2024-01-24 13:09:58,942] [INFO] Running command: hmmsearch --tblout GCF_004309735.1_ASM430973v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8e186d31-42b6-4034-b14b-1e19f35198bf/dqc_reference/reference_markers.hmm GCF_004309735.1_ASM430973v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:59,226] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:59,228] [INFO] Found 6/6 markers.
[2024-01-24 13:09:59,255] [INFO] Query marker FASTA was written to GCF_004309735.1_ASM430973v1_genomic.fna/markers.fasta
[2024-01-24 13:09:59,256] [INFO] Task started: Blastn
[2024-01-24 13:09:59,256] [INFO] Running command: blastn -query GCF_004309735.1_ASM430973v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e186d31-42b6-4034-b14b-1e19f35198bf/dqc_reference/reference_markers.fasta -out GCF_004309735.1_ASM430973v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:59,911] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:59,915] [INFO] Selected 11 target genomes.
[2024-01-24 13:09:59,916] [INFO] Target genome list was writen to GCF_004309735.1_ASM430973v1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:59,945] [INFO] Task started: fastANI
[2024-01-24 13:09:59,945] [INFO] Running command: fastANI --query /var/lib/cwl/stg637bb33e-6bc8-498a-a894-955b8ace89e3/GCF_004309735.1_ASM430973v1_genomic.fna.gz --refList GCF_004309735.1_ASM430973v1_genomic.fna/target_genomes.txt --output GCF_004309735.1_ASM430973v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:07,819] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:07,820] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8e186d31-42b6-4034-b14b-1e19f35198bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:07,820] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8e186d31-42b6-4034-b14b-1e19f35198bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:07,830] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:07,830] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:07,830] [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 legallii	strain=H1T	GCA_004309735.1	571438	571438	type	True	100.0	875	875	95	conclusive
Desulfovibrio porci	strain=PG-178-WT-4	GCA_009696265.1	2605782	2605782	type	True	80.2624	473	875	95	below_threshold
Desulfovibrio piger	strain=ATCC 29098	GCA_000156375.1	901	901	suspected-type	True	79.0409	336	875	95	below_threshold
Desulfovibrio intestinalis	strain=DSM 11275	GCA_014202345.1	58621	58621	type	True	78.8152	357	875	95	below_threshold
Cupidesulfovibrio liaohensis	strain=XJ01	GCA_011682075.1	2604158	2604158	type	True	77.38	185	875	95	below_threshold
Cupidesulfovibrio termitidis	strain=HI1	GCA_000504305.1	42252	42252	type	True	77.1072	222	875	95	below_threshold
Mailhella massiliensis	strain=Marseille-P3199	GCA_900155525.1	1903261	1903261	type	True	77.0877	115	875	95	below_threshold
Megalodesulfovibrio gigas	strain=DSM 1382	GCA_000429285.1	879	879	type	True	76.871	126	875	95	below_threshold
Bilophila wadsworthia	strain=ATCC 49260	GCA_000701705.1	35833	35833	type	True	76.3442	96	875	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:07,832] [INFO] DFAST Taxonomy check result was written to GCF_004309735.1_ASM430973v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:07,832] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:07,832] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:07,833] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8e186d31-42b6-4034-b14b-1e19f35198bf/dqc_reference/checkm_data
[2024-01-24 13:10:07,834] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:07,861] [INFO] Task started: CheckM
[2024-01-24 13:10:07,861] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004309735.1_ASM430973v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004309735.1_ASM430973v1_genomic.fna/checkm_input GCF_004309735.1_ASM430973v1_genomic.fna/checkm_result
[2024-01-24 13:10:36,075] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:36,077] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:36,098] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:36,099] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:36,100] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004309735.1_ASM430973v1_genomic.fna/markers.fasta)
[2024-01-24 13:10:36,100] [INFO] Task started: Blastn
[2024-01-24 13:10:36,100] [INFO] Running command: blastn -query GCF_004309735.1_ASM430973v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e186d31-42b6-4034-b14b-1e19f35198bf/dqc_reference/reference_markers_gtdb.fasta -out GCF_004309735.1_ASM430973v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:37,079] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:37,083] [INFO] Selected 13 target genomes.
[2024-01-24 13:10:37,084] [INFO] Target genome list was writen to GCF_004309735.1_ASM430973v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:37,270] [INFO] Task started: fastANI
[2024-01-24 13:10:37,270] [INFO] Running command: fastANI --query /var/lib/cwl/stg637bb33e-6bc8-498a-a894-955b8ace89e3/GCF_004309735.1_ASM430973v1_genomic.fna.gz --refList GCF_004309735.1_ASM430973v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004309735.1_ASM430973v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:10:46,029] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:46,039] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:10:46,040] [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_004309735.1	s__Desulfovibrio legallii	100.0	875	875	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	99.59	99.44	0.93	0.93	5	conclusive
GCF_900102485.1	s__Desulfovibrio legallii_A	87.1657	724	875	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	99.86	99.86	0.97	0.97	2	-
GCF_009696265.1	s__Desulfovibrio porci	80.2701	471	875	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	99.64	99.64	0.91	0.91	2	-
GCA_015062205.1	s__Desulfovibrio desulfuricans_D	80.0989	415	875	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_001553605.1	s__Desulfovibrio fairfieldensis	80.0283	493	875	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	97.09	95.23	0.86	0.83	6	-
GCA_910575755.1	s__Desulfovibrio sp910575755	79.6243	417	875	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_004801255.1	s__Desulfovibrio desulfuricans_C	79.4866	494	875	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_000420465.1	s__Desulfovibrio desulfuricans	79.2685	452	875	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	96.33	95.61	0.91	0.89	6	-
GCA_009712225.1	s__Desulfovibrio sp009712225	79.262	431	875	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_011039085.1	s__Desulfovibrio sp011039085	79.2252	372	875	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	96.72	96.72	0.85	0.85	2	-
GCF_900116045.1	s__Desulfovibrio piger_A	79.0905	351	875	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	99.11	98.95	0.94	0.93	3	-
GCF_000022125.1	s__Desulfovibrio desulfuricans_A	78.929	379	875	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	99.36	99.22	0.93	0.89	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:10:46,041] [INFO] GTDB search result was written to GCF_004309735.1_ASM430973v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:10:46,042] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:10:46,045] [INFO] DFAST_QC result json was written to GCF_004309735.1_ASM430973v1_genomic.fna/dqc_result.json
[2024-01-24 13:10:46,045] [INFO] DFAST_QC completed!
[2024-01-24 13:10:46,045] [INFO] Total running time: 0h0m57s