[2024-01-24 12:40:20,760] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:20,761] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:20,762] [INFO] DQC Reference Directory: /var/lib/cwl/stgb634b9e9-8c77-4b73-b2b0-451cf87d9762/dqc_reference
[2024-01-24 12:40:21,984] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:21,985] [INFO] Task started: Prodigal
[2024-01-24 12:40:21,985] [INFO] Running command: gunzip -c /var/lib/cwl/stg6cd2c0bd-d500-43f4-97bf-7b063f2ec6a9/GCF_002959635.1_ASM295963v1_genomic.fna.gz | prodigal -d GCF_002959635.1_ASM295963v1_genomic.fna/cds.fna -a GCF_002959635.1_ASM295963v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:54,372] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:54,372] [INFO] Task started: HMMsearch
[2024-01-24 12:40:54,373] [INFO] Running command: hmmsearch --tblout GCF_002959635.1_ASM295963v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb634b9e9-8c77-4b73-b2b0-451cf87d9762/dqc_reference/reference_markers.hmm GCF_002959635.1_ASM295963v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:54,720] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:54,721] [INFO] Found 6/6 markers.
[2024-01-24 12:40:54,773] [INFO] Query marker FASTA was written to GCF_002959635.1_ASM295963v1_genomic.fna/markers.fasta
[2024-01-24 12:40:54,773] [INFO] Task started: Blastn
[2024-01-24 12:40:54,773] [INFO] Running command: blastn -query GCF_002959635.1_ASM295963v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb634b9e9-8c77-4b73-b2b0-451cf87d9762/dqc_reference/reference_markers.fasta -out GCF_002959635.1_ASM295963v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:55,388] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:55,392] [INFO] Selected 9 target genomes.
[2024-01-24 12:40:55,393] [INFO] Target genome list was writen to GCF_002959635.1_ASM295963v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:55,398] [INFO] Task started: fastANI
[2024-01-24 12:40:55,399] [INFO] Running command: fastANI --query /var/lib/cwl/stg6cd2c0bd-d500-43f4-97bf-7b063f2ec6a9/GCF_002959635.1_ASM295963v1_genomic.fna.gz --refList GCF_002959635.1_ASM295963v1_genomic.fna/target_genomes.txt --output GCF_002959635.1_ASM295963v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:41:09,966] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:09,967] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb634b9e9-8c77-4b73-b2b0-451cf87d9762/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:41:09,967] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb634b9e9-8c77-4b73-b2b0-451cf87d9762/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:41:09,975] [INFO] Found 9 fastANI hits (6 hits with ANI > threshold)
[2024-01-24 12:41:09,975] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:41:09,976] [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=ATCC 8483	GCA_002959635.1	28116	28116	suspected-type	True	100.0	2222	2234	95	conclusive
Bacteroides ovatus	strain=ATCC 8483	GCA_001314995.1	28116	28116	suspected-type	True	99.9993	2154	2234	95	conclusive
Bacteroides ovatus	strain=FDAARGOS_1516	GCA_020149745.1	28116	28116	suspected-type	True	99.9977	2142	2234	95	conclusive
Bacteroides ovatus	strain=ATCC 8483	GCA_025146775.1	28116	28116	suspected-type	True	99.9965	2152	2234	95	conclusive
Bacteroides ovatus	strain=NCTC11153	GCA_900445505.1	28116	28116	suspected-type	True	99.9949	2164	2234	95	conclusive
Bacteroides ovatus	strain=DSM 1896	GCA_900107475.1	28116	28116	suspected-type	True	99.965	2087	2234	95	conclusive
Bacteroides caecimuris	strain=I48	GCA_023277905.1	1796613	1796613	type	True	89.6018	1011	2234	95	below_threshold
Bacteroides caccae	strain=ATCC 43185	GCA_025146315.1	47678	47678	suspected-type	True	83.3747	869	2234	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI 5482	GCA_022453665.1	818	818	type	True	82.0867	961	2234	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:41:09,978] [INFO] DFAST Taxonomy check result was written to GCF_002959635.1_ASM295963v1_genomic.fna/tc_result.tsv
[2024-01-24 12:41:09,978] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:41:09,979] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:41:09,979] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb634b9e9-8c77-4b73-b2b0-451cf87d9762/dqc_reference/checkm_data
[2024-01-24 12:41:09,981] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:41:10,044] [INFO] Task started: CheckM
[2024-01-24 12:41:10,044] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002959635.1_ASM295963v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002959635.1_ASM295963v1_genomic.fna/checkm_input GCF_002959635.1_ASM295963v1_genomic.fna/checkm_result
[2024-01-24 12:42:37,324] [INFO] Task succeeded: CheckM
[2024-01-24 12:42:37,325] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:42:37,347] [INFO] ===== Completeness check finished =====
[2024-01-24 12:42:37,347] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:42:37,347] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002959635.1_ASM295963v1_genomic.fna/markers.fasta)
[2024-01-24 12:42:37,348] [INFO] Task started: Blastn
[2024-01-24 12:42:37,348] [INFO] Running command: blastn -query GCF_002959635.1_ASM295963v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb634b9e9-8c77-4b73-b2b0-451cf87d9762/dqc_reference/reference_markers_gtdb.fasta -out GCF_002959635.1_ASM295963v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:42:38,198] [INFO] Task succeeded: Blastn
[2024-01-24 12:42:38,202] [INFO] Selected 9 target genomes.
[2024-01-24 12:42:38,202] [INFO] Target genome list was writen to GCF_002959635.1_ASM295963v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:42:38,229] [INFO] Task started: fastANI
[2024-01-24 12:42:38,229] [INFO] Running command: fastANI --query /var/lib/cwl/stg6cd2c0bd-d500-43f4-97bf-7b063f2ec6a9/GCF_002959635.1_ASM295963v1_genomic.fna.gz --refList GCF_002959635.1_ASM295963v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002959635.1_ASM295963v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:42:50,344] [INFO] Task succeeded: fastANI
[2024-01-24 12:42:50,353] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:42:50,353] [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	99.9993	2154	2234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.48	95.28	0.79	0.72	126	conclusive
GCA_900755095.1	s__Bacteroides sp900755095	94.5222	765	2234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014334015.1	s__Bacteroides intestinigallinarum	94.1381	1549	2234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.71	95.47	0.80	0.53	8	-
GCA_902362375.1	s__Bacteroides sp902362375	92.7952	1446	2234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.74	98.46	0.82	0.77	13	-
GCF_000210075.1	s__Bacteroides xylanisolvens	92.7161	1435	2234	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	91.2894	1342	2234	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	89.6624	1010	2234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.14	95.76	0.86	0.68	7	-
GCF_000156195.1	s__Bacteroides finegoldii	85.7794	940	2234	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	85.168	996	2234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.8579	97.65	96.82	0.72	0.66	9	-
--------------------------------------------------------------------------------
[2024-01-24 12:42:50,355] [INFO] GTDB search result was written to GCF_002959635.1_ASM295963v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:42:50,355] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:42:50,359] [INFO] DFAST_QC result json was written to GCF_002959635.1_ASM295963v1_genomic.fna/dqc_result.json
[2024-01-24 12:42:50,359] [INFO] DFAST_QC completed!
[2024-01-24 12:42:50,359] [INFO] Total running time: 0h2m30s