[2024-01-24 13:55:19,845] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:19,850] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:19,851] [INFO] DQC Reference Directory: /var/lib/cwl/stgf2877a29-967e-4a0e-a659-cfb0083bcba7/dqc_reference
[2024-01-24 13:55:21,324] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:21,324] [INFO] Task started: Prodigal
[2024-01-24 13:55:21,325] [INFO] Running command: gunzip -c /var/lib/cwl/stg58e34536-d30e-4e8c-8f81-33fe85ae381a/GCF_020735945.1_ASM2073594v1_genomic.fna.gz | prodigal -d GCF_020735945.1_ASM2073594v1_genomic.fna/cds.fna -a GCF_020735945.1_ASM2073594v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:46,388] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:46,389] [INFO] Task started: HMMsearch
[2024-01-24 13:55:46,389] [INFO] Running command: hmmsearch --tblout GCF_020735945.1_ASM2073594v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf2877a29-967e-4a0e-a659-cfb0083bcba7/dqc_reference/reference_markers.hmm GCF_020735945.1_ASM2073594v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:46,728] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:46,729] [INFO] Found 6/6 markers.
[2024-01-24 13:55:46,773] [INFO] Query marker FASTA was written to GCF_020735945.1_ASM2073594v1_genomic.fna/markers.fasta
[2024-01-24 13:55:46,774] [INFO] Task started: Blastn
[2024-01-24 13:55:46,774] [INFO] Running command: blastn -query GCF_020735945.1_ASM2073594v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2877a29-967e-4a0e-a659-cfb0083bcba7/dqc_reference/reference_markers.fasta -out GCF_020735945.1_ASM2073594v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:47,421] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:47,430] [INFO] Selected 15 target genomes.
[2024-01-24 13:55:47,431] [INFO] Target genome list was writen to GCF_020735945.1_ASM2073594v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:47,443] [INFO] Task started: fastANI
[2024-01-24 13:55:47,444] [INFO] Running command: fastANI --query /var/lib/cwl/stg58e34536-d30e-4e8c-8f81-33fe85ae381a/GCF_020735945.1_ASM2073594v1_genomic.fna.gz --refList GCF_020735945.1_ASM2073594v1_genomic.fna/target_genomes.txt --output GCF_020735945.1_ASM2073594v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:55:59,293] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:59,294] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf2877a29-967e-4a0e-a659-cfb0083bcba7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:55:59,294] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf2877a29-967e-4a0e-a659-cfb0083bcba7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:55:59,308] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:55:59,308] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:55:59,308] [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=FDAARGOS_1565	GCA_020735945.1	823	823	type	True	100.0	1604	1604	95	conclusive
Parabacteroides distasonis	strain=NCTC11152	GCA_900445525.1	823	823	type	True	99.9991	1604	1604	95	conclusive
Parabacteroides distasonis	strain=ATCC 8503	GCA_000012845.1	823	823	type	True	99.9967	1602	1604	95	conclusive
Parabacteroides merdae	strain=ATCC 43184	GCA_025151215.1	46503	46503	type	True	79.786	350	1604	95	below_threshold
Parabacteroides timonensis	strain=Marseille-P3236	GCA_900128505.1	1871013	1871013	type	True	78.8138	333	1604	95	below_threshold
Parabacteroides johnsonii	strain=DSM 18315	GCA_025151045.1	387661	387661	type	True	78.6096	338	1604	95	below_threshold
Parabacteroides johnsonii	strain=DSM 18315	GCA_000156495.1	387661	387661	type	True	78.2752	336	1604	95	below_threshold
Parabacteroides acidifaciens	strain=426_9	GCA_014385205.1	2290935	2290935	type	True	78.2005	313	1604	95	below_threshold
Parabacteroides acidifaciens	strain=426-9	GCA_003363715.1	2290935	2290935	type	True	78.189	314	1604	95	below_threshold
Bacteroides caccae	strain=FDAARGOS_1097	GCA_016726305.1	47678	47678	suspected-type	True	78.0392	69	1604	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:55:59,310] [INFO] DFAST Taxonomy check result was written to GCF_020735945.1_ASM2073594v1_genomic.fna/tc_result.tsv
[2024-01-24 13:55:59,311] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:55:59,311] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:55:59,312] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf2877a29-967e-4a0e-a659-cfb0083bcba7/dqc_reference/checkm_data
[2024-01-24 13:55:59,314] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:55:59,364] [INFO] Task started: CheckM
[2024-01-24 13:55:59,364] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020735945.1_ASM2073594v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020735945.1_ASM2073594v1_genomic.fna/checkm_input GCF_020735945.1_ASM2073594v1_genomic.fna/checkm_result
[2024-01-24 13:57:04,720] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:04,722] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:04,743] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:04,743] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:04,744] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020735945.1_ASM2073594v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:04,744] [INFO] Task started: Blastn
[2024-01-24 13:57:04,744] [INFO] Running command: blastn -query GCF_020735945.1_ASM2073594v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2877a29-967e-4a0e-a659-cfb0083bcba7/dqc_reference/reference_markers_gtdb.fasta -out GCF_020735945.1_ASM2073594v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:05,613] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:05,617] [INFO] Selected 18 target genomes.
[2024-01-24 13:57:05,617] [INFO] Target genome list was writen to GCF_020735945.1_ASM2073594v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:05,637] [INFO] Task started: fastANI
[2024-01-24 13:57:05,637] [INFO] Running command: fastANI --query /var/lib/cwl/stg58e34536-d30e-4e8c-8f81-33fe85ae381a/GCF_020735945.1_ASM2073594v1_genomic.fna.gz --refList GCF_020735945.1_ASM2073594v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020735945.1_ASM2073594v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:19,478] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:19,504] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:19,504] [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	99.9967	1603	1604	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	94.1331	973	1604	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	89.8369	773	1604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015550595.1	s__Parabacteroides sp900540715	78.8842	320	1604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.96	99.96	0.98	0.97	3	-
GCA_905196875.1	s__Parabacteroides sp905196875	78.3476	287	1604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000156495.1	s__Parabacteroides johnsonii	78.2578	336	1604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.42	96.67	0.88	0.77	13	-
GCF_003363715.1	s__Parabacteroides acidifaciens	78.2324	309	1604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.21	97.25	0.91	0.84	7	-
GCA_900770835.1	s__Parabacteroides sp900770835	78.2004	216	1604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014287585.1	s__Parabacteroides sp014287585	78.0863	353	1604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.33	98.97	0.95	0.91	4	-
GCA_019114945.1	s__Parabacteroides intestinigallinarum	78.0799	310	1604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900760525.1	s__Parabacteroides sp900760525	77.9137	300	1604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.93	98.92	0.84	0.82	3	-
GCA_900552465.1	s__Parabacteroides sp900552465	77.6812	276	1604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.92	99.92	0.93	0.93	2	-
GCF_012113595.1	s__Bacteroides sp012113595	77.6284	82	1604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552415.1	s__Parabacteroides intestinipullorum	77.3024	156	1604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	97.21	97.01	0.88	0.87	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:19,506] [INFO] GTDB search result was written to GCF_020735945.1_ASM2073594v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:19,506] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:19,509] [INFO] DFAST_QC result json was written to GCF_020735945.1_ASM2073594v1_genomic.fna/dqc_result.json
[2024-01-24 13:57:19,510] [INFO] DFAST_QC completed!
[2024-01-24 13:57:19,510] [INFO] Total running time: 0h1m60s