[2024-01-24 14:14:02,027] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:02,028] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:02,029] [INFO] DQC Reference Directory: /var/lib/cwl/stg72f8b0ca-5851-4a67-8547-e7320898c449/dqc_reference
[2024-01-24 14:14:03,391] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:03,397] [INFO] Task started: Prodigal
[2024-01-24 14:14:03,397] [INFO] Running command: gunzip -c /var/lib/cwl/stga6a88664-4ca3-46c7-b76c-bf78426d8a0a/GCF_004342845.1_ASM434284v1_genomic.fna.gz | prodigal -d GCF_004342845.1_ASM434284v1_genomic.fna/cds.fna -a GCF_004342845.1_ASM434284v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:25,725] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:25,725] [INFO] Task started: HMMsearch
[2024-01-24 14:14:25,725] [INFO] Running command: hmmsearch --tblout GCF_004342845.1_ASM434284v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg72f8b0ca-5851-4a67-8547-e7320898c449/dqc_reference/reference_markers.hmm GCF_004342845.1_ASM434284v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:26,016] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:26,017] [INFO] Found 6/6 markers.
[2024-01-24 14:14:26,049] [INFO] Query marker FASTA was written to GCF_004342845.1_ASM434284v1_genomic.fna/markers.fasta
[2024-01-24 14:14:26,050] [INFO] Task started: Blastn
[2024-01-24 14:14:26,050] [INFO] Running command: blastn -query GCF_004342845.1_ASM434284v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg72f8b0ca-5851-4a67-8547-e7320898c449/dqc_reference/reference_markers.fasta -out GCF_004342845.1_ASM434284v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:26,663] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:26,666] [INFO] Selected 17 target genomes.
[2024-01-24 14:14:26,667] [INFO] Target genome list was writen to GCF_004342845.1_ASM434284v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:26,674] [INFO] Task started: fastANI
[2024-01-24 14:14:26,674] [INFO] Running command: fastANI --query /var/lib/cwl/stga6a88664-4ca3-46c7-b76c-bf78426d8a0a/GCF_004342845.1_ASM434284v1_genomic.fna.gz --refList GCF_004342845.1_ASM434284v1_genomic.fna/target_genomes.txt --output GCF_004342845.1_ASM434284v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:14:39,390] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:39,391] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg72f8b0ca-5851-4a67-8547-e7320898c449/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:14:39,391] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg72f8b0ca-5851-4a67-8547-e7320898c449/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:14:39,409] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:14:39,409] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:14:39,409] [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 heparinolyticus	strain=DSM 23917	GCA_004342845.1	28113	28113	type	True	100.0	1173	1177	95	conclusive
Bacteroides zoogleoformans	strain=ATCC 33285	GCA_007830715.1	28119	28119	type	True	88.8539	829	1177	95	below_threshold
Bacteroides zoogleoformans	strain=ATCC 33285	GCA_002998435.1	28119	28119	type	True	88.8385	846	1177	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_000154205.1	820	820	type	True	79.7889	523	1177	95	below_threshold
Bacteroides uniformis	strain=FDAARGOS_901	GCA_016117815.1	820	820	type	True	79.7795	524	1177	95	below_threshold
Bacteroides muris	strain=KH365_2	GCA_024704915.1	2937417	2937417	type	True	79.6986	469	1177	95	below_threshold
Bacteroides rodentium	strain=JCM 16496	GCA_000614125.1	691816	691816	type	True	79.6825	519	1177	95	below_threshold
Bacteroides humanifaecis	strain=KGMB07931	GCA_017309675.2	2792859	2792859	type	True	79.5812	515	1177	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	79.3394	367	1177	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_025146565.1	28111	28111	type	True	79.0104	345	1177	95	below_threshold
Bacteroides propionicigenes	strain=NSJ-90	GCA_018390535.1	2834112	2834112	type	True	78.9935	358	1177	95	below_threshold
Bacteroides gallinarum	strain=JCM 13658	GCA_000613665.1	376806	376806	type	True	78.6433	378	1177	95	below_threshold
Bacteroides gallinarum	strain=DSM 18171	GCA_000374365.1	376806	376806	type	True	78.5972	384	1177	95	below_threshold
Bacteroides stercorirosoris	strain=JCM 17103	GCA_000614165.1	871324	871324	type	True	78.4607	342	1177	95	below_threshold
Bacteroides stercorirosoris	strain=DSM 26884	GCA_900142015.1	871324	871324	type	True	78.3918	351	1177	95	below_threshold
Bacteroides fragilis	strain=ATCC 25285	GCA_001997325.1	817	817	type	True	77.8109	196	1177	95	below_threshold
Bacteroides fragilis	strain=NCTC 9343	GCA_900445515.1	817	817	type	True	77.7136	200	1177	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:14:39,411] [INFO] DFAST Taxonomy check result was written to GCF_004342845.1_ASM434284v1_genomic.fna/tc_result.tsv
