[2023-06-28 07:22:01,154] [INFO] DFAST_QC pipeline started.
[2023-06-28 07:22:01,164] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 07:22:01,165] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a306a4e-9f26-455e-9fd6-2e1b12618769/dqc_reference
[2023-06-28 07:22:03,331] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 07:22:03,332] [INFO] Task started: Prodigal
[2023-06-28 07:22:03,332] [INFO] Running command: gunzip -c /var/lib/cwl/stga63e5dbe-93c2-45b9-94c6-b03b4379c77f/GCA_017449865.1_ASM1744986v1_genomic.fna.gz | prodigal -d GCA_017449865.1_ASM1744986v1_genomic.fna/cds.fna -a GCA_017449865.1_ASM1744986v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 07:22:16,237] [INFO] Task succeeded: Prodigal
[2023-06-28 07:22:16,237] [INFO] Task started: HMMsearch
[2023-06-28 07:22:16,237] [INFO] Running command: hmmsearch --tblout GCA_017449865.1_ASM1744986v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a306a4e-9f26-455e-9fd6-2e1b12618769/dqc_reference/reference_markers.hmm GCA_017449865.1_ASM1744986v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 07:22:16,413] [INFO] Task succeeded: HMMsearch
[2023-06-28 07:22:16,415] [INFO] Found 6/6 markers.
[2023-06-28 07:22:16,444] [INFO] Query marker FASTA was written to GCA_017449865.1_ASM1744986v1_genomic.fna/markers.fasta
[2023-06-28 07:22:16,445] [INFO] Task started: Blastn
[2023-06-28 07:22:16,445] [INFO] Running command: blastn -query GCA_017449865.1_ASM1744986v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a306a4e-9f26-455e-9fd6-2e1b12618769/dqc_reference/reference_markers.fasta -out GCA_017449865.1_ASM1744986v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 07:22:17,016] [INFO] Task succeeded: Blastn
[2023-06-28 07:22:17,019] [INFO] Selected 32 target genomes.
[2023-06-28 07:22:17,020] [INFO] Target genome list was writen to GCA_017449865.1_ASM1744986v1_genomic.fna/target_genomes.txt
[2023-06-28 07:22:17,021] [INFO] Task started: fastANI
[2023-06-28 07:22:17,021] [INFO] Running command: fastANI --query /var/lib/cwl/stga63e5dbe-93c2-45b9-94c6-b03b4379c77f/GCA_017449865.1_ASM1744986v1_genomic.fna.gz --refList GCA_017449865.1_ASM1744986v1_genomic.fna/target_genomes.txt --output GCA_017449865.1_ASM1744986v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 07:22:35,736] [INFO] Task succeeded: fastANI
[2023-06-28 07:22:35,737] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a306a4e-9f26-455e-9fd6-2e1b12618769/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 07:22:35,737] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a306a4e-9f26-455e-9fd6-2e1b12618769/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 07:22:35,745] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 07:22:35,745] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 07:22:35,745] [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
Bacteroides eggerthii	strain=DSM 20697	GCA_000155815.1	28111	28111	type	True	76.5864	50	756	95	below_threshold
Phocaeicola plebeius	strain=DSM 17135	GCA_000187895.1	310297	310297	suspected-type	True	76.4402	54	756	95	below_threshold
Bacteroides humanifaecis	strain=KGMB07931	GCA_017309675.2	2792859	2792859	type	True	76.3342	62	756	95	below_threshold
Bacteroides fluxus	strain=YIT 12057	GCA_000195635.1	626930	626930	type	True	76.147	54	756	95	below_threshold
Bacteroides timonensis		GCA_000513195.1	1470345	1470345	type	True	75.935	60	756	95	below_threshold
Bacteroides cellulosilyticus	strain=DSM 14838	GCA_000158035.1	246787	246787	type	True	75.9091	53	756	95	below_threshold
Bacteroides intestinalis	strain=DSM 17393	GCA_000172175.1	329854	329854	type	True	75.8052	53	756	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 07:22:35,747] [INFO] DFAST Taxonomy check result was written to GCA_017449865.1_ASM1744986v1_genomic.fna/tc_result.tsv
[2023-06-28 07:22:35,747] [INFO] ===== Taxonomy check completed =====
[2023-06-28 07:22:35,747] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 07:22:35,748] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a306a4e-9f26-455e-9fd6-2e1b12618769/dqc_reference/checkm_data
[2023-06-28 07:22:35,749] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 07:22:35,776] [INFO] Task started: CheckM
