[2024-01-24 13:19:01,239] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:01,241] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:01,241] [INFO] DQC Reference Directory: /var/lib/cwl/stg5ab34be4-1875-48ee-bd4d-75ae91524143/dqc_reference
[2024-01-24 13:19:02,655] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:02,655] [INFO] Task started: Prodigal
[2024-01-24 13:19:02,656] [INFO] Running command: gunzip -c /var/lib/cwl/stge5631456-299f-4d9f-a97b-2cb296cec67c/GCF_009688965.1_ASM968896v1_genomic.fna.gz | prodigal -d GCF_009688965.1_ASM968896v1_genomic.fna/cds.fna -a GCF_009688965.1_ASM968896v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:24,999] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:24,999] [INFO] Task started: HMMsearch
[2024-01-24 13:19:24,999] [INFO] Running command: hmmsearch --tblout GCF_009688965.1_ASM968896v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5ab34be4-1875-48ee-bd4d-75ae91524143/dqc_reference/reference_markers.hmm GCF_009688965.1_ASM968896v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:25,454] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:25,455] [INFO] Found 6/6 markers.
[2024-01-24 13:19:25,520] [INFO] Query marker FASTA was written to GCF_009688965.1_ASM968896v1_genomic.fna/markers.fasta
[2024-01-24 13:19:25,520] [INFO] Task started: Blastn
[2024-01-24 13:19:25,521] [INFO] Running command: blastn -query GCF_009688965.1_ASM968896v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ab34be4-1875-48ee-bd4d-75ae91524143/dqc_reference/reference_markers.fasta -out GCF_009688965.1_ASM968896v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:26,178] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:26,182] [INFO] Selected 19 target genomes.
[2024-01-24 13:19:26,182] [INFO] Target genome list was writen to GCF_009688965.1_ASM968896v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:26,217] [INFO] Task started: fastANI
[2024-01-24 13:19:26,217] [INFO] Running command: fastANI --query /var/lib/cwl/stge5631456-299f-4d9f-a97b-2cb296cec67c/GCF_009688965.1_ASM968896v1_genomic.fna.gz --refList GCF_009688965.1_ASM968896v1_genomic.fna/target_genomes.txt --output GCF_009688965.1_ASM968896v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:45,339] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:45,339] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5ab34be4-1875-48ee-bd4d-75ae91524143/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:45,340] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5ab34be4-1875-48ee-bd4d-75ae91524143/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:45,353] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:45,353] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:45,353] [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
Desulfosarcina widdelii	strain=PP31	GCA_009688965.1	947919	947919	type	True	100.0	2430	2432	95	conclusive
Desulfosarcina alkanivorans	strain=PL12	GCA_009688945.1	571177	571177	type	True	79.583	917	2432	95	below_threshold
Desulfosarcina ovata subsp. ovata	strain=oXyS1	GCA_009689005.1	2752305	83564	type	True	78.9291	652	2432	95	below_threshold
Desulfosarcina ovata subsp. sediminis	strain=28bB2T	GCA_009688985.1	885957	83564	type	True	78.699	625	2432	95	below_threshold
Desulfosarcina cetonica	strain=JCM 12296	GCA_001311845.1	90730	90730	type	True	78.4774	529	2432	95	below_threshold
Desulfosudis oleivorans	strain=Hxd3	GCA_000018405.1	181663	181663	type	True	76.9027	117	2432	95	below_threshold
Desulfococcus multivorans	strain=DSM 2059	GCA_900167235.1	897	897	type	True	76.8462	111	2432	95	below_threshold
Desulfonema ishimotonii	strain=Tokyo 01	GCA_003851005.1	45657	45657	type	True	76.7345	152	2432	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	75.596	50	2432	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	75.1911	52	2432	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:45,354] [INFO] DFAST Taxonomy check result was written to GCF_009688965.1_ASM968896v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:45,355] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:45,355] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:45,355] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5ab34be4-1875-48ee-bd4d-75ae91524143/dqc_reference/checkm_data
[2024-01-24 13:19:45,356] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:45,421] [INFO] Task started: CheckM
[2024-01-24 13:19:45,421] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009688965.1_ASM968896v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009688965.1_ASM968896v1_genomic.fna/checkm_input GCF_009688965.1_ASM968896v1_genomic.fna/checkm_result
[2024-01-24 13:20:48,112] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:48,113] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:48,136] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:48,136] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:48,136] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009688965.1_ASM968896v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:48,137] [INFO] Task started: Blastn
[2024-01-24 13:20:48,137] [INFO] Running command: blastn -query GCF_009688965.1_ASM968896v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ab34be4-1875-48ee-bd4d-75ae91524143/dqc_reference/reference_markers_gtdb.fasta -out GCF_009688965.1_ASM968896v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:49,057] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:49,061] [INFO] Selected 10 target genomes.
[2024-01-24 13:20:49,061] [INFO] Target genome list was writen to GCF_009688965.1_ASM968896v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:49,070] [INFO] Task started: fastANI
[2024-01-24 13:20:49,071] [INFO] Running command: fastANI --query /var/lib/cwl/stge5631456-299f-4d9f-a97b-2cb296cec67c/GCF_009688965.1_ASM968896v1_genomic.fna.gz --refList GCF_009688965.1_ASM968896v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009688965.1_ASM968896v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:21:00,401] [INFO] Task succeeded: fastANI
[2024-01-24 13:21:00,413] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:21:00,413] [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_009688965.1	s__Desulfosarcina widdelii	100.0	2430	2432	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009688945.1	s__Desulfosarcina alkanivorans	79.574	916	2432	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009689005.1	s__Desulfosarcina ovata	78.9329	651	2432	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina	95.0	97.03	97.03	0.77	0.77	2	-
GCA_014237405.1	s__Desulfosarcina sp014237405	78.9227	651	2432	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina	95.0	99.69	99.69	0.89	0.89	3	-
GCA_002352605.1	s__Desulfosarcina sp002352605	78.6962	376	2432	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018224455.1	s__Desulfosarcina sp018224455	78.5952	501	2432	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001311845.1	s__Desulfosarcina cetonica	78.5068	525	2432	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina	95.0	99.91	99.91	0.98	0.98	2	-
GCA_002747175.1	s__Desulfosarcina sp002747175	77.8173	167	2432	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina	95.0	97.81	97.81	0.57	0.57	2	-
GCA_018224505.1	s__Desulfatitalea sp018224505	76.5165	152	2432	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfatitalea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:21:00,415] [INFO] GTDB search result was written to GCF_009688965.1_ASM968896v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:21:00,415] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:21:00,418] [INFO] DFAST_QC result json was written to GCF_009688965.1_ASM968896v1_genomic.fna/dqc_result.json
[2024-01-24 13:21:00,419] [INFO] DFAST_QC completed!
[2024-01-24 13:21:00,419] [INFO] Total running time: 0h1m59s