[2024-01-24 13:25:31,046] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:31,048] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:31,048] [INFO] DQC Reference Directory: /var/lib/cwl/stg692f4aa2-1afd-466a-8d62-a9f92a14208b/dqc_reference
[2024-01-24 13:25:32,357] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:32,358] [INFO] Task started: Prodigal
[2024-01-24 13:25:32,358] [INFO] Running command: gunzip -c /var/lib/cwl/stg005b61b8-13f7-426a-b9de-c90cde6014b6/GCF_014385165.1_ASM1438516v1_genomic.fna.gz | prodigal -d GCF_014385165.1_ASM1438516v1_genomic.fna/cds.fna -a GCF_014385165.1_ASM1438516v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:56,088] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:56,088] [INFO] Task started: HMMsearch
[2024-01-24 13:25:56,088] [INFO] Running command: hmmsearch --tblout GCF_014385165.1_ASM1438516v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg692f4aa2-1afd-466a-8d62-a9f92a14208b/dqc_reference/reference_markers.hmm GCF_014385165.1_ASM1438516v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:56,370] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:56,371] [INFO] Found 6/6 markers.
[2024-01-24 13:25:56,413] [INFO] Query marker FASTA was written to GCF_014385165.1_ASM1438516v1_genomic.fna/markers.fasta
[2024-01-24 13:25:56,414] [INFO] Task started: Blastn
[2024-01-24 13:25:56,414] [INFO] Running command: blastn -query GCF_014385165.1_ASM1438516v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg692f4aa2-1afd-466a-8d62-a9f92a14208b/dqc_reference/reference_markers.fasta -out GCF_014385165.1_ASM1438516v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:57,061] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:57,066] [INFO] Selected 20 target genomes.
[2024-01-24 13:25:57,067] [INFO] Target genome list was writen to GCF_014385165.1_ASM1438516v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:57,082] [INFO] Task started: fastANI
[2024-01-24 13:25:57,083] [INFO] Running command: fastANI --query /var/lib/cwl/stg005b61b8-13f7-426a-b9de-c90cde6014b6/GCF_014385165.1_ASM1438516v1_genomic.fna.gz --refList GCF_014385165.1_ASM1438516v1_genomic.fna/target_genomes.txt --output GCF_014385165.1_ASM1438516v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:12,203] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:12,203] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg692f4aa2-1afd-466a-8d62-a9f92a14208b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:12,203] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg692f4aa2-1afd-466a-8d62-a9f92a14208b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:12,218] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:26:12,218] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:26:12,218] [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 salyersiae	strain=DSM 18765	GCA_000381365.1	291644	291644	type	True	79.9761	506	1577	95	below_threshold
Bacteroides nordii	strain=FDAARGOS_1461	GCA_019930665.1	291645	291645	type	True	79.7576	509	1577	95	below_threshold
Bacteroides faecalis	strain=KCTC 15687	GCA_003865075.1	2447885	2447885	type	True	79.6969	321	1577	95	below_threshold
Bacteroides fragilis	strain=NCTC 9343	GCA_900445515.1	817	817	type	True	79.5863	364	1577	95	below_threshold
Bacteroides fragilis	strain=FDAARGOS_1512	GCA_020097275.1	817	817	type	True	79.5535	368	1577	95	below_threshold
Bacteroides fragilis	strain=NCTC 9343	GCA_000025985.1	817	817	type	True	79.4708	371	1577	95	below_threshold
Bacteroides fragilis	strain=ATCC 25285	GCA_001997325.1	817	817	type	True	79.1897	364	1577	95	below_threshold
Bacteroides propionicigenes	strain=NSJ-90	GCA_018390535.1	2834112	2834112	type	True	79.1351	239	1577	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_002221665.1	1796613	1796613	type	True	78.9497	314	1577	95	below_threshold
Bacteroides bouchesdurhonensis	strain=Marseille-P2653	GCA_900155865.1	1841855	1841855	type	True	78.9299	296	1577	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_016697125.1	1796613	1796613	type	True	78.9108	310	1577	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_023277905.1	1796613	1796613	type	True	78.8917	311	1577	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI 5482	GCA_022453665.1	818	818	type	True	78.7125	337	1577	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI-5482	GCA_002959695.1	818	818	type	True	78.6434	335	1577	95	below_threshold
Bacteroides thetaiotaomicron	strain=NCTC10582	GCA_900445595.1	818	818	type	True	78.6121	325	1577	95	below_threshold
Bacteroides humanifaecis	strain=KGMB07931	GCA_017309675.2	2792859	2792859	type	True	78.605	238	1577	95	below_threshold
