[2023-06-18 17:33:03,105] [INFO] DFAST_QC pipeline started.
[2023-06-18 17:33:03,107] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 17:33:03,107] [INFO] DQC Reference Directory: /var/lib/cwl/stgd67fb68a-7652-4583-b82c-e5d38fb25f6f/dqc_reference
[2023-06-18 17:33:04,452] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 17:33:04,453] [INFO] Task started: Prodigal
[2023-06-18 17:33:04,453] [INFO] Running command: gunzip -c /var/lib/cwl/stg3c6ec288-e288-4f5d-8be3-9b259409d694/GCA_018003515.1_ASM1800351v1_genomic.fna.gz | prodigal -d GCA_018003515.1_ASM1800351v1_genomic.fna/cds.fna -a GCA_018003515.1_ASM1800351v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 17:33:24,638] [INFO] Task succeeded: Prodigal
[2023-06-18 17:33:24,639] [INFO] Task started: HMMsearch
[2023-06-18 17:33:24,639] [INFO] Running command: hmmsearch --tblout GCA_018003515.1_ASM1800351v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd67fb68a-7652-4583-b82c-e5d38fb25f6f/dqc_reference/reference_markers.hmm GCA_018003515.1_ASM1800351v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 17:33:25,051] [INFO] Task succeeded: HMMsearch
[2023-06-18 17:33:25,052] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3c6ec288-e288-4f5d-8be3-9b259409d694/GCA_018003515.1_ASM1800351v1_genomic.fna.gz]
[2023-06-18 17:33:25,176] [INFO] Query marker FASTA was written to GCA_018003515.1_ASM1800351v1_genomic.fna/markers.fasta
[2023-06-18 17:33:25,177] [INFO] Task started: Blastn
[2023-06-18 17:33:25,177] [INFO] Running command: blastn -query GCA_018003515.1_ASM1800351v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd67fb68a-7652-4583-b82c-e5d38fb25f6f/dqc_reference/reference_markers.fasta -out GCA_018003515.1_ASM1800351v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 17:33:25,908] [INFO] Task succeeded: Blastn
[2023-06-18 17:33:25,920] [INFO] Selected 23 target genomes.
[2023-06-18 17:33:25,921] [INFO] Target genome list was writen to GCA_018003515.1_ASM1800351v1_genomic.fna/target_genomes.txt
[2023-06-18 17:33:25,928] [INFO] Task started: fastANI
[2023-06-18 17:33:25,928] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c6ec288-e288-4f5d-8be3-9b259409d694/GCA_018003515.1_ASM1800351v1_genomic.fna.gz --refList GCA_018003515.1_ASM1800351v1_genomic.fna/target_genomes.txt --output GCA_018003515.1_ASM1800351v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 17:33:40,860] [INFO] Task succeeded: fastANI
[2023-06-18 17:33:40,861] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd67fb68a-7652-4583-b82c-e5d38fb25f6f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 17:33:40,861] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd67fb68a-7652-4583-b82c-e5d38fb25f6f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 17:33:40,866] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 17:33:40,866] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 17:33:40,866] [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
Litorilinea aerophila	strain=ATCC BAA-2444	GCA_006569185.2	1204385	1204385	type	True	77.0288	327	1847	95	below_threshold
Caldilinea aerophila	strain=DSM 14535	GCA_000281175.1	133453	133453	type	True	76.1694	111	1847	95	below_threshold
Falsiroseomonas tokyonensis	strain=K-20	GCA_019024325.1	430521	430521	type	True	74.671	58	1847	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 17:33:40,869] [INFO] DFAST Taxonomy check result was written to GCA_018003515.1_ASM1800351v1_genomic.fna/tc_result.tsv
[2023-06-18 17:33:40,871] [INFO] ===== Taxonomy check completed =====
[2023-06-18 17:33:40,872] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 17:33:40,872] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd67fb68a-7652-4583-b82c-e5d38fb25f6f/dqc_reference/checkm_data
[2023-06-18 17:33:40,873] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 17:33:40,936] [INFO] Task started: CheckM
[2023-06-18 17:33:40,936] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018003515.1_ASM1800351v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018003515.1_ASM1800351v1_genomic.fna/checkm_input GCA_018003515.1_ASM1800351v1_genomic.fna/checkm_result
