[2023-06-17 08:40:30,728] [INFO] DFAST_QC pipeline started.
[2023-06-17 08:40:30,738] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 08:40:30,738] [INFO] DQC Reference Directory: /var/lib/cwl/stg79a6ff68-9ead-4091-8034-c4af84715958/dqc_reference
[2023-06-17 08:40:32,497] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 08:40:32,504] [INFO] Task started: Prodigal
[2023-06-17 08:40:32,505] [INFO] Running command: gunzip -c /var/lib/cwl/stg87771210-1ee9-4f12-9fdf-27003b3662d2/GCA_028721825.1_ASM2872182v1_genomic.fna.gz | prodigal -d GCA_028721825.1_ASM2872182v1_genomic.fna/cds.fna -a GCA_028721825.1_ASM2872182v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 08:40:39,219] [INFO] Task succeeded: Prodigal
[2023-06-17 08:40:39,219] [INFO] Task started: HMMsearch
[2023-06-17 08:40:39,219] [INFO] Running command: hmmsearch --tblout GCA_028721825.1_ASM2872182v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg79a6ff68-9ead-4091-8034-c4af84715958/dqc_reference/reference_markers.hmm GCA_028721825.1_ASM2872182v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 08:40:39,427] [INFO] Task succeeded: HMMsearch
[2023-06-17 08:40:39,429] [INFO] Found 6/6 markers.
[2023-06-17 08:40:39,453] [INFO] Query marker FASTA was written to GCA_028721825.1_ASM2872182v1_genomic.fna/markers.fasta
[2023-06-17 08:40:39,454] [INFO] Task started: Blastn
[2023-06-17 08:40:39,454] [INFO] Running command: blastn -query GCA_028721825.1_ASM2872182v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg79a6ff68-9ead-4091-8034-c4af84715958/dqc_reference/reference_markers.fasta -out GCA_028721825.1_ASM2872182v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 08:40:40,207] [INFO] Task succeeded: Blastn
[2023-06-17 08:40:40,212] [INFO] Selected 18 target genomes.
[2023-06-17 08:40:40,213] [INFO] Target genome list was writen to GCA_028721825.1_ASM2872182v1_genomic.fna/target_genomes.txt
[2023-06-17 08:40:40,218] [INFO] Task started: fastANI
[2023-06-17 08:40:40,218] [INFO] Running command: fastANI --query /var/lib/cwl/stg87771210-1ee9-4f12-9fdf-27003b3662d2/GCA_028721825.1_ASM2872182v1_genomic.fna.gz --refList GCA_028721825.1_ASM2872182v1_genomic.fna/target_genomes.txt --output GCA_028721825.1_ASM2872182v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 08:40:55,169] [INFO] Task succeeded: fastANI
[2023-06-17 08:40:55,170] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg79a6ff68-9ead-4091-8034-c4af84715958/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 08:40:55,170] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg79a6ff68-9ead-4091-8034-c4af84715958/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 08:40:55,175] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2023-06-17 08:40:55,175] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-17 08:40:55,176] [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
Phascolarctobacterium succinatutens	strain=YIT 12067	GCA_000188175.1	626940	626940	type	True	99.4136	538	577	95	conclusive
Phascolarctobacterium faecium	strain=DSM 14760	GCA_003269275.1	33025	33025	type	True	77.2193	95	577	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 08:40:55,177] [INFO] DFAST Taxonomy check result was written to GCA_028721825.1_ASM2872182v1_genomic.fna/tc_result.tsv
[2023-06-17 08:40:55,178] [INFO] ===== Taxonomy check completed =====
[2023-06-17 08:40:55,178] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 08:40:55,178] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg79a6ff68-9ead-4091-8034-c4af84715958/dqc_reference/checkm_data
[2023-06-17 08:40:55,179] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 08:40:55,202] [INFO] Task started: CheckM
[2023-06-17 08:40:55,202] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028721825.1_ASM2872182v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028721825.1_ASM2872182v1_genomic.fna/checkm_input GCA_028721825.1_ASM2872182v1_genomic.fna/checkm_result
[2023-06-17 08:41:23,523] [INFO] Task succeeded: CheckM
[2023-06-17 08:41:23,524] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.58%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 08:41:23,662] [INFO] ===== Completeness check finished =====
[2023-06-17 08:41:23,662] [INFO] ===== Start GTDB Search =====
[2023-06-17 08:41:23,662] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028721825.1_ASM2872182v1_genomic.fna/markers.fasta)
[2023-06-17 08:41:23,663] [INFO] Task started: Blastn
[2023-06-17 08:41:23,663] [INFO] Running command: blastn -query GCA_028721825.1_ASM2872182v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg79a6ff68-9ead-4091-8034-c4af84715958/dqc_reference/reference_markers_gtdb.fasta -out GCA_028721825.1_ASM2872182v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 08:41:24,720] [INFO] Task succeeded: Blastn
[2023-06-17 08:41:24,724] [INFO] Selected 7 target genomes.
[2023-06-17 08:41:24,724] [INFO] Target genome list was writen to GCA_028721825.1_ASM2872182v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 08:41:24,727] [INFO] Task started: fastANI
[2023-06-17 08:41:24,727] [INFO] Running command: fastANI --query /var/lib/cwl/stg87771210-1ee9-4f12-9fdf-27003b3662d2/GCA_028721825.1_ASM2872182v1_genomic.fna.gz --refList GCA_028721825.1_ASM2872182v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028721825.1_ASM2872182v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 08:41:29,007] [INFO] Task succeeded: fastANI
[2023-06-17 08:41:29,015] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 08:41:29,016] [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_000188175.1	s__Phascolarctobacterium_A succinatutens	99.4136	538	577	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A	95.0	97.32	95.06	0.90	0.84	17	conclusive
GCA_900753045.1	s__Phascolarctobacterium_A sp900753045	94.975	521	577	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000434895.1	s__Phascolarctobacterium_A succinatutens_A	94.5358	527	577	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A	95.0	95.38	95.36	0.85	0.80	4	-
GCA_900770955.1	s__Phascolarctobacterium_A sp900770955	92.8721	522	577	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551335.1	s__Phascolarctobacterium_A sp900551335	82.1043	275	577	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A	95.0	96.01	95.96	0.95	0.94	3	-
GCA_905212365.1	s__Phascolarctobacterium_A sp905212365	79.303	272	577	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900553055.1	s__Phascolarctobacterium_A sp900553055	78.8235	188	577	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A	95.0	98.03	96.65	0.77	0.68	4	-
--------------------------------------------------------------------------------
[2023-06-17 08:41:29,017] [INFO] GTDB search result was written to GCA_028721825.1_ASM2872182v1_genomic.fna/result_gtdb.tsv
[2023-06-17 08:41:29,018] [INFO] ===== GTDB Search completed =====
[2023-06-17 08:41:29,021] [INFO] DFAST_QC result json was written to GCA_028721825.1_ASM2872182v1_genomic.fna/dqc_result.json
[2023-06-17 08:41:29,021] [INFO] DFAST_QC completed!
[2023-06-17 08:41:29,021] [INFO] Total running time: 0h0m58s