[2024-01-24 14:22:33,527] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:33,529] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:33,530] [INFO] DQC Reference Directory: /var/lib/cwl/stg9b3cbc5c-2f44-40e5-990f-5b5579bab749/dqc_reference
[2024-01-24 14:22:34,840] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:34,841] [INFO] Task started: Prodigal
[2024-01-24 14:22:34,841] [INFO] Running command: gunzip -c /var/lib/cwl/stgf940835e-1119-410b-8a72-35f48210c9c5/GCF_008121885.1_ASM812188v1_genomic.fna.gz | prodigal -d GCF_008121885.1_ASM812188v1_genomic.fna/cds.fna -a GCF_008121885.1_ASM812188v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:41,089] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:41,089] [INFO] Task started: HMMsearch
[2024-01-24 14:22:41,090] [INFO] Running command: hmmsearch --tblout GCF_008121885.1_ASM812188v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9b3cbc5c-2f44-40e5-990f-5b5579bab749/dqc_reference/reference_markers.hmm GCF_008121885.1_ASM812188v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:41,395] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:41,482] [INFO] Found 6/6 markers.
[2024-01-24 14:22:41,601] [INFO] Query marker FASTA was written to GCF_008121885.1_ASM812188v1_genomic.fna/markers.fasta
[2024-01-24 14:22:41,602] [INFO] Task started: Blastn
[2024-01-24 14:22:41,602] [INFO] Running command: blastn -query GCF_008121885.1_ASM812188v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b3cbc5c-2f44-40e5-990f-5b5579bab749/dqc_reference/reference_markers.fasta -out GCF_008121885.1_ASM812188v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:42,187] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:42,190] [INFO] Selected 10 target genomes.
[2024-01-24 14:22:42,191] [INFO] Target genome list was writen to GCF_008121885.1_ASM812188v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:42,203] [INFO] Task started: fastANI
[2024-01-24 14:22:42,204] [INFO] Running command: fastANI --query /var/lib/cwl/stgf940835e-1119-410b-8a72-35f48210c9c5/GCF_008121885.1_ASM812188v1_genomic.fna.gz --refList GCF_008121885.1_ASM812188v1_genomic.fna/target_genomes.txt --output GCF_008121885.1_ASM812188v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:47,725] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:47,726] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9b3cbc5c-2f44-40e5-990f-5b5579bab749/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:47,726] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9b3cbc5c-2f44-40e5-990f-5b5579bab749/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:47,734] [INFO] Found 7 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:22:47,734] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:47,734] [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
Moorella thermoacetica	strain=ATCC 35608	GCA_008121885.1	1525	1525	type	True	100.0	859	860	95	conclusive
Moorella thermoacetica	strain=DSM 2955	GCA_001267435.1	1525	1525	type	True	99.9957	860	860	95	conclusive
Moorella thermoacetica	strain=DSM 521	GCA_001267405.1	1525	1525	type	True	99.9078	829	860	95	conclusive
Moorella mulderi	strain=DSM 14980	GCA_001594015.1	202604	202604	type	True	81.5906	507	860	95	below_threshold
Moorella stamsii	strain=DSM 26217	GCA_002995805.1	1266720	1266720	type	True	80.9771	501	860	95	below_threshold
Moorella glycerini	strain=DSM 11254	GCA_009735625.1	55779	55779	type	True	80.8247	525	860	95	below_threshold
Moorella humiferrea	strain=DSM 23265	GCA_002995755.1	676965	676965	type	True	80.1443	309	860	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:47,736] [INFO] DFAST Taxonomy check result was written to GCF_008121885.1_ASM812188v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:47,736] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:47,736] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:47,737] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9b3cbc5c-2f44-40e5-990f-5b5579bab749/dqc_reference/checkm_data
[2024-01-24 14:22:47,738] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:47,784] [INFO] Task started: CheckM
[2024-01-24 14:22:47,784] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008121885.1_ASM812188v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008121885.1_ASM812188v1_genomic.fna/checkm_input GCF_008121885.1_ASM812188v1_genomic.fna/checkm_result
[2024-01-24 14:23:12,729] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:12,730] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:12,754] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:12,754] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:12,755] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008121885.1_ASM812188v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:12,755] [INFO] Task started: Blastn
[2024-01-24 14:23:12,755] [INFO] Running command: blastn -query GCF_008121885.1_ASM812188v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b3cbc5c-2f44-40e5-990f-5b5579bab749/dqc_reference/reference_markers_gtdb.fasta -out GCF_008121885.1_ASM812188v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:13,620] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:13,624] [INFO] Selected 12 target genomes.
[2024-01-24 14:23:13,624] [INFO] Target genome list was writen to GCF_008121885.1_ASM812188v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:13,635] [INFO] Task started: fastANI
[2024-01-24 14:23:13,635] [INFO] Running command: fastANI --query /var/lib/cwl/stgf940835e-1119-410b-8a72-35f48210c9c5/GCF_008121885.1_ASM812188v1_genomic.fna.gz --refList GCF_008121885.1_ASM812188v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008121885.1_ASM812188v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:22,183] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:22,192] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:22,192] [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_001267405.1	s__Moorella thermoacetica	99.9037	829	860	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__Moorellales;f__Moorellaceae;g__Moorella	95.0	99.27	98.11	0.95	0.88	17	conclusive
GCF_001875325.1	s__Moorella thermoacetica_A	93.0756	642	860	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__Moorellales;f__Moorellaceae;g__Moorella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003116935.1	s__Moorella sp003116935	83.3043	624	860	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__Moorellales;f__Moorellaceae;g__Moorella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001594015.1	s__Moorella mulderi	81.5709	506	860	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__Moorellales;f__Moorellaceae;g__Moorella	95.265	N/A	N/A	N/A	N/A	1	-
GCF_006538365.1	s__Moorella sp006538365	81.3706	493	860	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__Moorellales;f__Moorellaceae;g__Moorella	95.0	99.18	99.18	0.87	0.87	2	-
GCF_002995805.1	s__Moorella stamsii	80.981	502	860	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__Moorellales;f__Moorellaceae;g__Moorella	95.265	99.99	99.99	0.99	0.99	2	-
GCF_009735625.1	s__Moorella glycerini	80.8433	522	860	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__Moorellales;f__Moorellaceae;g__Moorella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002995755.1	s__Moorella humiferrea	80.1496	308	860	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__Moorellales;f__Moorellaceae;g__Moorella	95.0	97.49	97.49	0.85	0.85	2	-
GCA_002383405.1	s__Moorella sp002383405	78.8523	230	860	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__Moorellales;f__Moorellaceae;g__Moorella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012727745.1	s__JAAYGJ01 sp012727745	76.5032	62	860	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__Moorellales;f__Moorellaceae;g__JAAYGJ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:22,194] [INFO] GTDB search result was written to GCF_008121885.1_ASM812188v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:22,195] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:22,197] [INFO] DFAST_QC result json was written to GCF_008121885.1_ASM812188v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:22,198] [INFO] DFAST_QC completed!
[2024-01-24 14:23:22,198] [INFO] Total running time: 0h0m49s