[2024-01-24 13:28:28,967] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:28,969] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:28,969] [INFO] DQC Reference Directory: /var/lib/cwl/stg50d10de4-2b14-4878-8b4a-68e4ae79f8e8/dqc_reference
[2024-01-24 13:28:30,192] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:30,193] [INFO] Task started: Prodigal
[2024-01-24 13:28:30,193] [INFO] Running command: gunzip -c /var/lib/cwl/stgb15e7824-9cd4-4038-8094-c88479a4233b/GCF_000169015.1_ASM16901v1_genomic.fna.gz | prodigal -d GCF_000169015.1_ASM16901v1_genomic.fna/cds.fna -a GCF_000169015.1_ASM16901v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:51,890] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:51,891] [INFO] Task started: HMMsearch
[2024-01-24 13:28:51,891] [INFO] Running command: hmmsearch --tblout GCF_000169015.1_ASM16901v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg50d10de4-2b14-4878-8b4a-68e4ae79f8e8/dqc_reference/reference_markers.hmm GCF_000169015.1_ASM16901v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:52,176] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:52,178] [INFO] Found 6/6 markers.
[2024-01-24 13:28:52,220] [INFO] Query marker FASTA was written to GCF_000169015.1_ASM16901v1_genomic.fna/markers.fasta
[2024-01-24 13:28:52,220] [INFO] Task started: Blastn
[2024-01-24 13:28:52,220] [INFO] Running command: blastn -query GCF_000169015.1_ASM16901v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50d10de4-2b14-4878-8b4a-68e4ae79f8e8/dqc_reference/reference_markers.fasta -out GCF_000169015.1_ASM16901v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:52,847] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:52,851] [INFO] Selected 9 target genomes.
[2024-01-24 13:28:52,852] [INFO] Target genome list was writen to GCF_000169015.1_ASM16901v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:52,858] [INFO] Task started: fastANI
[2024-01-24 13:28:52,858] [INFO] Running command: fastANI --query /var/lib/cwl/stgb15e7824-9cd4-4038-8094-c88479a4233b/GCF_000169015.1_ASM16901v1_genomic.fna.gz --refList GCF_000169015.1_ASM16901v1_genomic.fna/target_genomes.txt --output GCF_000169015.1_ASM16901v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:29:02,749] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:02,750] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg50d10de4-2b14-4878-8b4a-68e4ae79f8e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:29:02,750] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg50d10de4-2b14-4878-8b4a-68e4ae79f8e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:29:02,758] [INFO] Found 9 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 13:29:02,758] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:29:02,759] [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 caccae	strain=ATCC 43185	GCA_000169015.1	47678	47678	suspected-type	True	100.0	1507	1511	95	conclusive
Bacteroides caccae	strain=ATCC 43185	GCA_002222615.2	47678	47678	suspected-type	True	99.9982	1508	1511	95	conclusive
Bacteroides caccae	strain=ATCC 43185	GCA_002959715.1	47678	47678	suspected-type	True	99.9981	1511	1511	95	conclusive
Bacteroides caccae	strain=ATCC 43185	GCA_025146315.1	47678	47678	suspected-type	True	99.9979	1508	1511	95	conclusive
Bacteroides caccae	strain=FDAARGOS_1097	GCA_016726305.1	47678	47678	suspected-type	True	99.9972	1510	1511	95	conclusive
Bacteroides caecimuris	strain=I48	GCA_023277905.1	1796613	1796613	type	True	83.5333	731	1511	95	below_threshold
Bacteroides ovatus	strain=FDAARGOS_1516	GCA_020149745.1	28116	28116	suspected-type	True	83.3845	858	1511	95	below_threshold
Bacteroides ovatus	strain=ATCC 8483	GCA_025146775.1	28116	28116	suspected-type	True	83.2945	870	1511	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI 5482	GCA_022453665.1	818	818	type	True	82.0556	816	1511	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:29:02,760] [INFO] DFAST Taxonomy check result was written to GCF_000169015.1_ASM16901v1_genomic.fna/tc_result.tsv
[2024-01-24 13:29:02,761] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:29:02,761] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:29:02,761] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg50d10de4-2b14-4878-8b4a-68e4ae79f8e8/dqc_reference/checkm_data
[2024-01-24 13:29:02,762] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:29:02,807] [INFO] Task started: CheckM
[2024-01-24 13:29:02,807] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000169015.1_ASM16901v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000169015.1_ASM16901v1_genomic.fna/checkm_input GCF_000169015.1_ASM16901v1_genomic.fna/checkm_result
[2024-01-24 13:30:05,233] [INFO] Task succeeded: CheckM
[2024-01-24 13:30:05,234] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:30:05,253] [INFO] ===== Completeness check finished =====
[2024-01-24 13:30:05,253] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:30:05,254] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000169015.1_ASM16901v1_genomic.fna/markers.fasta)
[2024-01-24 13:30:05,254] [INFO] Task started: Blastn
[2024-01-24 13:30:05,254] [INFO] Running command: blastn -query GCF_000169015.1_ASM16901v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50d10de4-2b14-4878-8b4a-68e4ae79f8e8/dqc_reference/reference_markers_gtdb.fasta -out GCF_000169015.1_ASM16901v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:30:06,140] [INFO] Task succeeded: Blastn
[2024-01-24 13:30:06,145] [INFO] Selected 19 target genomes.
