[2024-01-24 14:31:14,461] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:14,463] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:14,463] [INFO] DQC Reference Directory: /var/lib/cwl/stg0cf4d596-7c0f-4e56-a05d-c8d9555bc2ac/dqc_reference
[2024-01-24 14:31:15,786] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:15,787] [INFO] Task started: Prodigal
[2024-01-24 14:31:15,787] [INFO] Running command: gunzip -c /var/lib/cwl/stg097cd5ca-f056-44bd-88bd-b34efebb20e1/GCF_002008145.1_ASM200814v1_genomic.fna.gz | prodigal -d GCF_002008145.1_ASM200814v1_genomic.fna/cds.fna -a GCF_002008145.1_ASM200814v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:22,404] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:22,404] [INFO] Task started: HMMsearch
[2024-01-24 14:31:22,404] [INFO] Running command: hmmsearch --tblout GCF_002008145.1_ASM200814v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0cf4d596-7c0f-4e56-a05d-c8d9555bc2ac/dqc_reference/reference_markers.hmm GCF_002008145.1_ASM200814v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:22,735] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:22,736] [INFO] Found 6/6 markers.
[2024-01-24 14:31:22,772] [INFO] Query marker FASTA was written to GCF_002008145.1_ASM200814v1_genomic.fna/markers.fasta
[2024-01-24 14:31:22,772] [INFO] Task started: Blastn
[2024-01-24 14:31:22,772] [INFO] Running command: blastn -query GCF_002008145.1_ASM200814v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0cf4d596-7c0f-4e56-a05d-c8d9555bc2ac/dqc_reference/reference_markers.fasta -out GCF_002008145.1_ASM200814v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:23,383] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:23,386] [INFO] Selected 10 target genomes.
[2024-01-24 14:31:23,386] [INFO] Target genome list was writen to GCF_002008145.1_ASM200814v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:23,390] [INFO] Task started: fastANI
[2024-01-24 14:31:23,391] [INFO] Running command: fastANI --query /var/lib/cwl/stg097cd5ca-f056-44bd-88bd-b34efebb20e1/GCF_002008145.1_ASM200814v1_genomic.fna.gz --refList GCF_002008145.1_ASM200814v1_genomic.fna/target_genomes.txt --output GCF_002008145.1_ASM200814v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:34,364] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:34,365] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0cf4d596-7c0f-4e56-a05d-c8d9555bc2ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:34,366] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0cf4d596-7c0f-4e56-a05d-c8d9555bc2ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:34,379] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 14:31:34,379] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:34,380] [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
Clostridium sporogenes	strain=ATCC 3584	GCA_002008145.1	1509	1509	type	True	100.0	1348	1350	95	conclusive
Clostridium sporogenes	strain=NCIMB 10696	GCA_000973705.1	1509	1509	type	True	99.9974	1349	1350	95	conclusive
Clostridium sporogenes	strain=DSM 795	GCA_001020205.1	1509	1509	type	True	99.997	1350	1350	95	conclusive
Clostridium sporogenes	strain=NCTC13020	GCA_900461305.1	1509	1509	type	True	99.997	1348	1350	95	conclusive
Clostridium sporogenes	strain=DSM 795	GCA_000685115.1	1509	1509	type	True	99.9713	1346	1350	95	conclusive
Clostridium tetanomorphum	strain=DSM 4474	GCA_017873215.1	1553	1553	type	True	77.9778	349	1350	95	below_threshold
Clostridium muellerianum	strain=P21	GCA_012926525.1	2716538	2716538	type	True	77.5203	327	1350	95	below_threshold
Clostridium acetireducens	strain=DSM 10703	GCA_001758365.1	76489	76489	type	True	77.0439	262	1350	95	below_threshold
Clostridium liquoris	strain=DSM 100320	GCA_002995785.1	1289519	1289519	type	True	76.9194	214	1350	95	below_threshold
Oceanirhabdus seepicola	strain=ZWT	GCA_023684385.1	2828781	2828781	type	True	76.2438	144	1350	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:34,386] [INFO] DFAST Taxonomy check result was written to GCF_002008145.1_ASM200814v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:34,386] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:34,386] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:34,387] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0cf4d596-7c0f-4e56-a05d-c8d9555bc2ac/dqc_reference/checkm_data
[2024-01-24 14:31:34,388] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:34,431] [INFO] Task started: CheckM
[2024-01-24 14:31:34,432] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002008145.1_ASM200814v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002008145.1_ASM200814v1_genomic.fna/checkm_input GCF_002008145.1_ASM200814v1_genomic.fna/checkm_result
[2024-01-24 14:32:00,470] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:00,471] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:00,493] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:00,493] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:00,494] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002008145.1_ASM200814v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:00,494] [INFO] Task started: Blastn
[2024-01-24 14:32:00,494] [INFO] Running command: blastn -query GCF_002008145.1_ASM200814v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0cf4d596-7c0f-4e56-a05d-c8d9555bc2ac/dqc_reference/reference_markers_gtdb.fasta -out GCF_002008145.1_ASM200814v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:01,248] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:01,252] [INFO] Selected 5 target genomes.
[2024-01-24 14:32:01,252] [INFO] Target genome list was writen to GCF_002008145.1_ASM200814v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:01,273] [INFO] Task started: fastANI
[2024-01-24 14:32:01,273] [INFO] Running command: fastANI --query /var/lib/cwl/stg097cd5ca-f056-44bd-88bd-b34efebb20e1/GCF_002008145.1_ASM200814v1_genomic.fna.gz --refList GCF_002008145.1_ASM200814v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002008145.1_ASM200814v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:07,752] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:07,764] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:07,764] [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_001020205.1	s__Clostridium_F sporogenes	99.997	1350	1350	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	99.24	98.80	0.94	0.88	81	conclusive
GCF_001889325.1	s__Clostridium_F botulinum_A	94.2892	1147	1350	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	95.92	95.51	0.89	0.85	52	-
GCF_001276985.1	s__Clostridium_F botulinum	91.9398	1070	1350	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	97.69	95.97	0.92	0.83	213	-
GCF_001276215.1	s__Clostridium_F sp001276215	89.4286	1002	1350	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	97.32	95.44	0.88	0.82	10	-
GCF_002008345.1	s__Clostridium_F tepidum	88.301	813	1350	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	99.70	99.54	0.93	0.92	5	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:07,766] [INFO] GTDB search result was written to GCF_002008145.1_ASM200814v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:07,766] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:07,769] [INFO] DFAST_QC result json was written to GCF_002008145.1_ASM200814v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:07,770] [INFO] DFAST_QC completed!
[2024-01-24 14:32:07,770] [INFO] Total running time: 0h0m53s