[2023-06-13 08:07:28,132] [INFO] DFAST_QC pipeline started.
[2023-06-13 08:07:28,135] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 08:07:28,136] [INFO] DQC Reference Directory: /var/lib/cwl/stgcd1a89e3-8871-4c61-a018-1d0ec38101cd/dqc_reference
[2023-06-13 08:07:29,545] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 08:07:29,546] [INFO] Task started: Prodigal
[2023-06-13 08:07:29,546] [INFO] Running command: gunzip -c /var/lib/cwl/stg85386763-f3bd-496a-8322-a8f4676b3e49/GCA_022739435.1_ASM2273943v1_genomic.fna.gz | prodigal -d GCA_022739435.1_ASM2273943v1_genomic.fna/cds.fna -a GCA_022739435.1_ASM2273943v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 08:07:47,208] [INFO] Task succeeded: Prodigal
[2023-06-13 08:07:47,209] [INFO] Task started: HMMsearch
[2023-06-13 08:07:47,209] [INFO] Running command: hmmsearch --tblout GCA_022739435.1_ASM2273943v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcd1a89e3-8871-4c61-a018-1d0ec38101cd/dqc_reference/reference_markers.hmm GCA_022739435.1_ASM2273943v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 08:07:47,472] [INFO] Task succeeded: HMMsearch
[2023-06-13 08:07:47,474] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg85386763-f3bd-496a-8322-a8f4676b3e49/GCA_022739435.1_ASM2273943v1_genomic.fna.gz]
[2023-06-13 08:07:47,515] [INFO] Query marker FASTA was written to GCA_022739435.1_ASM2273943v1_genomic.fna/markers.fasta
[2023-06-13 08:07:47,516] [INFO] Task started: Blastn
[2023-06-13 08:07:47,516] [INFO] Running command: blastn -query GCA_022739435.1_ASM2273943v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd1a89e3-8871-4c61-a018-1d0ec38101cd/dqc_reference/reference_markers.fasta -out GCA_022739435.1_ASM2273943v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 08:07:48,113] [INFO] Task succeeded: Blastn
[2023-06-13 08:07:48,126] [INFO] Selected 12 target genomes.
[2023-06-13 08:07:48,127] [INFO] Target genome list was writen to GCA_022739435.1_ASM2273943v1_genomic.fna/target_genomes.txt
[2023-06-13 08:07:48,132] [INFO] Task started: fastANI
[2023-06-13 08:07:48,133] [INFO] Running command: fastANI --query /var/lib/cwl/stg85386763-f3bd-496a-8322-a8f4676b3e49/GCA_022739435.1_ASM2273943v1_genomic.fna.gz --refList GCA_022739435.1_ASM2273943v1_genomic.fna/target_genomes.txt --output GCA_022739435.1_ASM2273943v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 08:07:56,871] [INFO] Task succeeded: fastANI
[2023-06-13 08:07:56,872] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcd1a89e3-8871-4c61-a018-1d0ec38101cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 08:07:56,873] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcd1a89e3-8871-4c61-a018-1d0ec38101cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 08:07:56,888] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2023-06-13 08:07:56,888] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 08:07:56,888] [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 distasonis	strain=NCTC11152	GCA_900445525.1	823	823	type	True	96.5899	528	632	95	conclusive
Parabacteroides distasonis	strain=ATCC 8503	GCA_000012845.1	823	823	type	True	96.5896	531	632	95	conclusive
Parabacteroides distasonis	strain=FDAARGOS_1565	GCA_020735945.1	823	823	type	True	96.5443	529	632	95	conclusive
Parabacteroides merdae	strain=ATCC 43184	GCA_025151215.1	46503	46503	type	True	77.9133	136	632	95	below_threshold
Parabacteroides merdae	strain=ATCC 43184	GCA_000154105.1	46503	46503	type	True	77.8714	135	632	95	below_threshold
Parabacteroides acidifaciens	strain=426-9	GCA_003363715.1	2290935	2290935	type	True	77.4025	136	632	95	below_threshold
Parabacteroides acidifaciens	strain=426_9	GCA_014385205.1	2290935	2290935	type	True	77.4025	136	632	95	below_threshold
Parabacteroides faecis	strain=JCM 18682	GCA_014647375.1	1217282	1217282	type	True	77.3869	126	632	95	below_threshold
Parabacteroides faecis	strain=DSM 102983	GCA_014199665.1	1217282	1217282	type	True	77.3283	126	632	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 08:07:56,890] [INFO] DFAST Taxonomy check result was written to GCA_022739435.1_ASM2273943v1_genomic.fna/tc_result.tsv
[2023-06-13 08:07:56,891] [INFO] ===== Taxonomy check completed =====
