[2023-06-28 08:44:20,835] [INFO] DFAST_QC pipeline started.
[2023-06-28 08:44:20,840] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 08:44:20,840] [INFO] DQC Reference Directory: /var/lib/cwl/stg425c38b5-4880-4a28-88f0-376fada5e219/dqc_reference
[2023-06-28 08:44:22,051] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 08:44:22,052] [INFO] Task started: Prodigal
[2023-06-28 08:44:22,052] [INFO] Running command: gunzip -c /var/lib/cwl/stg586e098b-1503-4283-9f94-d099d5bc5b19/GCA_017396965.1_ASM1739696v1_genomic.fna.gz | prodigal -d GCA_017396965.1_ASM1739696v1_genomic.fna/cds.fna -a GCA_017396965.1_ASM1739696v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 08:44:27,271] [INFO] Task succeeded: Prodigal
[2023-06-28 08:44:27,272] [INFO] Task started: HMMsearch
[2023-06-28 08:44:27,272] [INFO] Running command: hmmsearch --tblout GCA_017396965.1_ASM1739696v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg425c38b5-4880-4a28-88f0-376fada5e219/dqc_reference/reference_markers.hmm GCA_017396965.1_ASM1739696v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 08:44:27,515] [INFO] Task succeeded: HMMsearch
[2023-06-28 08:44:27,517] [INFO] Found 6/6 markers.
[2023-06-28 08:44:27,542] [INFO] Query marker FASTA was written to GCA_017396965.1_ASM1739696v1_genomic.fna/markers.fasta
[2023-06-28 08:44:27,542] [INFO] Task started: Blastn
[2023-06-28 08:44:27,542] [INFO] Running command: blastn -query GCA_017396965.1_ASM1739696v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg425c38b5-4880-4a28-88f0-376fada5e219/dqc_reference/reference_markers.fasta -out GCA_017396965.1_ASM1739696v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 08:44:28,150] [INFO] Task succeeded: Blastn
[2023-06-28 08:44:28,155] [INFO] Selected 46 target genomes.
[2023-06-28 08:44:28,156] [INFO] Target genome list was writen to GCA_017396965.1_ASM1739696v1_genomic.fna/target_genomes.txt
[2023-06-28 08:44:28,168] [INFO] Task started: fastANI
[2023-06-28 08:44:28,168] [INFO] Running command: fastANI --query /var/lib/cwl/stg586e098b-1503-4283-9f94-d099d5bc5b19/GCA_017396965.1_ASM1739696v1_genomic.fna.gz --refList GCA_017396965.1_ASM1739696v1_genomic.fna/target_genomes.txt --output GCA_017396965.1_ASM1739696v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 08:44:57,576] [INFO] Task succeeded: fastANI
[2023-06-28 08:44:57,577] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg425c38b5-4880-4a28-88f0-376fada5e219/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 08:44:57,577] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg425c38b5-4880-4a28-88f0-376fada5e219/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 08:44:57,588] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 08:44:57,588] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 08:44:57,588] [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
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	76.1928	53	528	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	76.0996	56	528	95	below_threshold
Streptomyces varsoviensis	strain=NRRL ISP-5346	GCA_000718635.1	67373	67373	type	True	74.7303	55	528	95	below_threshold
Streptomyces varsoviensis	strain=NRRL B-3589	GCA_000719255.1	67373	67373	type	True	74.7303	55	528	95	below_threshold
Streptomyces hydrogenans	strain=JCM 4771	GCA_014656075.1	1873719	1873719	type	True	74.6833	67	528	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 08:44:57,590] [INFO] DFAST Taxonomy check result was written to GCA_017396965.1_ASM1739696v1_genomic.fna/tc_result.tsv
[2023-06-28 08:44:57,591] [INFO] ===== Taxonomy check completed =====
[2023-06-28 08:44:57,591] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 08:44:57,591] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg425c38b5-4880-4a28-88f0-376fada5e219/dqc_reference/checkm_data
[2023-06-28 08:44:57,592] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 08:44:57,621] [INFO] Task started: CheckM
[2023-06-28 08:44:57,622] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017396965.1_ASM1739696v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017396965.1_ASM1739696v1_genomic.fna/checkm_input GCA_017396965.1_ASM1739696v1_genomic.fna/checkm_result
[2023-06-28 08:45:19,274] [INFO] Task succeeded: CheckM
[2023-06-28 08:45:19,276] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 2.55%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-28 08:45:19,297] [INFO] ===== Completeness check finished =====
[2023-06-28 08:45:19,297] [INFO] ===== Start GTDB Search =====
[2023-06-28 08:45:19,298] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017396965.1_ASM1739696v1_genomic.fna/markers.fasta)
[2023-06-28 08:45:19,298] [INFO] Task started: Blastn
[2023-06-28 08:45:19,298] [INFO] Running command: blastn -query GCA_017396965.1_ASM1739696v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg425c38b5-4880-4a28-88f0-376fada5e219/dqc_reference/reference_markers_gtdb.fasta -out GCA_017396965.1_ASM1739696v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 08:45:20,164] [INFO] Task succeeded: Blastn
[2023-06-28 08:45:20,181] [INFO] Selected 24 target genomes.
[2023-06-28 08:45:20,181] [INFO] Target genome list was writen to GCA_017396965.1_ASM1739696v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 08:45:20,195] [INFO] Task started: fastANI
[2023-06-28 08:45:20,195] [INFO] Running command: fastANI --query /var/lib/cwl/stg586e098b-1503-4283-9f94-d099d5bc5b19/GCA_017396965.1_ASM1739696v1_genomic.fna.gz --refList GCA_017396965.1_ASM1739696v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017396965.1_ASM1739696v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 08:45:30,858] [INFO] Task succeeded: fastANI
[2023-06-28 08:45:30,871] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 08:45:30,871] [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_017396965.1	s__Galloscillospira_B sp017396965	99.9999	518	528	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__BX7;g__Galloscillospira_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018714125.1	s__Galloscillospira_B excrementipullorum	78.1385	160	528	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__BX7;g__Galloscillospira_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017427525.1	s__Galloscillospira_B sp017427525	77.5329	85	528	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__BX7;g__Galloscillospira_B	95.0	97.15	95.98	0.81	0.80	3	-
GCA_012719075.1	s__JAAYBB01 sp012719075	77.4696	124	528	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__BX7;g__JAAYBB01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900626285.1	s__Flavonifractor massiliensis_A	76.3747	53	528	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018228705.1	s__Dysosmobacter sp018228705	76.0933	58	528	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002161215.1	s__Flavonifractor avistercoris	75.9979	74	528	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	96.82	96.45	0.91	0.89	7	-
GCF_016899775.1	s__Lawsonibacter sp900545895	75.7584	50	528	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	96.62	96.12	0.85	0.79	4	-
GCF_000718635.1	s__Streptomyces varsoviensis	74.7215	57	528	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-06-28 08:45:30,873] [INFO] GTDB search result was written to GCA_017396965.1_ASM1739696v1_genomic.fna/result_gtdb.tsv
[2023-06-28 08:45:30,874] [INFO] ===== GTDB Search completed =====
[2023-06-28 08:45:30,876] [INFO] DFAST_QC result json was written to GCA_017396965.1_ASM1739696v1_genomic.fna/dqc_result.json
[2023-06-28 08:45:30,877] [INFO] DFAST_QC completed!
[2023-06-28 08:45:30,877] [INFO] Total running time: 0h1m10s