[2023-06-28 12:02:15,941] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:02:15,944] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:02:15,945] [INFO] DQC Reference Directory: /var/lib/cwl/stg6054e86d-5121-4e9b-a102-3a4dc734fe2b/dqc_reference
[2023-06-28 12:02:17,393] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:02:17,394] [INFO] Task started: Prodigal
[2023-06-28 12:02:17,394] [INFO] Running command: gunzip -c /var/lib/cwl/stgd30f7ed5-18d0-49a4-b093-8c2f033e9a55/GCA_020433585.1_ASM2043358v1_genomic.fna.gz | prodigal -d GCA_020433585.1_ASM2043358v1_genomic.fna/cds.fna -a GCA_020433585.1_ASM2043358v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:02:32,761] [INFO] Task succeeded: Prodigal
[2023-06-28 12:02:32,761] [INFO] Task started: HMMsearch
[2023-06-28 12:02:32,761] [INFO] Running command: hmmsearch --tblout GCA_020433585.1_ASM2043358v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6054e86d-5121-4e9b-a102-3a4dc734fe2b/dqc_reference/reference_markers.hmm GCA_020433585.1_ASM2043358v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:02:33,108] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:02:33,109] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgd30f7ed5-18d0-49a4-b093-8c2f033e9a55/GCA_020433585.1_ASM2043358v1_genomic.fna.gz]
[2023-06-28 12:02:33,166] [INFO] Query marker FASTA was written to GCA_020433585.1_ASM2043358v1_genomic.fna/markers.fasta
[2023-06-28 12:02:33,167] [INFO] Task started: Blastn
[2023-06-28 12:02:33,167] [INFO] Running command: blastn -query GCA_020433585.1_ASM2043358v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6054e86d-5121-4e9b-a102-3a4dc734fe2b/dqc_reference/reference_markers.fasta -out GCA_020433585.1_ASM2043358v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:02:33,860] [INFO] Task succeeded: Blastn
[2023-06-28 12:02:33,865] [INFO] Selected 23 target genomes.
[2023-06-28 12:02:33,866] [INFO] Target genome list was writen to GCA_020433585.1_ASM2043358v1_genomic.fna/target_genomes.txt
[2023-06-28 12:02:33,868] [INFO] Task started: fastANI
[2023-06-28 12:02:33,868] [INFO] Running command: fastANI --query /var/lib/cwl/stgd30f7ed5-18d0-49a4-b093-8c2f033e9a55/GCA_020433585.1_ASM2043358v1_genomic.fna.gz --refList GCA_020433585.1_ASM2043358v1_genomic.fna/target_genomes.txt --output GCA_020433585.1_ASM2043358v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:02:52,504] [INFO] Task succeeded: fastANI
[2023-06-28 12:02:52,505] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6054e86d-5121-4e9b-a102-3a4dc734fe2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:02:52,505] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6054e86d-5121-4e9b-a102-3a4dc734fe2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:02:52,518] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:02:52,518] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 12:02:52,519] [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
Caldilinea aerophila	strain=DSM 14535	GCA_000281175.1	133453	133453	type	True	77.0637	174	845	95	below_threshold
Litorilinea aerophila	strain=ATCC BAA-2444	GCA_006569185.2	1204385	1204385	type	True	76.3879	96	845	95	below_threshold
Roseomonas cervicalis	strain=ATCC 49957	GCA_000164635.1	204525	204525	type	True	75.0066	73	845	95	below_threshold
Nonomuraea deserti	strain=KC310	GCA_004348685.1	1848322	1848322	type	True	74.9544	61	845	95	below_threshold
Nonomuraea harbinensis	strain=CGMCC 4.7106	GCA_019396385.1	1286938	1286938	type	True	74.904	59	845	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000420125.1	316997	316997	type	True	74.7777	62	845	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	74.7768	60	845	95	below_threshold
Nonomuraea spiralis	strain=JCM 3286	GCA_014648435.1	46182	46182	type	True	74.7494	68	845	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 12:02:52,521] [INFO] DFAST Taxonomy check result was written to GCA_020433585.1_ASM2043358v1_genomic.fna/tc_result.tsv
[2023-06-28 12:02:52,521] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:02:52,522] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:02:52,522] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6054e86d-5121-4e9b-a102-3a4dc734fe2b/dqc_reference/checkm_data
