[2024-01-25 19:37:20,632] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:37:20,634] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:37:20,634] [INFO] DQC Reference Directory: /var/lib/cwl/stg8d6955df-943a-4421-9c76-36fc1ee0c15c/dqc_reference
[2024-01-25 19:37:21,880] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:37:21,881] [INFO] Task started: Prodigal
[2024-01-25 19:37:21,881] [INFO] Running command: gunzip -c /var/lib/cwl/stgd32b6ade-96cd-49fb-8f81-fcab780fa86f/GCF_030404055.1_ASM3040405v1_genomic.fna.gz | prodigal -d GCF_030404055.1_ASM3040405v1_genomic.fna/cds.fna -a GCF_030404055.1_ASM3040405v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:37:29,402] [INFO] Task succeeded: Prodigal
[2024-01-25 19:37:29,403] [INFO] Task started: HMMsearch
[2024-01-25 19:37:29,403] [INFO] Running command: hmmsearch --tblout GCF_030404055.1_ASM3040405v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8d6955df-943a-4421-9c76-36fc1ee0c15c/dqc_reference/reference_markers.hmm GCF_030404055.1_ASM3040405v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:37:29,611] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:37:29,612] [INFO] Found 6/6 markers.
[2024-01-25 19:37:29,647] [INFO] Query marker FASTA was written to GCF_030404055.1_ASM3040405v1_genomic.fna/markers.fasta
[2024-01-25 19:37:29,647] [INFO] Task started: Blastn
[2024-01-25 19:37:29,647] [INFO] Running command: blastn -query GCF_030404055.1_ASM3040405v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d6955df-943a-4421-9c76-36fc1ee0c15c/dqc_reference/reference_markers.fasta -out GCF_030404055.1_ASM3040405v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:37:30,185] [INFO] Task succeeded: Blastn
[2024-01-25 19:37:30,188] [INFO] Selected 29 target genomes.
[2024-01-25 19:37:30,189] [INFO] Target genome list was writen to GCF_030404055.1_ASM3040405v1_genomic.fna/target_genomes.txt
[2024-01-25 19:37:30,198] [INFO] Task started: fastANI
[2024-01-25 19:37:30,198] [INFO] Running command: fastANI --query /var/lib/cwl/stgd32b6ade-96cd-49fb-8f81-fcab780fa86f/GCF_030404055.1_ASM3040405v1_genomic.fna.gz --refList GCF_030404055.1_ASM3040405v1_genomic.fna/target_genomes.txt --output GCF_030404055.1_ASM3040405v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:37:51,783] [INFO] Task succeeded: fastANI
[2024-01-25 19:37:51,783] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8d6955df-943a-4421-9c76-36fc1ee0c15c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:37:51,784] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8d6955df-943a-4421-9c76-36fc1ee0c15c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:37:51,790] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:37:51,790] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:37:51,790] [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
Alkalihalobacillus macyae	strain=DSM 16346	GCA_001039475.1	157733	157733	type	True	96.3842	1250	1356	95	conclusive
Fictibacillus macauensis	strain=ZFHKF-1	GCA_000269865.1	245160	245160	type	True	76.928	57	1356	95	below_threshold
Litchfieldia salsa	strain=IBRC-M10078	GCA_900104555.1	930152	930152	type	True	76.8417	52	1356	95	below_threshold
Fictibacillus arsenicus	strain=Con a/3	GCA_001999465.1	255247	255247	type	True	76.584	64	1356	95	below_threshold
Metabacillus schmidteae	strain=Marseille-P9898	GCA_903166545.1	2730405	2730405	type	True	76.3393	55	1356	95	below_threshold
Lottiidibacillus patelloidae	strain=SA5d-4	GCA_002262935.1	2670334	2670334	type	True	76.1862	53	1356	95	below_threshold
Bacillus massiliogorillae	strain=G2	GCA_000380245.2	1243664	1243664	type	True	75.9339	56	1356	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:37:51,792] [INFO] DFAST Taxonomy check result was written to GCF_030404055.1_ASM3040405v1_genomic.fna/tc_result.tsv
[2024-01-25 19:37:51,793] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:37:51,793] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:37:51,793] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8d6955df-943a-4421-9c76-36fc1ee0c15c/dqc_reference/checkm_data
[2024-01-25 19:37:51,794] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:37:51,838] [INFO] Task started: CheckM
[2024-01-25 19:37:51,839] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030404055.1_ASM3040405v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030404055.1_ASM3040405v1_genomic.fna/checkm_input GCF_030404055.1_ASM3040405v1_genomic.fna/checkm_result
[2024-01-25 19:38:18,475] [INFO] Task succeeded: CheckM
[2024-01-25 19:38:18,477] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:38:18,510] [INFO] ===== Completeness check finished =====
[2024-01-25 19:38:18,510] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:38:18,511] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030404055.1_ASM3040405v1_genomic.fna/markers.fasta)
[2024-01-25 19:38:18,511] [INFO] Task started: Blastn
[2024-01-25 19:38:18,512] [INFO] Running command: blastn -query GCF_030404055.1_ASM3040405v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d6955df-943a-4421-9c76-36fc1ee0c15c/dqc_reference/reference_markers_gtdb.fasta -out GCF_030404055.1_ASM3040405v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:38:19,305] [INFO] Task succeeded: Blastn
[2024-01-25 19:38:19,307] [INFO] Selected 8 target genomes.
[2024-01-25 19:38:19,307] [INFO] Target genome list was writen to GCF_030404055.1_ASM3040405v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:38:19,315] [INFO] Task started: fastANI
[2024-01-25 19:38:19,315] [INFO] Running command: fastANI --query /var/lib/cwl/stgd32b6ade-96cd-49fb-8f81-fcab780fa86f/GCF_030404055.1_ASM3040405v1_genomic.fna.gz --refList GCF_030404055.1_ASM3040405v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030404055.1_ASM3040405v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:38:28,055] [INFO] Task succeeded: fastANI
[2024-01-25 19:38:28,060] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:38:28,061] [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_001039475.1	s__Anaerobacillus_A macyae	96.3842	1250	1356	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__HB172195;g__Anaerobacillus_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005144865.1	s__Anaerobacillus_A hwajinpoensis_A	87.3606	1137	1356	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__HB172195;g__Anaerobacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017303315.1	s__Anaerobacillus_A sp017303315	87.176	1101	1356	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__HB172195;g__Anaerobacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009818105.1	s__Anaerobacillus_A sp009818105	80.9419	671	1356	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__HB172195;g__Anaerobacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015234585.1	s__Anaerobacillus_A hwajinpoensis_B	80.7664	712	1356	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__HB172195;g__Anaerobacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002563635.1	s__Anaerobacillus_A sp002563635	80.7532	690	1356	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__HB172195;g__Anaerobacillus_A	95.0	96.09	95.80	0.90	0.90	3	-
GCF_003667865.1	s__Bacillus_BQ marisflavi_A	75.9846	58	1356	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Bacillus_BQ	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:38:28,062] [INFO] GTDB search result was written to GCF_030404055.1_ASM3040405v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:38:28,063] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:38:28,065] [INFO] DFAST_QC result json was written to GCF_030404055.1_ASM3040405v1_genomic.fna/dqc_result.json
[2024-01-25 19:38:28,065] [INFO] DFAST_QC completed!
[2024-01-25 19:38:28,065] [INFO] Total running time: 0h1m7s