[2023-06-18 13:50:56,494] [INFO] DFAST_QC pipeline started.
[2023-06-18 13:50:56,500] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 13:50:56,500] [INFO] DQC Reference Directory: /var/lib/cwl/stga83dbf47-c67b-47f8-b280-6981adc95de5/dqc_reference
[2023-06-18 13:50:58,696] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 13:50:58,697] [INFO] Task started: Prodigal
[2023-06-18 13:50:58,698] [INFO] Running command: gunzip -c /var/lib/cwl/stgeba6e92f-de17-42f1-9975-a9326f5467b5/GCA_018377515.1_ASM1837751v1_genomic.fna.gz | prodigal -d GCA_018377515.1_ASM1837751v1_genomic.fna/cds.fna -a GCA_018377515.1_ASM1837751v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 13:51:29,298] [INFO] Task succeeded: Prodigal
[2023-06-18 13:51:29,298] [INFO] Task started: HMMsearch
[2023-06-18 13:51:29,299] [INFO] Running command: hmmsearch --tblout GCA_018377515.1_ASM1837751v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga83dbf47-c67b-47f8-b280-6981adc95de5/dqc_reference/reference_markers.hmm GCA_018377515.1_ASM1837751v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 13:51:29,634] [INFO] Task succeeded: HMMsearch
[2023-06-18 13:51:29,635] [INFO] Found 6/6 markers.
[2023-06-18 13:51:29,707] [INFO] Query marker FASTA was written to GCA_018377515.1_ASM1837751v1_genomic.fna/markers.fasta
[2023-06-18 13:51:29,708] [INFO] Task started: Blastn
[2023-06-18 13:51:29,708] [INFO] Running command: blastn -query GCA_018377515.1_ASM1837751v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga83dbf47-c67b-47f8-b280-6981adc95de5/dqc_reference/reference_markers.fasta -out GCA_018377515.1_ASM1837751v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 13:51:30,325] [INFO] Task succeeded: Blastn
[2023-06-18 13:51:30,330] [INFO] Selected 14 target genomes.
[2023-06-18 13:51:30,330] [INFO] Target genome list was writen to GCA_018377515.1_ASM1837751v1_genomic.fna/target_genomes.txt
[2023-06-18 13:51:30,333] [INFO] Task started: fastANI
[2023-06-18 13:51:30,333] [INFO] Running command: fastANI --query /var/lib/cwl/stgeba6e92f-de17-42f1-9975-a9326f5467b5/GCA_018377515.1_ASM1837751v1_genomic.fna.gz --refList GCA_018377515.1_ASM1837751v1_genomic.fna/target_genomes.txt --output GCA_018377515.1_ASM1837751v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 13:51:47,408] [INFO] Task succeeded: fastANI
[2023-06-18 13:51:47,408] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga83dbf47-c67b-47f8-b280-6981adc95de5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 13:51:47,409] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga83dbf47-c67b-47f8-b280-6981adc95de5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 13:51:47,425] [INFO] Found 14 fastANI hits (6 hits with ANI > threshold)
[2023-06-18 13:51:47,425] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-18 13:51:47,425] [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 ovatus	strain=DSM 1896	GCA_900107475.1	28116	28116	suspected-type	True	96.8024	1541	2079	95	conclusive
Bacteroides ovatus	strain=ATCC 8483	GCA_002959635.1	28116	28116	suspected-type	True	96.757	1563	2079	95	conclusive
Bacteroides ovatus	strain=FDAARGOS_1516	GCA_020149745.1	28116	28116	suspected-type	True	96.7349	1555	2079	95	conclusive
Bacteroides ovatus	strain=ATCC 8483	GCA_025146775.1	28116	28116	suspected-type	True	96.7234	1566	2079	95	conclusive
Bacteroides ovatus	strain=ATCC 8483	GCA_001314995.1	28116	28116	suspected-type	True	96.7156	1570	2079	95	conclusive
Bacteroides ovatus	strain=NCTC11153	GCA_900445505.1	28116	28116	suspected-type	True	96.6779	1571	2079	95	conclusive
Bacteroides xylanisolvens	strain=XB1A	GCA_000210075.1	371601	371601	suspected-type	True	93.5043	1425	2079	95	below_threshold
Bacteroides luhongzhouii	strain=HF-5141	GCA_009193295.2	2650158	2650158	type	True	91.4626	1307	2079	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_002221665.1	1796613	1796613	type	True	90.04	974	2079	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_016697125.1	1796613	1796613	type	True	89.9397	992	2079	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_023277905.1	1796613	1796613	type	True	89.8941	988	2079	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_001688725.2	1796613	1796613	type	True	89.8718	987	2079	95	below_threshold
Bacteroides caccae	strain=ATCC 43185	GCA_025146315.1	47678	47678	suspected-type	True	82.9177	841	2079	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI 5482	GCA_022453665.1	818	818	type	True	82.2522	940	2079	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 13:51:47,427] [INFO] DFAST Taxonomy check result was written to GCA_018377515.1_ASM1837751v1_genomic.fna/tc_result.tsv