[2023-06-28 07:22:35,776] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017449865.1_ASM1744986v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017449865.1_ASM1744986v1_genomic.fna/checkm_input GCA_017449865.1_ASM1744986v1_genomic.fna/checkm_result
[2023-06-28 07:23:15,893] [INFO] Task succeeded: CheckM
[2023-06-28 07:23:15,894] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 07:23:15,907] [INFO] ===== Completeness check finished =====
[2023-06-28 07:23:15,908] [INFO] ===== Start GTDB Search =====
[2023-06-28 07:23:15,908] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017449865.1_ASM1744986v1_genomic.fna/markers.fasta)
[2023-06-28 07:23:15,908] [INFO] Task started: Blastn
[2023-06-28 07:23:15,908] [INFO] Running command: blastn -query GCA_017449865.1_ASM1744986v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a306a4e-9f26-455e-9fd6-2e1b12618769/dqc_reference/reference_markers_gtdb.fasta -out GCA_017449865.1_ASM1744986v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 07:23:16,691] [INFO] Task succeeded: Blastn
[2023-06-28 07:23:16,695] [INFO] Selected 16 target genomes.
[2023-06-28 07:23:16,695] [INFO] Target genome list was writen to GCA_017449865.1_ASM1744986v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 07:23:16,698] [INFO] Task started: fastANI
[2023-06-28 07:23:16,698] [INFO] Running command: fastANI --query /var/lib/cwl/stga63e5dbe-93c2-45b9-94c6-b03b4379c77f/GCA_017449865.1_ASM1744986v1_genomic.fna.gz --refList GCA_017449865.1_ASM1744986v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017449865.1_ASM1744986v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 07:23:25,147] [INFO] Task succeeded: fastANI
[2023-06-28 07:23:25,158] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 07:23:25,158] [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_017471185.1	s__UBA2918 sp017471185	97.9934	615	756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA2918	95.0	98.22	98.01	0.82	0.81	3	conclusive
GCA_902775375.1	s__UBA2918 sp002349865	80.0639	275	756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA2918	95.0	98.32	97.59	0.93	0.86	10	-
GCA_902779085.1	s__UBA2918 sp902779085	79.4358	276	756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA2918	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017442855.1	s__UBA2918 sp017442855	79.1882	278	756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA2918	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017534535.1	s__UBA2918 sp017534535	78.9989	301	756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA2918	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017649485.1	s__UBA2918 sp017649485	78.9648	297	756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA2918	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017651505.1	s__UBA2918 sp017651505	78.9525	188	756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA2918	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902783615.1	s__UBA2918 sp902783615	78.7005	268	756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA2918	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016284115.1	s__UBA2918 sp016284115	78.6876	198	756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA2918	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900313715.1	s__UBA2918 sp900313715	78.3643	212	756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA2918	95.0	100.00	100.00	0.98	0.98	2	-
GCF_000195635.1	s__Bacteroides fluxus	76.147	54	756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.66	99.32	0.94	0.88	3	-
GCF_903181435.1	s__Bacteroides sp900765785	75.581	50	756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.28	97.12	0.65	0.59	3	-
--------------------------------------------------------------------------------
[2023-06-28 07:23:25,160] [INFO] GTDB search result was written to GCA_017449865.1_ASM1744986v1_genomic.fna/result_gtdb.tsv
[2023-06-28 07:23:25,160] [INFO] ===== GTDB Search completed =====
[2023-06-28 07:23:25,163] [INFO] DFAST_QC result json was written to GCA_017449865.1_ASM1744986v1_genomic.fna/dqc_result.json
[2023-06-28 07:23:25,164] [INFO] DFAST_QC completed!
[2023-06-28 07:23:25,164] [INFO] Total running time: 0h1m24s