Bacteroides faecichinchillae	strain=DSM 26883	GCA_900129065.1	871325	871325	type	True	78.5732	287	1577	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI-5482	GCA_020179495.1	818	818	type	True	78.4281	325	1577	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_025147485.1	820	820	type	True	78.2081	243	1577	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:12,220] [INFO] DFAST Taxonomy check result was written to GCF_014385165.1_ASM1438516v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:12,221] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:12,221] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:12,221] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg692f4aa2-1afd-466a-8d62-a9f92a14208b/dqc_reference/checkm_data
[2024-01-24 13:26:12,222] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:12,271] [INFO] Task started: CheckM
[2024-01-24 13:26:12,271] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014385165.1_ASM1438516v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014385165.1_ASM1438516v1_genomic.fna/checkm_input GCF_014385165.1_ASM1438516v1_genomic.fna/checkm_result
[2024-01-24 13:27:17,475] [INFO] Task succeeded: CheckM
[2024-01-24 13:27:17,477] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:27:17,499] [INFO] ===== Completeness check finished =====
[2024-01-24 13:27:17,499] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:27:17,499] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014385165.1_ASM1438516v1_genomic.fna/markers.fasta)
[2024-01-24 13:27:17,500] [INFO] Task started: Blastn
[2024-01-24 13:27:17,500] [INFO] Running command: blastn -query GCF_014385165.1_ASM1438516v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg692f4aa2-1afd-466a-8d62-a9f92a14208b/dqc_reference/reference_markers_gtdb.fasta -out GCF_014385165.1_ASM1438516v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:18,330] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:18,334] [INFO] Selected 16 target genomes.
[2024-01-24 13:27:18,334] [INFO] Target genome list was writen to GCF_014385165.1_ASM1438516v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:27:18,380] [INFO] Task started: fastANI
[2024-01-24 13:27:18,380] [INFO] Running command: fastANI --query /var/lib/cwl/stg005b61b8-13f7-426a-b9de-c90cde6014b6/GCF_014385165.1_ASM1438516v1_genomic.fna.gz --refList GCF_014385165.1_ASM1438516v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014385165.1_ASM1438516v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:27:33,475] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:33,493] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:27:33,493] [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_014385165.1	s__Bacteroides sp014385165	100.0	1570	1577	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.97	99.97	0.99	0.99	2	conclusive
GCF_000381365.1	s__Bacteroides salyersiae	79.9711	506	1577	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.03	96.77	0.88	0.58	55	-
GCF_009193325.2	s__Bacteroides zhangwenhongi	79.8127	310	1577	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.8579	97.65	96.82	0.72	0.66	9	-
GCF_002849695.1	s__Bacteroides fragilis_A	79.7346	359	1577	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.30	97.98	0.84	0.80	39	-
GCF_003865075.1	s__Bacteroides faecalis	79.6227	323	1577	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000613465.1	s__Bacteroides nordii	79.5821	509	1577	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.55	98.11	0.85	0.80	13	-
GCF_000025985.1	s__Bacteroides fragilis	79.4651	371	1577	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.01	98.63	0.88	0.79	194	-
GCF_014750685.1	s__Bacteroides sp014750685	79.1643	320	1577	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155865.1	s__Bacteroides bouchesdurhonensis	78.9441	295	1577	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.60	98.60	0.88	0.88	2	-
GCF_000210075.1	s__Bacteroides xylanisolvens	78.7593	305	1577	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.52	96.81	0.77	0.68	125	-
GCA_900762525.1	s__Bacteroides sp900762525	78.6564	399	1577	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	78.6013	334	1577	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.45	97.24	0.84	0.75	121	-
GCA_902362375.1	s__Bacteroides sp902362375	78.5608	328	1577	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.74	98.46	0.82	0.77	13	-
GCF_012113595.1	s__Bacteroides sp012113595	78.5574	324	1577	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900547205.1	s__Bacteroides sp900547205	78.1311	280	1577	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	77.2724	102	1577	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 13:27:33,495] [INFO] GTDB search result was written to GCF_014385165.1_ASM1438516v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:27:33,496] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:27:33,501] [INFO] DFAST_QC result json was written to GCF_014385165.1_ASM1438516v1_genomic.fna/dqc_result.json
[2024-01-24 13:27:33,501] [INFO] DFAST_QC completed!
[2024-01-24 13:27:33,501] [INFO] Total running time: 0h2m2s