[2023-06-13 09:11:57,700] [INFO] DFAST_QC pipeline started.
[2023-06-13 09:11:57,702] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 09:11:57,703] [INFO] DQC Reference Directory: /var/lib/cwl/stg15cab386-e136-41d7-b92e-2d7627e70a2d/dqc_reference
[2023-06-13 09:11:59,174] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 09:11:59,176] [INFO] Task started: Prodigal
[2023-06-13 09:11:59,177] [INFO] Running command: gunzip -c /var/lib/cwl/stg7ce87a28-c4d5-4a3c-8838-2cd683356931/GCA_022737795.1_ASM2273779v1_genomic.fna.gz | prodigal -d GCA_022737795.1_ASM2273779v1_genomic.fna/cds.fna -a GCA_022737795.1_ASM2273779v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 09:12:23,034] [INFO] Task succeeded: Prodigal
[2023-06-13 09:12:23,034] [INFO] Task started: HMMsearch
[2023-06-13 09:12:23,034] [INFO] Running command: hmmsearch --tblout GCA_022737795.1_ASM2273779v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg15cab386-e136-41d7-b92e-2d7627e70a2d/dqc_reference/reference_markers.hmm GCA_022737795.1_ASM2273779v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 09:12:23,400] [INFO] Task succeeded: HMMsearch
[2023-06-13 09:12:23,404] [INFO] Found 6/6 markers.
[2023-06-13 09:12:23,482] [INFO] Query marker FASTA was written to GCA_022737795.1_ASM2273779v1_genomic.fna/markers.fasta
[2023-06-13 09:12:23,483] [INFO] Task started: Blastn
[2023-06-13 09:12:23,483] [INFO] Running command: blastn -query GCA_022737795.1_ASM2273779v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15cab386-e136-41d7-b92e-2d7627e70a2d/dqc_reference/reference_markers.fasta -out GCA_022737795.1_ASM2273779v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 09:12:24,254] [INFO] Task succeeded: Blastn
[2023-06-13 09:12:24,259] [INFO] Selected 11 target genomes.
[2023-06-13 09:12:24,259] [INFO] Target genome list was writen to GCA_022737795.1_ASM2273779v1_genomic.fna/target_genomes.txt
[2023-06-13 09:12:24,262] [INFO] Task started: fastANI
[2023-06-13 09:12:24,263] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ce87a28-c4d5-4a3c-8838-2cd683356931/GCA_022737795.1_ASM2273779v1_genomic.fna.gz --refList GCA_022737795.1_ASM2273779v1_genomic.fna/target_genomes.txt --output GCA_022737795.1_ASM2273779v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 09:12:35,720] [INFO] Task succeeded: fastANI
[2023-06-13 09:12:35,721] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg15cab386-e136-41d7-b92e-2d7627e70a2d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 09:12:35,721] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg15cab386-e136-41d7-b92e-2d7627e70a2d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 09:12:35,731] [INFO] Found 11 fastANI hits (5 hits with ANI > threshold)
[2023-06-13 09:12:35,731] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 09:12:35,731] [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 fragilis	strain=ATCC 25285	GCA_001997325.1	817	817	type	True	99.0647	1406	1550	95	conclusive
Bacteroides fragilis	strain=NCTC 9343	GCA_000025985.1	817	817	type	True	99.0509	1421	1550	95	conclusive
Bacteroides fragilis	strain=CCUG4856T	GCA_005706655.1	817	817	type	True	99.0464	1421	1550	95	conclusive
Bacteroides fragilis	strain=NCTC 9343	GCA_900445515.1	817	817	type	True	99.0454	1419	1550	95	conclusive
Bacteroides fragilis	strain=FDAARGOS_1512	GCA_020097275.1	817	817	type	True	99.0372	1421	1550	95	conclusive
Bacteroides thetaiotaomicron	strain=VPI 5482	GCA_022453665.1	818	818	type	True	79.2022	382	1550	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_023277905.1	1796613	1796613	type	True	79.0907	338	1550	95	below_threshold
Bacteroides ovatus	strain=FDAARGOS_1516	GCA_020149745.1	28116	28116	suspected-type	True	78.7533	343	1550	95	below_threshold
Bacteroides propionicigenes	strain=NSJ-90	GCA_018390535.1	2834112	2834112	type	True	78.746	289	1550	95	below_threshold
Bacteroides ovatus	strain=ATCC 8483	GCA_025146775.1	28116	28116	suspected-type	True	78.6898	355	1550	95	below_threshold
Bacteroides caccae	strain=ATCC 43185	GCA_025146315.1	47678	47678	suspected-type	True	78.5353	368	1550	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 09:12:35,734] [INFO] DFAST Taxonomy check result was written to GCA_022737795.1_ASM2273779v1_genomic.fna/tc_result.tsv
[2023-06-13 09:12:35,734] [INFO] ===== Taxonomy check completed =====
[2023-06-13 09:12:35,734] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 09:12:35,735] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg15cab386-e136-41d7-b92e-2d7627e70a2d/dqc_reference/checkm_data
[2023-06-13 09:12:35,736] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 09:12:35,792] [INFO] Task started: CheckM
[2023-06-13 09:12:35,792] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022737795.1_ASM2273779v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022737795.1_ASM2273779v1_genomic.fna/checkm_input GCA_022737795.1_ASM2273779v1_genomic.fna/checkm_result
[2023-06-13 09:13:42,817] [INFO] Task succeeded: CheckM
[2023-06-13 09:13:42,819] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 09:13:42,845] [INFO] ===== Completeness check finished =====
[2023-06-13 09:13:42,845] [INFO] ===== Start GTDB Search =====
[2023-06-13 09:13:42,845] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022737795.1_ASM2273779v1_genomic.fna/markers.fasta)
[2023-06-13 09:13:42,846] [INFO] Task started: Blastn
[2023-06-13 09:13:42,846] [INFO] Running command: blastn -query GCA_022737795.1_ASM2273779v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15cab386-e136-41d7-b92e-2d7627e70a2d/dqc_reference/reference_markers_gtdb.fasta -out GCA_022737795.1_ASM2273779v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 09:13:43,672] [INFO] Task succeeded: Blastn
[2023-06-13 09:13:43,677] [INFO] Selected 21 target genomes.
