[2024-01-24 13:10:03,967] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:10:03,969] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:10:03,969] [INFO] DQC Reference Directory: /var/lib/cwl/stg449d9359-0fe1-4346-9135-64168e537f9c/dqc_reference
[2024-01-24 13:10:05,340] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:10:05,341] [INFO] Task started: Prodigal
[2024-01-24 13:10:05,341] [INFO] Running command: gunzip -c /var/lib/cwl/stg0fc3ce35-e9be-47c3-9415-0391e4d7b705/GCF_009688945.1_ASM968894v1_genomic.fna.gz | prodigal -d GCF_009688945.1_ASM968894v1_genomic.fna/cds.fna -a GCF_009688945.1_ASM968894v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:28,087] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:28,087] [INFO] Task started: HMMsearch
[2024-01-24 13:10:28,087] [INFO] Running command: hmmsearch --tblout GCF_009688945.1_ASM968894v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg449d9359-0fe1-4346-9135-64168e537f9c/dqc_reference/reference_markers.hmm GCF_009688945.1_ASM968894v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:28,534] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:28,535] [INFO] Found 6/6 markers.
[2024-01-24 13:10:28,594] [INFO] Query marker FASTA was written to GCF_009688945.1_ASM968894v1_genomic.fna/markers.fasta
[2024-01-24 13:10:28,595] [INFO] Task started: Blastn
[2024-01-24 13:10:28,595] [INFO] Running command: blastn -query GCF_009688945.1_ASM968894v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg449d9359-0fe1-4346-9135-64168e537f9c/dqc_reference/reference_markers.fasta -out GCF_009688945.1_ASM968894v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:29,276] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:29,279] [INFO] Selected 16 target genomes.
[2024-01-24 13:10:29,279] [INFO] Target genome list was writen to GCF_009688945.1_ASM968894v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:29,285] [INFO] Task started: fastANI
[2024-01-24 13:10:29,285] [INFO] Running command: fastANI --query /var/lib/cwl/stg0fc3ce35-e9be-47c3-9415-0391e4d7b705/GCF_009688945.1_ASM968894v1_genomic.fna.gz --refList GCF_009688945.1_ASM968894v1_genomic.fna/target_genomes.txt --output GCF_009688945.1_ASM968894v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:45,495] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:45,496] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg449d9359-0fe1-4346-9135-64168e537f9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:45,497] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg449d9359-0fe1-4346-9135-64168e537f9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:45,509] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:45,509] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:45,510] [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 alkanivorans	strain=PL12	GCA_009688945.1	571177	571177	type	True	100.0	2438	2441	95	conclusive
Desulfosarcina widdelii	strain=PP31	GCA_009688965.1	947919	947919	type	True	79.6398	896	2441	95	below_threshold
Desulfosarcina ovata subsp. ovata	strain=oXyS1	GCA_009689005.1	2752305	83564	type	True	79.276	734	2441	95	below_threshold
Desulfosarcina ovata subsp. sediminis	strain=28bB2T	GCA_009688985.1	885957	83564	type	True	78.5137	688	2441	95	below_threshold
Desulfosarcina cetonica	strain=JCM 12296	GCA_001311845.1	90730	90730	type	True	78.182	549	2441	95	below_threshold
Desulfosudis oleivorans	strain=Hxd3	GCA_000018405.1	181663	181663	type	True	77.2529	154	2441	95	below_threshold
Desulfonema ishimotonii	strain=Tokyo 01	GCA_003851005.1	45657	45657	type	True	76.5225	173	2441	95	below_threshold
Desulfatirhabdium butyrativorans	strain=DSM 18734	GCA_000429925.1	340467	340467	type	True	76.373	93	2441	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	75.5011	60	2441	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	75.3659	64	2441	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	75.1749	59	2441	95	below_threshold
Alcanivorax gelatiniphagus	strain=MEBiC 08158	GCA_005938655.1	1194167	1194167	type	True	74.8852	53	2441	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:45,511] [INFO] DFAST Taxonomy check result was written to GCF_009688945.1_ASM968894v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:45,512] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:45,512] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:45,512] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg449d9359-0fe1-4346-9135-64168e537f9c/dqc_reference/checkm_data
[2024-01-24 13:10:45,514] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:45,585] [INFO] Task started: CheckM
[2024-01-24 13:10:45,586] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009688945.1_ASM968894v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009688945.1_ASM968894v1_genomic.fna/checkm_input GCF_009688945.1_ASM968894v1_genomic.fna/checkm_result
[2024-01-24 13:11:51,346] [INFO] Task succeeded: CheckM
[2024-01-24 13:11:51,348] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:11:51,372] [INFO] ===== Completeness check finished =====
[2024-01-24 13:11:51,372] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:11:51,372] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009688945.1_ASM968894v1_genomic.fna/markers.fasta)
[2024-01-24 13:11:51,373] [INFO] Task started: Blastn
[2024-01-24 13:11:51,373] [INFO] Running command: blastn -query GCF_009688945.1_ASM968894v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg449d9359-0fe1-4346-9135-64168e537f9c/dqc_reference/reference_markers_gtdb.fasta -out GCF_009688945.1_ASM968894v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:52,433] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:52,438] [INFO] Selected 9 target genomes.
[2024-01-24 13:11:52,438] [INFO] Target genome list was writen to GCF_009688945.1_ASM968894v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:52,447] [INFO] Task started: fastANI
[2024-01-24 13:11:52,447] [INFO] Running command: fastANI --query /var/lib/cwl/stg0fc3ce35-e9be-47c3-9415-0391e4d7b705/GCF_009688945.1_ASM968894v1_genomic.fna.gz --refList GCF_009688945.1_ASM968894v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009688945.1_ASM968894v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:12:02,258] [INFO] Task succeeded: fastANI
[2024-01-24 13:12:02,273] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:12:02,273] [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_009688945.1	s__Desulfosarcina alkanivorans	100.0	2438	2441	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014237405.1	s__Desulfosarcina sp014237405	81.4452	875	2441	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina	95.0	99.69	99.69	0.89	0.89	3	-
GCA_018224455.1	s__Desulfosarcina sp018224455	80.7063	702	2441	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002352605.1	s__Desulfosarcina sp002352605	80.5683	576	2441	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009688965.1	s__Desulfosarcina widdelii	79.6313	901	2441	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	79.2733	732	2441	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina	95.0	97.03	97.03	0.77	0.77	2	-
GCF_000018405.1	s__Desulfosudis oleovorans	77.2363	155	2441	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosudaceae;g__Desulfosudis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016218685.1	s__Desulfatitalea sp016218685	76.8509	192	2441	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfatitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390315.1	s__JAABSQ01 sp011390315	76.4499	130	2441	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfococcaceae;g__JAABSQ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:12:02,275] [INFO] GTDB search result was written to GCF_009688945.1_ASM968894v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:12:02,276] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:12:02,278] [INFO] DFAST_QC result json was written to GCF_009688945.1_ASM968894v1_genomic.fna/dqc_result.json
[2024-01-24 13:12:02,279] [INFO] DFAST_QC completed!
[2024-01-24 13:12:02,279] [INFO] Total running time: 0h1m58s