[2023-06-28 12:02:52,523] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:02:52,589] [INFO] Task started: CheckM
[2023-06-28 12:02:52,589] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020433585.1_ASM2043358v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020433585.1_ASM2043358v1_genomic.fna/checkm_input GCA_020433585.1_ASM2043358v1_genomic.fna/checkm_result
[2023-06-28 12:03:36,056] [INFO] Task succeeded: CheckM
[2023-06-28 12:03:36,057] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.55%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:03:36,085] [INFO] ===== Completeness check finished =====
[2023-06-28 12:03:36,085] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:03:36,086] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020433585.1_ASM2043358v1_genomic.fna/markers.fasta)
[2023-06-28 12:03:36,086] [INFO] Task started: Blastn
[2023-06-28 12:03:36,086] [INFO] Running command: blastn -query GCA_020433585.1_ASM2043358v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6054e86d-5121-4e9b-a102-3a4dc734fe2b/dqc_reference/reference_markers_gtdb.fasta -out GCA_020433585.1_ASM2043358v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:03:37,409] [INFO] Task succeeded: Blastn
[2023-06-28 12:03:37,415] [INFO] Selected 13 target genomes.
[2023-06-28 12:03:37,415] [INFO] Target genome list was writen to GCA_020433585.1_ASM2043358v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:03:37,421] [INFO] Task started: fastANI
[2023-06-28 12:03:37,421] [INFO] Running command: fastANI --query /var/lib/cwl/stgd30f7ed5-18d0-49a4-b093-8c2f033e9a55/GCA_020433585.1_ASM2043358v1_genomic.fna.gz --refList GCA_020433585.1_ASM2043358v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020433585.1_ASM2043358v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:03:50,701] [INFO] Task succeeded: fastANI
[2023-06-28 12:03:50,713] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 12:03:50,713] [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_903879975.1	s__Caldilinea sp903879975	80.2078	347	845	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Caldilinea	95.0	98.69	98.69	0.81	0.81	2	-
GCA_016710365.1	s__Caldilinea sp016710365	78.9989	319	845	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Caldilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014879855.1	s__Caldilinea sp014879855	78.149	294	845	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Caldilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016861025.1	s__Caldilinea sp016861025	78.0992	282	845	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Caldilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003451595.1	s__Caldilinea sp003451595	77.7313	291	845	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Caldilinea	95.0	99.85	99.85	0.94	0.94	2	-
GCA_002391565.1	s__Caldilinea sp002391565	77.7022	283	845	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Caldilinea	95.0	99.77	99.77	0.90	0.90	2	-
GCF_000281175.1	s__Caldilinea aerophila	77.0499	175	845	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Caldilinea	95.0	97.04	95.81	0.94	0.92	4	-
GCA_016713335.1	s__JADJPH01 sp016713335	76.6391	109	845	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__JADJPH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003577005.1	s__CFX5 sp003577005	76.0332	94	845	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	75.9925	82	845	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__JAAEKA01;f__JAAEKA01;g__JAAEKA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008017515.1	s__Nonomuraea sp008017515	74.8684	70	845	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 12:03:50,716] [INFO] GTDB search result was written to GCA_020433585.1_ASM2043358v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:03:50,717] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:03:50,723] [INFO] DFAST_QC result json was written to GCA_020433585.1_ASM2043358v1_genomic.fna/dqc_result.json
[2023-06-28 12:03:50,723] [INFO] DFAST_QC completed!
[2023-06-28 12:03:50,724] [INFO] Total running time: 0h1m35s