[2024-01-24 13:22:25,281] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:25,283] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:25,283] [INFO] DQC Reference Directory: /var/lib/cwl/stg578217e8-b31b-40d8-bac5-1e93457a173c/dqc_reference
[2024-01-24 13:22:26,595] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:26,596] [INFO] Task started: Prodigal
[2024-01-24 13:22:26,597] [INFO] Running command: gunzip -c /var/lib/cwl/stg38f8ec83-7a49-4e6c-99fc-28ad0c874236/GCF_001293685.1_ASM129368v1_genomic.fna.gz | prodigal -d GCF_001293685.1_ASM129368v1_genomic.fna/cds.fna -a GCF_001293685.1_ASM129368v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:45,292] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:45,292] [INFO] Task started: HMMsearch
[2024-01-24 13:22:45,292] [INFO] Running command: hmmsearch --tblout GCF_001293685.1_ASM129368v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg578217e8-b31b-40d8-bac5-1e93457a173c/dqc_reference/reference_markers.hmm GCF_001293685.1_ASM129368v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:45,727] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:45,728] [INFO] Found 6/6 markers.
[2024-01-24 13:22:45,788] [INFO] Query marker FASTA was written to GCF_001293685.1_ASM129368v1_genomic.fna/markers.fasta
[2024-01-24 13:22:45,789] [INFO] Task started: Blastn
[2024-01-24 13:22:45,789] [INFO] Running command: blastn -query GCF_001293685.1_ASM129368v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg578217e8-b31b-40d8-bac5-1e93457a173c/dqc_reference/reference_markers.fasta -out GCF_001293685.1_ASM129368v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:46,440] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:46,444] [INFO] Selected 26 target genomes.
[2024-01-24 13:22:46,444] [INFO] Target genome list was writen to GCF_001293685.1_ASM129368v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:46,453] [INFO] Task started: fastANI
[2024-01-24 13:22:46,453] [INFO] Running command: fastANI --query /var/lib/cwl/stg38f8ec83-7a49-4e6c-99fc-28ad0c874236/GCF_001293685.1_ASM129368v1_genomic.fna.gz --refList GCF_001293685.1_ASM129368v1_genomic.fna/target_genomes.txt --output GCF_001293685.1_ASM129368v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:07,461] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:07,462] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg578217e8-b31b-40d8-bac5-1e93457a173c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:07,462] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg578217e8-b31b-40d8-bac5-1e93457a173c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:07,475] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:23:07,475] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:07,475] [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
Desulfatitalea tepidiphila	strain=S28bF	GCA_001293685.1	1185843	1185843	type	True	100.0	1869	1869	95	conclusive
Desulfosarcina alkanivorans	strain=PL12	GCA_009688945.1	571177	571177	type	True	78.8536	275	1869	95	below_threshold
Desulfococcus multivorans	strain=DSM 2059	GCA_002009335.2	897	897	type	True	78.1254	129	1869	95	below_threshold
Desulfococcus multivorans	strain=DSM 2059	GCA_900167235.1	897	897	type	True	77.9611	128	1869	95	below_threshold
Desulfococcus multivorans	strain=DSM 2059	GCA_000422185.1	897	897	type	True	77.8923	127	1869	95	below_threshold
Desulfosarcina widdelii	strain=PP31	GCA_009688965.1	947919	947919	type	True	77.5697	261	1869	95	below_threshold
Desulfosudis oleivorans	strain=Hxd3	GCA_000018405.1	181663	181663	type	True	77.3141	99	1869	95	below_threshold
Desulfosarcina ovata subsp. ovata	strain=oXyS1	GCA_009689005.1	2752305	83564	type	True	77.0878	239	1869	95	below_threshold
Desulfosarcina ovata subsp. sediminis	strain=28bB2T	GCA_009688985.1	885957	83564	type	True	76.9287	230	1869	95	below_threshold
Desulfosalsimonas propionicica	strain=DSM 17721	GCA_013761005.1	332175	332175	type	True	76.272	92	1869	95	below_threshold
Pseudodesulfovibrio hydrargyri	strain=BerOc1	GCA_001874525.1	2125990	2125990	type	True	76.1816	64	1869	95	below_threshold
Desulfacinum infernum	strain=DSM 9756	GCA_900129305.1	35837	35837	type	True	75.7064	81	1869	95	below_threshold
Solidesulfovibrio carbinolicus	strain=DSM 3852	GCA_004135975.1	296842	296842	type	True	75.5852	73	1869	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	75.3647	53	1869	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	75.2406	55	1869	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:07,477] [INFO] DFAST Taxonomy check result was written to GCF_001293685.1_ASM129368v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:07,478] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:07,478] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:07,478] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg578217e8-b31b-40d8-bac5-1e93457a173c/dqc_reference/checkm_data
