[2024-01-24 13:31:56,828] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:56,836] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:56,836] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e255bd1-5b18-4b26-b1b5-181bae33137f/dqc_reference
[2024-01-24 13:31:58,119] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:58,120] [INFO] Task started: Prodigal
[2024-01-24 13:31:58,120] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a2addd3-0844-48ff-8130-71b695821c4e/GCF_014287585.1_ASM1428758v1_genomic.fna.gz | prodigal -d GCF_014287585.1_ASM1428758v1_genomic.fna/cds.fna -a GCF_014287585.1_ASM1428758v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:26,017] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:26,017] [INFO] Task started: HMMsearch
[2024-01-24 13:32:26,017] [INFO] Running command: hmmsearch --tblout GCF_014287585.1_ASM1428758v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e255bd1-5b18-4b26-b1b5-181bae33137f/dqc_reference/reference_markers.hmm GCF_014287585.1_ASM1428758v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:26,317] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:26,318] [INFO] Found 6/6 markers.
[2024-01-24 13:32:26,395] [INFO] Query marker FASTA was written to GCF_014287585.1_ASM1428758v1_genomic.fna/markers.fasta
[2024-01-24 13:32:26,395] [INFO] Task started: Blastn
[2024-01-24 13:32:26,395] [INFO] Running command: blastn -query GCF_014287585.1_ASM1428758v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e255bd1-5b18-4b26-b1b5-181bae33137f/dqc_reference/reference_markers.fasta -out GCF_014287585.1_ASM1428758v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:27,016] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:27,019] [INFO] Selected 12 target genomes.
[2024-01-24 13:32:27,020] [INFO] Target genome list was writen to GCF_014287585.1_ASM1428758v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:27,025] [INFO] Task started: fastANI
[2024-01-24 13:32:27,025] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a2addd3-0844-48ff-8130-71b695821c4e/GCF_014287585.1_ASM1428758v1_genomic.fna.gz --refList GCF_014287585.1_ASM1428758v1_genomic.fna/target_genomes.txt --output GCF_014287585.1_ASM1428758v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:37,468] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:37,468] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e255bd1-5b18-4b26-b1b5-181bae33137f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:37,468] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e255bd1-5b18-4b26-b1b5-181bae33137f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:37,476] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:32:37,476] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:32:37,476] [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
Parabacteroides merdae	strain=ATCC 43184	GCA_000154105.1	46503	46503	type	True	89.6684	1088	1676	95	below_threshold
Parabacteroides merdae	strain=NCTC13052	GCA_900445495.1	46503	46503	type	True	89.6595	1088	1676	95	below_threshold
Parabacteroides merdae	strain=ATCC 43184	GCA_025151215.1	46503	46503	type	True	89.5638	1093	1676	95	below_threshold
Parabacteroides johnsonii	strain=DSM 18315	GCA_025151045.1	387661	387661	type	True	89.5197	1181	1676	95	below_threshold
Parabacteroides johnsonii	strain=DSM 18315	GCA_000156495.1	387661	387661	type	True	89.3975	1172	1676	95	below_threshold
Phocaeicola intestinalis	strain=Sa1CVN1	GCA_014837065.1	2762212	2762212	type	True	79.4174	69	1676	95	below_threshold
Bacteroides ovatus	strain=ATCC 8483	GCA_025146775.1	28116	28116	suspected-type	True	77.097	103	1676	95	below_threshold
Bacteroides ovatus	strain=FDAARGOS_1516	GCA_020149745.1	28116	28116	suspected-type	True	77.0928	107	1676	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:37,478] [INFO] DFAST Taxonomy check result was written to GCF_014287585.1_ASM1428758v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:37,479] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:37,479] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:37,479] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e255bd1-5b18-4b26-b1b5-181bae33137f/dqc_reference/checkm_data
[2024-01-24 13:32:37,480] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:37,531] [INFO] Task started: CheckM
[2024-01-24 13:32:37,532] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014287585.1_ASM1428758v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014287585.1_ASM1428758v1_genomic.fna/checkm_input GCF_014287585.1_ASM1428758v1_genomic.fna/checkm_result
[2024-01-24 13:33:53,361] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:53,363] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:53,385] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:53,386] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:53,386] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014287585.1_ASM1428758v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:53,386] [INFO] Task started: Blastn
[2024-01-24 13:33:53,387] [INFO] Running command: blastn -query GCF_014287585.1_ASM1428758v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e255bd1-5b18-4b26-b1b5-181bae33137f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014287585.1_ASM1428758v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:54,316] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:54,320] [INFO] Selected 10 target genomes.
[2024-01-24 13:33:54,321] [INFO] Target genome list was writen to GCF_014287585.1_ASM1428758v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:54,338] [INFO] Task started: fastANI
[2024-01-24 13:33:54,338] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a2addd3-0844-48ff-8130-71b695821c4e/GCF_014287585.1_ASM1428758v1_genomic.fna.gz --refList GCF_014287585.1_ASM1428758v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014287585.1_ASM1428758v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:04,281] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:04,291] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:04,291] [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_014287585.1	s__Parabacteroides sp014287585	100.0	1670	1676	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.33	98.97	0.95	0.91	4	conclusive
GCF_000154105.1	s__Parabacteroides merdae	89.6684	1088	1676	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.97	97.44	0.89	0.77	85	-
GCF_000156495.1	s__Parabacteroides johnsonii	89.3915	1173	1676	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.42	96.67	0.88	0.77	13	-
GCA_900760525.1	s__Parabacteroides sp900760525	88.7425	1059	1676	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.93	98.92	0.84	0.82	3	-
GCF_900155425.1	s__Parabacteroides massiliensis	88.3829	1053	1676	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.33	99.33	0.93	0.93	2	-
GCA_017937385.1	s__Parabacteroides sp017937385	84.9492	802	1676	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:04,293] [INFO] GTDB search result was written to GCF_014287585.1_ASM1428758v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:04,293] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:04,296] [INFO] DFAST_QC result json was written to GCF_014287585.1_ASM1428758v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:04,296] [INFO] DFAST_QC completed!
[2024-01-24 13:34:04,296] [INFO] Total running time: 0h2m7s