[2023-06-13 08:07:56,891] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 08:07:56,892] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcd1a89e3-8871-4c61-a018-1d0ec38101cd/dqc_reference/checkm_data
[2023-06-13 08:07:56,893] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 08:07:56,941] [INFO] Task started: CheckM
[2023-06-13 08:07:56,942] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022739435.1_ASM2273943v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022739435.1_ASM2273943v1_genomic.fna/checkm_input GCA_022739435.1_ASM2273943v1_genomic.fna/checkm_result
[2023-06-13 08:08:47,407] [INFO] Task succeeded: CheckM
[2023-06-13 08:08:47,408] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.89%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 08:08:47,432] [INFO] ===== Completeness check finished =====
[2023-06-13 08:08:47,433] [INFO] ===== Start GTDB Search =====
[2023-06-13 08:08:47,433] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022739435.1_ASM2273943v1_genomic.fna/markers.fasta)
[2023-06-13 08:08:47,433] [INFO] Task started: Blastn
[2023-06-13 08:08:47,434] [INFO] Running command: blastn -query GCA_022739435.1_ASM2273943v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd1a89e3-8871-4c61-a018-1d0ec38101cd/dqc_reference/reference_markers_gtdb.fasta -out GCA_022739435.1_ASM2273943v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 08:08:48,215] [INFO] Task succeeded: Blastn
[2023-06-13 08:08:48,220] [INFO] Selected 12 target genomes.
[2023-06-13 08:08:48,220] [INFO] Target genome list was writen to GCA_022739435.1_ASM2273943v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 08:08:48,229] [INFO] Task started: fastANI
[2023-06-13 08:08:48,229] [INFO] Running command: fastANI --query /var/lib/cwl/stg85386763-f3bd-496a-8322-a8f4676b3e49/GCA_022739435.1_ASM2273943v1_genomic.fna.gz --refList GCA_022739435.1_ASM2273943v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022739435.1_ASM2273943v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 08:08:56,182] [INFO] Task succeeded: fastANI
[2023-06-13 08:08:56,195] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 08:08:56,195] [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_000012845.1	s__Parabacteroides distasonis	96.5896	531	632	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.16	96.57	0.86	0.75	191	conclusive
GCF_004793765.1	s__Parabacteroides distasonis_A	93.3657	422	632	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.06	98.88	0.88	0.86	4	-
GCF_011038785.1	s__Parabacteroides sp011038785	88.6969	354	632	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108035.1	s__Parabacteroides chinchillae	78.148	88	632	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	97.95	97.95	0.87	0.87	3	-
GCF_000154105.1	s__Parabacteroides merdae	77.8562	134	632	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.97	97.44	0.89	0.77	85	-
GCA_019114945.1	s__Parabacteroides intestinigallinarum	77.6452	110	632	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003363715.1	s__Parabacteroides acidifaciens	77.3941	135	632	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.21	97.25	0.91	0.84	7	-
GCF_014647375.1	s__Parabacteroides faecis	77.3869	126	632	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.52	97.91	0.91	0.84	9	-
GCA_900552465.1	s__Parabacteroides sp900552465	77.1594	114	632	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.92	99.92	0.93	0.93	2	-
GCA_900760525.1	s__Parabacteroides sp900760525	77.0573	111	632	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.93	98.92	0.84	0.82	3	-
GCA_900552415.1	s__Parabacteroides intestinipullorum	76.6503	64	632	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	97.21	97.01	0.88	0.87	3	-
--------------------------------------------------------------------------------
[2023-06-13 08:08:56,197] [INFO] GTDB search result was written to GCA_022739435.1_ASM2273943v1_genomic.fna/result_gtdb.tsv
[2023-06-13 08:08:56,198] [INFO] ===== GTDB Search completed =====
[2023-06-13 08:08:56,201] [INFO] DFAST_QC result json was written to GCA_022739435.1_ASM2273943v1_genomic.fna/dqc_result.json
[2023-06-13 08:08:56,201] [INFO] DFAST_QC completed!
[2023-06-13 08:08:56,201] [INFO] Total running time: 0h1m28s