[2024-01-24 14:50:04,376] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:50:04,377] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:50:04,378] [INFO] DQC Reference Directory: /var/lib/cwl/stg8753ea7e-5c6f-4e98-b450-89945bac1a27/dqc_reference
[2024-01-24 14:50:05,796] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:50:05,797] [INFO] Task started: Prodigal
[2024-01-24 14:50:05,797] [INFO] Running command: gunzip -c /var/lib/cwl/stgbfc9fe35-b039-4a8b-b16e-7a4c0592e22d/GCF_002008345.1_ASM200834v1_genomic.fna.gz | prodigal -d GCF_002008345.1_ASM200834v1_genomic.fna/cds.fna -a GCF_002008345.1_ASM200834v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:50:10,310] [INFO] Task succeeded: Prodigal
[2024-01-24 14:50:10,310] [INFO] Task started: HMMsearch
[2024-01-24 14:50:10,311] [INFO] Running command: hmmsearch --tblout GCF_002008345.1_ASM200834v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8753ea7e-5c6f-4e98-b450-89945bac1a27/dqc_reference/reference_markers.hmm GCF_002008345.1_ASM200834v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:50:10,613] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:50:10,615] [INFO] Found 6/6 markers.
[2024-01-24 14:50:10,648] [INFO] Query marker FASTA was written to GCF_002008345.1_ASM200834v1_genomic.fna/markers.fasta
[2024-01-24 14:50:10,648] [INFO] Task started: Blastn
[2024-01-24 14:50:10,648] [INFO] Running command: blastn -query GCF_002008345.1_ASM200834v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8753ea7e-5c6f-4e98-b450-89945bac1a27/dqc_reference/reference_markers.fasta -out GCF_002008345.1_ASM200834v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:50:11,287] [INFO] Task succeeded: Blastn
[2024-01-24 14:50:11,291] [INFO] Selected 15 target genomes.
[2024-01-24 14:50:11,292] [INFO] Target genome list was writen to GCF_002008345.1_ASM200834v1_genomic.fna/target_genomes.txt
[2024-01-24 14:50:11,299] [INFO] Task started: fastANI
[2024-01-24 14:50:11,299] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfc9fe35-b039-4a8b-b16e-7a4c0592e22d/GCF_002008345.1_ASM200834v1_genomic.fna.gz --refList GCF_002008345.1_ASM200834v1_genomic.fna/target_genomes.txt --output GCF_002008345.1_ASM200834v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:50:24,148] [INFO] Task succeeded: fastANI
[2024-01-24 14:50:24,148] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8753ea7e-5c6f-4e98-b450-89945bac1a27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:50:24,148] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8753ea7e-5c6f-4e98-b450-89945bac1a27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:50:24,160] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:50:24,161] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:50:24,161] [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 tepidum	strain=IEH 97212	GCA_002008345.1	1962263	1962263	type	True	100.0	968	970	95	conclusive
Clostridium sporogenes	strain=NCTC13020	GCA_900461305.1	1509	1509	type	True	88.4828	822	970	95	below_threshold
Clostridium sporogenes	strain=DSM 795	GCA_001020205.1	1509	1509	type	True	88.4001	828	970	95	below_threshold
Clostridium sporogenes	strain=DSM 795	GCA_000685115.1	1509	1509	type	True	88.3765	833	970	95	below_threshold
Clostridium sporogenes	strain=NCIMB 10696	GCA_000973705.1	1509	1509	type	True	88.3749	832	970	95	below_threshold
Clostridium botulinum	strain=ATCC 25763	GCA_001276985.1	1491	1491	type	True	88.244	809	970	95	below_threshold
Clostridium botulinum	strain=ATCC 25763	GCA_011017965.1	1491	1491	type	True	88.1383	790	970	95	below_threshold
Clostridium combesii	strain=DSM 20696	GCA_002749945.1	39481	39481	type	True	88.0406	817	970	95	below_threshold
Clostridium faecium	strain=N37	GCA_014836835.1	2762223	2762223	type	True	77.7905	232	970	95	below_threshold
Clostridium acetireducens	strain=DSM 10703	GCA_001758365.1	76489	76489	type	True	77.2748	263	970	95	below_threshold