[2024-01-24 13:23:07,479] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:07,531] [INFO] Task started: CheckM
[2024-01-24 13:23:07,531] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001293685.1_ASM129368v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001293685.1_ASM129368v1_genomic.fna/checkm_input GCF_001293685.1_ASM129368v1_genomic.fna/checkm_result
[2024-01-24 13:24:02,038] [INFO] Task succeeded: CheckM
[2024-01-24 13:24:02,039] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:24:02,063] [INFO] ===== Completeness check finished =====
[2024-01-24 13:24:02,063] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:24:02,064] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001293685.1_ASM129368v1_genomic.fna/markers.fasta)
[2024-01-24 13:24:02,064] [INFO] Task started: Blastn
[2024-01-24 13:24:02,065] [INFO] Running command: blastn -query GCF_001293685.1_ASM129368v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg578217e8-b31b-40d8-bac5-1e93457a173c/dqc_reference/reference_markers_gtdb.fasta -out GCF_001293685.1_ASM129368v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:03,010] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:03,013] [INFO] Selected 21 target genomes.
[2024-01-24 13:24:03,014] [INFO] Target genome list was writen to GCF_001293685.1_ASM129368v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:24:03,069] [INFO] Task started: fastANI
[2024-01-24 13:24:03,069] [INFO] Running command: fastANI --query /var/lib/cwl/stg38f8ec83-7a49-4e6c-99fc-28ad0c874236/GCF_001293685.1_ASM129368v1_genomic.fna.gz --refList GCF_001293685.1_ASM129368v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001293685.1_ASM129368v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:20,169] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:20,179] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:20,180] [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_001293685.1	s__Desulfatitalea tepidiphila	100.0	1869	1869	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfatitalea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002402905.1	s__Desulfatitalea sp002402905	93.5464	1131	1869	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfatitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009688945.1	s__Desulfosarcina alkanivorans	78.9203	270	1869	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016218685.1	s__Desulfatitalea sp016218685	78.4952	349	1869	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfatitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018224505.1	s__Desulfatitalea sp018224505	77.6145	273	1869	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfatitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009688965.1	s__Desulfosarcina widdelii	77.5999	257	1869	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000961655.1	s__Desulfatitalea sp000961655	77.4839	336	1869	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfatitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003599575.1	s__Desulfatitalea sp003599575	77.3541	335	1869	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfatitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013041835.1	s__Desulfatitalea sp013041835	76.8885	168	1869	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfatitalea	95.0	99.91	99.91	0.92	0.92	2	-
GCA_002352605.1	s__Desulfosarcina sp002352605	76.8739	111	1869	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014237405.1	s__Desulfosarcina sp014237405	76.6976	154	1869	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina	95.0	99.69	99.69	0.89	0.89	3	-
GCA_903953895.1	s__RAAP-1 sp903953895	75.66	62	1869	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfatirhabdiaceae;g__RAAP-1	95.0	99.36	98.92	0.95	0.91	7	-
--------------------------------------------------------------------------------
[2024-01-24 13:24:20,182] [INFO] GTDB search result was written to GCF_001293685.1_ASM129368v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:20,183] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:20,189] [INFO] DFAST_QC result json was written to GCF_001293685.1_ASM129368v1_genomic.fna/dqc_result.json
[2024-01-24 13:24:20,189] [INFO] DFAST_QC completed!
[2024-01-24 13:24:20,189] [INFO] Total running time: 0h1m55s