[2024-01-24 14:14:39,411] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:14:39,411] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:14:39,412] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg72f8b0ca-5851-4a67-8547-e7320898c449/dqc_reference/checkm_data
[2024-01-24 14:14:39,413] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:14:39,450] [INFO] Task started: CheckM
[2024-01-24 14:14:39,451] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004342845.1_ASM434284v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004342845.1_ASM434284v1_genomic.fna/checkm_input GCF_004342845.1_ASM434284v1_genomic.fna/checkm_result
[2024-01-24 14:15:39,493] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:39,494] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:39,641] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:39,641] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:39,642] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004342845.1_ASM434284v1_genomic.fna/markers.fasta)
[2024-01-24 14:15:39,642] [INFO] Task started: Blastn
[2024-01-24 14:15:39,642] [INFO] Running command: blastn -query GCF_004342845.1_ASM434284v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg72f8b0ca-5851-4a67-8547-e7320898c449/dqc_reference/reference_markers_gtdb.fasta -out GCF_004342845.1_ASM434284v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:40,511] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:40,515] [INFO] Selected 16 target genomes.
[2024-01-24 14:15:40,515] [INFO] Target genome list was writen to GCF_004342845.1_ASM434284v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:40,552] [INFO] Task started: fastANI
[2024-01-24 14:15:40,552] [INFO] Running command: fastANI --query /var/lib/cwl/stga6a88664-4ca3-46c7-b76c-bf78426d8a0a/GCF_004342845.1_ASM434284v1_genomic.fna.gz --refList GCF_004342845.1_ASM434284v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004342845.1_ASM434284v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:54,617] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:54,637] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:54,637] [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_004342845.1	s__Bacteroides heparinolyticus	100.0	1173	1177	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.64	97.08	0.84	0.81	4	conclusive
GCF_002998435.1	s__Bacteroides zoogleoformans	88.8355	846	1177	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000154205.1	s__Bacteroides uniformis	79.7888	523	1177	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.42	95.87	0.83	0.69	301	-
GCF_000614125.1	s__Bacteroides rodentium	79.6825	519	1177	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902388495.1	s__Bacteroides sp902388495	79.6693	444	1177	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.99	99.99	0.98	0.98	2	-
GCF_004793475.1	s__Bacteroides sp002491635	79.6653	486	1177	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.51	98.46	0.94	0.83	13	-
GCA_910578895.1	s__Bacteroides sp910578895	79.0274	359	1177	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905203765.1	s__Bacteroides sp905203765	79.0066	333	1177	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129655.1	s__Bacteroides clarus	78.98	363	1177	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.75	98.47	0.87	0.82	18	-
GCF_000374365.1	s__Bacteroides gallinarum	78.5974	384	1177	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.97	99.97	1.00	1.00	2	-
GCF_900142015.1	s__Bacteroides stercorirosoris	78.4164	348	1177	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.49	98.12	0.84	0.77	7	-
GCF_000315485.1	s__Bacteroides oleiciplenus	78.2975	338	1177	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.39	98.79	0.93	0.86	3	-
GCF_900130135.1	s__Bacteroides togonis	78.2777	257	1177	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.34	96.94	0.82	0.80	8	-
GCA_900555635.1	s__Bacteroides sp900555635	78.096	315	1177	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.02	98.02	0.75	0.75	2	-
GCF_000025985.1	s__Bacteroides fragilis	77.7409	199	1177	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.01	98.63	0.88	0.79	194	-
GCF_002849695.1	s__Bacteroides fragilis_A	77.7177	201	1177	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.30	97.98	0.84	0.80	39	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:54,639] [INFO] GTDB search result was written to GCF_004342845.1_ASM434284v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:54,639] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:54,643] [INFO] DFAST_QC result json was written to GCF_004342845.1_ASM434284v1_genomic.fna/dqc_result.json
[2024-01-24 14:15:54,644] [INFO] DFAST_QC completed!
[2024-01-24 14:15:54,644] [INFO] Total running time: 0h1m53s