Clostridium tetanomorphum	strain=DSM 4474	GCA_017873215.1	1553	1553	type	True	77.1293	291	970	95	below_threshold
Clostridium mobile	strain=MSJ-11	GCA_018918285.1	2841512	2841512	type	True	76.9294	224	970	95	below_threshold
Clostridium simiarum	strain=MSJ-4	GCA_018919175.1	2841506	2841506	type	True	76.3261	169	970	95	below_threshold
Clostridium acidisoli	strain=DSM 12555	GCA_900176305.1	91624	91624	type	True	76.0563	150	970	95	below_threshold
Clostridium weizhouense	strain=YB-6	GCA_019431045.1	2859781	2859781	type	True	76.029	218	970	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:50:24,169] [INFO] DFAST Taxonomy check result was written to GCF_002008345.1_ASM200834v1_genomic.fna/tc_result.tsv
[2024-01-24 14:50:24,170] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:50:24,170] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:50:24,171] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8753ea7e-5c6f-4e98-b450-89945bac1a27/dqc_reference/checkm_data
[2024-01-24 14:50:24,173] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:50:24,211] [INFO] Task started: CheckM
[2024-01-24 14:50:24,211] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002008345.1_ASM200834v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002008345.1_ASM200834v1_genomic.fna/checkm_input GCF_002008345.1_ASM200834v1_genomic.fna/checkm_result
[2024-01-24 14:50:44,953] [INFO] Task succeeded: CheckM
[2024-01-24 14:50:44,954] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:50:44,976] [INFO] ===== Completeness check finished =====
[2024-01-24 14:50:44,977] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:50:44,977] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002008345.1_ASM200834v1_genomic.fna/markers.fasta)
[2024-01-24 14:50:44,978] [INFO] Task started: Blastn
[2024-01-24 14:50:44,978] [INFO] Running command: blastn -query GCF_002008345.1_ASM200834v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8753ea7e-5c6f-4e98-b450-89945bac1a27/dqc_reference/reference_markers_gtdb.fasta -out GCF_002008345.1_ASM200834v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:50:45,783] [INFO] Task succeeded: Blastn
[2024-01-24 14:50:45,787] [INFO] Selected 5 target genomes.
[2024-01-24 14:50:45,787] [INFO] Target genome list was writen to GCF_002008345.1_ASM200834v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:50:45,791] [INFO] Task started: fastANI
[2024-01-24 14:50:45,792] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfc9fe35-b039-4a8b-b16e-7a4c0592e22d/GCF_002008345.1_ASM200834v1_genomic.fna.gz --refList GCF_002008345.1_ASM200834v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002008345.1_ASM200834v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:50:50,698] [INFO] Task succeeded: fastANI
[2024-01-24 14:50:50,703] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:50:50,703] [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_002008345.1	s__Clostridium_F tepidum	100.0	968	970	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	conclusive
GCF_001276215.1	s__Clostridium_F sp001276215	91.5762	816	970	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_001020205.1	s__Clostridium_F sporogenes	88.4071	827	970	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	-
GCF_001889325.1	s__Clostridium_F botulinum_A	88.3266	824	970	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	88.2443	809	970	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	-
--------------------------------------------------------------------------------
[2024-01-24 14:50:50,705] [INFO] GTDB search result was written to GCF_002008345.1_ASM200834v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:50:50,706] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:50:50,709] [INFO] DFAST_QC result json was written to GCF_002008345.1_ASM200834v1_genomic.fna/dqc_result.json
[2024-01-24 14:50:50,710] [INFO] DFAST_QC completed!
[2024-01-24 14:50:50,710] [INFO] Total running time: 0h0m46s