[2023-06-13 09:13:43,677] [INFO] Target genome list was writen to GCA_022737795.1_ASM2273779v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 09:13:43,681] [INFO] Task started: fastANI
[2023-06-13 09:13:43,682] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ce87a28-c4d5-4a3c-8838-2cd683356931/GCA_022737795.1_ASM2273779v1_genomic.fna.gz --refList GCA_022737795.1_ASM2273779v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022737795.1_ASM2273779v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 09:14:01,817] [INFO] Task succeeded: fastANI
[2023-06-13 09:14:01,841] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 09:14:01,842] [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_000025985.1	s__Bacteroides fragilis	99.0509	1421	1550	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.01	98.63	0.88	0.79	194	conclusive
GCF_002849695.1	s__Bacteroides fragilis_A	87.3937	1223	1550	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.30	97.98	0.84	0.80	39	-
GCF_000381365.1	s__Bacteroides salyersiae	79.2338	390	1550	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.03	96.77	0.88	0.58	55	-
GCF_000011065.1	s__Bacteroides thetaiotaomicron	79.1865	383	1550	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.45	97.24	0.84	0.75	121	-
GCF_009193295.2	s__Bacteroides luhongzhouii	79.1712	364	1550	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.19	98.73	0.86	0.78	4	-
GCF_000210075.1	s__Bacteroides xylanisolvens	79.1475	382	1550	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.52	96.81	0.77	0.68	125	-
GCA_000613465.1	s__Bacteroides nordii	79.0122	406	1550	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.55	98.11	0.85	0.80	13	-
GCF_001688725.2	s__Bacteroides caecimuris	79.011	336	1550	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.14	95.76	0.86	0.68	7	-
GCF_900106755.1	s__Bacteroides faecis	78.925	372	1550	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.27	98.92	0.88	0.84	29	-
GCF_903181435.1	s__Bacteroides sp900765785	78.9242	360	1550	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.28	97.12	0.65	0.59	3	-
GCF_014334015.1	s__Bacteroides intestinigallinarum	78.9072	382	1550	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.71	95.47	0.80	0.53	8	-
GCA_000613385.1	s__Bacteroides acidifaciens	78.7993	319	1550	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.33	97.99	0.81	0.75	18	-
GCF_009193325.2	s__Bacteroides zhangwenhongi	78.765	353	1550	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.8579	97.65	96.82	0.72	0.66	9	-
GCA_014385165.1	s__Bacteroides sp014385165	78.7541	350	1550	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.97	99.97	0.99	0.99	2	-
GCF_003438615.1	s__Bacteroides sp003545565	78.6901	288	1550	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.56	99.02	0.91	0.88	7	-
GCF_001314995.1	s__Bacteroides ovatus	78.6693	352	1550	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.48	95.28	0.79	0.72	126	-
GCA_902362375.1	s__Bacteroides sp902362375	78.4536	364	1550	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.74	98.46	0.82	0.77	13	-
GCA_900755095.1	s__Bacteroides sp900755095	78.4051	183	1550	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900556625.1	s__Bacteroides sp900556625	78.0095	219	1550	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.84	99.84	0.94	0.94	2	-
GCA_900544675.1	s__Phocaeicola sp900544675	77.4914	94	1550	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.98	99.96	0.94	0.90	3	-
--------------------------------------------------------------------------------
[2023-06-13 09:14:01,844] [INFO] GTDB search result was written to GCA_022737795.1_ASM2273779v1_genomic.fna/result_gtdb.tsv
[2023-06-13 09:14:01,844] [INFO] ===== GTDB Search completed =====
[2023-06-13 09:14:01,848] [INFO] DFAST_QC result json was written to GCA_022737795.1_ASM2273779v1_genomic.fna/dqc_result.json
[2023-06-13 09:14:01,849] [INFO] DFAST_QC completed!
[2023-06-13 09:14:01,849] [INFO] Total running time: 0h2m4s