[2023-06-18 13:51:47,427] [INFO] ===== Taxonomy check completed =====
[2023-06-18 13:51:47,428] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 13:51:47,428] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga83dbf47-c67b-47f8-b280-6981adc95de5/dqc_reference/checkm_data
[2023-06-18 13:51:47,429] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 13:51:47,491] [INFO] Task started: CheckM
[2023-06-18 13:51:47,491] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018377515.1_ASM1837751v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018377515.1_ASM1837751v1_genomic.fna/checkm_input GCA_018377515.1_ASM1837751v1_genomic.fna/checkm_result
[2023-06-18 13:53:11,060] [INFO] Task succeeded: CheckM
[2023-06-18 13:53:11,061] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 96.97%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 13:53:11,084] [INFO] ===== Completeness check finished =====
[2023-06-18 13:53:11,084] [INFO] ===== Start GTDB Search =====
[2023-06-18 13:53:11,084] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018377515.1_ASM1837751v1_genomic.fna/markers.fasta)
[2023-06-18 13:53:11,085] [INFO] Task started: Blastn
[2023-06-18 13:53:11,085] [INFO] Running command: blastn -query GCA_018377515.1_ASM1837751v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga83dbf47-c67b-47f8-b280-6981adc95de5/dqc_reference/reference_markers_gtdb.fasta -out GCA_018377515.1_ASM1837751v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 13:53:11,949] [INFO] Task succeeded: Blastn
[2023-06-18 13:53:11,954] [INFO] Selected 11 target genomes.
[2023-06-18 13:53:11,954] [INFO] Target genome list was writen to GCA_018377515.1_ASM1837751v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 13:53:11,961] [INFO] Task started: fastANI
[2023-06-18 13:53:11,961] [INFO] Running command: fastANI --query /var/lib/cwl/stgeba6e92f-de17-42f1-9975-a9326f5467b5/GCA_018377515.1_ASM1837751v1_genomic.fna.gz --refList GCA_018377515.1_ASM1837751v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018377515.1_ASM1837751v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 13:53:25,286] [INFO] Task succeeded: fastANI
[2023-06-18 13:53:25,307] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 13:53:25,307] [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_001314995.1	s__Bacteroides ovatus	96.7166	1570	2079	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.48	95.28	0.79	0.72	126	conclusive
GCF_014334015.1	s__Bacteroides intestinigallinarum	94.1046	1488	2079	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.71	95.47	0.80	0.53	8	-
GCA_900755095.1	s__Bacteroides sp900755095	93.8473	715	2079	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000210075.1	s__Bacteroides xylanisolvens	93.5012	1425	2079	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.52	96.81	0.77	0.68	125	-
GCA_902362375.1	s__Bacteroides sp902362375	92.6711	1419	2079	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.74	98.46	0.82	0.77	13	-
GCF_009193295.2	s__Bacteroides luhongzhouii	91.4737	1306	2079	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.19	98.73	0.86	0.78	4	-
GCF_001688725.2	s__Bacteroides caecimuris	89.8688	987	2079	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.14	95.76	0.86	0.68	7	-
GCA_900557355.1	s__Bacteroides sp900557355	89.3979	425	2079	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.57	98.57	0.54	0.54	2	-
GCF_000156195.1	s__Bacteroides finegoldii	85.9156	953	2079	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.8579	98.84	97.86	0.83	0.75	21	-
GCF_009193325.2	s__Bacteroides zhangwenhongi	84.8776	993	2079	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.8579	97.65	96.82	0.72	0.66	9	-
GCF_900106755.1	s__Bacteroides faecis	82.3541	912	2079	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.27	98.92	0.88	0.84	29	-
--------------------------------------------------------------------------------
[2023-06-18 13:53:25,311] [INFO] GTDB search result was written to GCA_018377515.1_ASM1837751v1_genomic.fna/result_gtdb.tsv
[2023-06-18 13:53:25,312] [INFO] ===== GTDB Search completed =====
[2023-06-18 13:53:25,315] [INFO] DFAST_QC result json was written to GCA_018377515.1_ASM1837751v1_genomic.fna/dqc_result.json
[2023-06-18 13:53:25,316] [INFO] DFAST_QC completed!
[2023-06-18 13:53:25,316] [INFO] Total running time: 0h2m29s