[2023-06-18 19:16:43,526] [INFO] DFAST_QC pipeline started.
[2023-06-18 19:16:43,529] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 19:16:43,529] [INFO] DQC Reference Directory: /var/lib/cwl/stg58144d64-0520-42ba-8815-0a770353cd70/dqc_reference
[2023-06-18 19:16:45,813] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 19:16:45,817] [INFO] Task started: Prodigal
[2023-06-18 19:16:45,818] [INFO] Running command: gunzip -c /var/lib/cwl/stgf4d4a14f-8167-4bb9-b89a-023d0a03db8a/GCA_018064005.1_ASM1806400v1_genomic.fna.gz | prodigal -d GCA_018064005.1_ASM1806400v1_genomic.fna/cds.fna -a GCA_018064005.1_ASM1806400v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 19:16:47,996] [INFO] Task succeeded: Prodigal
[2023-06-18 19:16:47,997] [INFO] Task started: HMMsearch
[2023-06-18 19:16:47,997] [INFO] Running command: hmmsearch --tblout GCA_018064005.1_ASM1806400v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg58144d64-0520-42ba-8815-0a770353cd70/dqc_reference/reference_markers.hmm GCA_018064005.1_ASM1806400v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 19:16:48,237] [INFO] Task succeeded: HMMsearch
[2023-06-18 19:16:48,239] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgf4d4a14f-8167-4bb9-b89a-023d0a03db8a/GCA_018064005.1_ASM1806400v1_genomic.fna.gz]
[2023-06-18 19:16:48,257] [INFO] Query marker FASTA was written to GCA_018064005.1_ASM1806400v1_genomic.fna/markers.fasta
[2023-06-18 19:16:48,257] [INFO] Task started: Blastn
[2023-06-18 19:16:48,258] [INFO] Running command: blastn -query GCA_018064005.1_ASM1806400v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58144d64-0520-42ba-8815-0a770353cd70/dqc_reference/reference_markers.fasta -out GCA_018064005.1_ASM1806400v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 19:16:50,268] [INFO] Task succeeded: Blastn
[2023-06-18 19:16:50,273] [INFO] Selected 16 target genomes.
[2023-06-18 19:16:50,274] [INFO] Target genome list was writen to GCA_018064005.1_ASM1806400v1_genomic.fna/target_genomes.txt
[2023-06-18 19:16:50,278] [INFO] Task started: fastANI
[2023-06-18 19:16:50,278] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4d4a14f-8167-4bb9-b89a-023d0a03db8a/GCA_018064005.1_ASM1806400v1_genomic.fna.gz --refList GCA_018064005.1_ASM1806400v1_genomic.fna/target_genomes.txt --output GCA_018064005.1_ASM1806400v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 19:16:58,190] [INFO] Task succeeded: fastANI
[2023-06-18 19:16:58,191] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg58144d64-0520-42ba-8815-0a770353cd70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 19:16:58,192] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg58144d64-0520-42ba-8815-0a770353cd70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 19:16:58,199] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 19:16:58,200] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 19:16:58,200] [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
Roseburia faecis	strain=M72	GCA_001406815.1	301302	301302	type	True	77.6794	80	282	95	below_threshold
Roseburia porci	strain=MUC/MUC-530-WT-4D	GCA_009695765.1	2605790	2605790	type	True	77.5962	59	282	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 19:16:58,202] [INFO] DFAST Taxonomy check result was written to GCA_018064005.1_ASM1806400v1_genomic.fna/tc_result.tsv
[2023-06-18 19:16:58,202] [INFO] ===== Taxonomy check completed =====
[2023-06-18 19:16:58,203] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 19:16:58,203] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg58144d64-0520-42ba-8815-0a770353cd70/dqc_reference/checkm_data
[2023-06-18 19:16:58,204] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 19:16:58,223] [INFO] Task started: CheckM
[2023-06-18 19:16:58,224] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018064005.1_ASM1806400v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018064005.1_ASM1806400v1_genomic.fna/checkm_input GCA_018064005.1_ASM1806400v1_genomic.fna/checkm_result
[2023-06-18 19:17:13,230] [INFO] Task succeeded: CheckM
[2023-06-18 19:17:13,231] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 19:17:13,258] [INFO] ===== Completeness check finished =====
[2023-06-18 19:17:13,258] [INFO] ===== Start GTDB Search =====
[2023-06-18 19:17:13,259] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018064005.1_ASM1806400v1_genomic.fna/markers.fasta)
[2023-06-18 19:17:13,259] [INFO] Task started: Blastn
[2023-06-18 19:17:13,259] [INFO] Running command: blastn -query GCA_018064005.1_ASM1806400v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58144d64-0520-42ba-8815-0a770353cd70/dqc_reference/reference_markers_gtdb.fasta -out GCA_018064005.1_ASM1806400v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 19:17:14,010] [INFO] Task succeeded: Blastn
[2023-06-18 19:17:14,015] [INFO] Selected 12 target genomes.
[2023-06-18 19:17:14,015] [INFO] Target genome list was writen to GCA_018064005.1_ASM1806400v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 19:17:14,022] [INFO] Task started: fastANI
[2023-06-18 19:17:14,023] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4d4a14f-8167-4bb9-b89a-023d0a03db8a/GCA_018064005.1_ASM1806400v1_genomic.fna.gz --refList GCA_018064005.1_ASM1806400v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018064005.1_ASM1806400v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 19:17:19,564] [INFO] Task succeeded: fastANI
[2023-06-18 19:17:19,576] [INFO] Found 6 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-18 19:17:19,576] [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_000020605.1	s__Agathobacter rectalis	98.8863	276	282	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	97.37	96.06	0.82	0.65	151	inconclusive
GCA_900546625.1	s__Agathobacter sp900546625	95.52	265	282	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	96.96	96.96	0.86	0.86	2	inconclusive
GCA_900317585.1	s__Agathobacter sp900317585	94.6723	246	282	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	98.18	95.52	0.87	0.83	5	-
GCA_905209075.1	s__Agathobacter sp905209075	81.2079	129	282	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	98.22	97.67	0.80	0.73	5	-
GCA_900552085.1	s__Agathobacter sp900552085	78.6392	57	282	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	97.03	95.54	0.78	0.69	7	-
GCA_900549895.1	s__Agathobacter sp900549895	77.3127	52	282	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 19:17:19,578] [INFO] GTDB search result was written to GCA_018064005.1_ASM1806400v1_genomic.fna/result_gtdb.tsv
[2023-06-18 19:17:19,579] [INFO] ===== GTDB Search completed =====
[2023-06-18 19:17:19,582] [INFO] DFAST_QC result json was written to GCA_018064005.1_ASM1806400v1_genomic.fna/dqc_result.json
[2023-06-18 19:17:19,582] [INFO] DFAST_QC completed!
[2023-06-18 19:17:19,583] [INFO] Total running time: 0h0m36s