[2023-06-18 17:34:39,474] [INFO] Task succeeded: CheckM
[2023-06-18 17:34:39,475] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.04%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 17:34:39,511] [INFO] ===== Completeness check finished =====
[2023-06-18 17:34:39,512] [INFO] ===== Start GTDB Search =====
[2023-06-18 17:34:39,514] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018003515.1_ASM1800351v1_genomic.fna/markers.fasta)
[2023-06-18 17:34:39,514] [INFO] Task started: Blastn
[2023-06-18 17:34:39,514] [INFO] Running command: blastn -query GCA_018003515.1_ASM1800351v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd67fb68a-7652-4583-b82c-e5d38fb25f6f/dqc_reference/reference_markers_gtdb.fasta -out GCA_018003515.1_ASM1800351v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 17:34:40,400] [INFO] Task succeeded: Blastn
[2023-06-18 17:34:40,408] [INFO] Selected 16 target genomes.
[2023-06-18 17:34:40,408] [INFO] Target genome list was writen to GCA_018003515.1_ASM1800351v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 17:34:40,421] [INFO] Task started: fastANI
[2023-06-18 17:34:40,421] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c6ec288-e288-4f5d-8be3-9b259409d694/GCA_018003515.1_ASM1800351v1_genomic.fna.gz --refList GCA_018003515.1_ASM1800351v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018003515.1_ASM1800351v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 17:34:58,631] [INFO] Task succeeded: fastANI
[2023-06-18 17:34:58,645] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 17:34:58,645] [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
GCA_018003515.1	s__JAGNDO01 sp018003515	100.0	1839	1847	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__JAGNDO01	95.0	99.87	99.85	0.92	0.92	4	conclusive
GCA_015494005.1	s__S144-5 sp015494005	77.2383	272	1847	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__S144-5	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006569185.1	s__Litorilinea aerophila	77.0435	325	1847	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Litorilinea	95.0	99.85	99.85	0.99	0.99	2	-
GCA_016199425.1	s__JACQGT01 sp016199425	76.5406	159	1847	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__JACQGT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124945.1	s__RI-153 sp016124945	76.092	155	1847	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__RI-153	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016861025.1	s__Caldilinea sp016861025	75.9685	113	1847	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Caldilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012032975.1	s__JAAUPU01 sp012032975	75.8596	82	1847	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__JAAUPU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003451595.1	s__Caldilinea sp003451595	75.8591	114	1847	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Caldilinea	95.0	99.85	99.85	0.94	0.94	2	-
GCA_003577005.1	s__CFX5 sp003577005	75.7937	126	1847	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__CFX5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014879765.1	s__JAAEKA01 sp014879765	75.7463	141	1847	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__JAAEKA01;f__JAAEKA01;g__JAAEKA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002391565.1	s__Caldilinea sp002391565	75.627	121	1847	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Caldilinea	95.0	99.77	99.77	0.90	0.90	2	-
GCF_003337555.1	s__Pseudorhodoferax soli	74.8708	50	1847	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudorhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 17:34:58,649] [INFO] GTDB search result was written to GCA_018003515.1_ASM1800351v1_genomic.fna/result_gtdb.tsv
[2023-06-18 17:34:58,649] [INFO] ===== GTDB Search completed =====
[2023-06-18 17:34:58,652] [INFO] DFAST_QC result json was written to GCA_018003515.1_ASM1800351v1_genomic.fna/dqc_result.json
[2023-06-18 17:34:58,653] [INFO] DFAST_QC completed!
[2023-06-18 17:34:58,653] [INFO] Total running time: 0h1m56s