[2024-01-24 13:30:06,145] [INFO] Target genome list was writen to GCF_000169015.1_ASM16901v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:30:06,157] [INFO] Task started: fastANI
[2024-01-24 13:30:06,157] [INFO] Running command: fastANI --query /var/lib/cwl/stgb15e7824-9cd4-4038-8094-c88479a4233b/GCF_000169015.1_ASM16901v1_genomic.fna.gz --refList GCF_000169015.1_ASM16901v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000169015.1_ASM16901v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:30:26,274] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:26,293] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:30:26,293] [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_002222615.2	s__Bacteroides caccae	99.9982	1509	1511	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.30	98.91	0.88	0.81	77	conclusive
GCA_900556625.1	s__Bacteroides sp900556625	91.2278	628	1511	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.84	99.84	0.94	0.94	2	-
GCF_903181435.1	s__Bacteroides sp900765785	84.4174	820	1511	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.28	97.12	0.65	0.59	3	-
GCF_012113595.1	s__Bacteroides sp012113595	84.3103	974	1511	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900130125.1	s__Bacteroides congonensis	83.9794	924	1511	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.81	97.60	0.79	0.75	6	-
GCA_000613385.1	s__Bacteroides acidifaciens	83.6718	730	1511	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.33	97.99	0.81	0.75	18	-
GCF_001688725.2	s__Bacteroides caecimuris	83.6118	739	1511	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.14	95.76	0.86	0.68	7	-
GCF_001314995.1	s__Bacteroides ovatus	83.3172	876	1511	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.48	95.28	0.79	0.72	126	-
GCF_000210075.1	s__Bacteroides xylanisolvens	83.1853	854	1511	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.52	96.81	0.77	0.68	125	-
GCF_009193295.2	s__Bacteroides luhongzhouii	83.144	840	1511	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.19	98.73	0.86	0.78	4	-
GCF_014334015.1	s__Bacteroides intestinigallinarum	83.051	892	1511	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.71	95.47	0.80	0.53	8	-
GCA_900761785.1	s__Bacteroides sp900761785	83.0421	814	1511	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902362375.1	s__Bacteroides sp902362375	82.9951	846	1511	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.74	98.46	0.82	0.77	13	-
GCF_014750685.1	s__Bacteroides sp014750685	82.8438	904	1511	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011065.1	s__Bacteroides thetaiotaomicron	82.0978	805	1511	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.45	97.24	0.84	0.75	121	-
GCF_900106755.1	s__Bacteroides faecis	82.0779	769	1511	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.27	98.92	0.88	0.84	29	-
GCA_900547205.1	s__Bacteroides sp900547205	81.7103	754	1511	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.99	99.99	0.95	0.95	2	-
GCA_900544675.1	s__Phocaeicola sp900544675	77.8069	92	1511	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.98	99.96	0.94	0.90	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:30:26,295] [INFO] GTDB search result was written to GCF_000169015.1_ASM16901v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:30:26,295] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:30:26,302] [INFO] DFAST_QC result json was written to GCF_000169015.1_ASM16901v1_genomic.fna/dqc_result.json
[2024-01-24 13:30:26,302] [INFO] DFAST_QC completed!
[2024-01-24 13:30:26,302] [INFO] Total running time: 0h1m57s