[2024-01-25 18:06:05,654] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:06:05,656] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:06:05,656] [INFO] DQC Reference Directory: /var/lib/cwl/stg3039896e-a71f-4e27-a8f8-252281cca2fd/dqc_reference
[2024-01-25 18:06:06,826] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:06:06,826] [INFO] Task started: Prodigal
[2024-01-25 18:06:06,827] [INFO] Running command: gunzip -c /var/lib/cwl/stg1ce8ac23-9ada-411a-b6e4-050d9eeaaa9e/GCF_022809355.1_ASM2280935v1_genomic.fna.gz | prodigal -d GCF_022809355.1_ASM2280935v1_genomic.fna/cds.fna -a GCF_022809355.1_ASM2280935v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:06:24,093] [INFO] Task succeeded: Prodigal
[2024-01-25 18:06:24,093] [INFO] Task started: HMMsearch
[2024-01-25 18:06:24,093] [INFO] Running command: hmmsearch --tblout GCF_022809355.1_ASM2280935v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3039896e-a71f-4e27-a8f8-252281cca2fd/dqc_reference/reference_markers.hmm GCF_022809355.1_ASM2280935v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:06:24,411] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:06:24,412] [INFO] Found 6/6 markers.
[2024-01-25 18:06:24,448] [INFO] Query marker FASTA was written to GCF_022809355.1_ASM2280935v1_genomic.fna/markers.fasta
[2024-01-25 18:06:24,449] [INFO] Task started: Blastn
[2024-01-25 18:06:24,449] [INFO] Running command: blastn -query GCF_022809355.1_ASM2280935v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3039896e-a71f-4e27-a8f8-252281cca2fd/dqc_reference/reference_markers.fasta -out GCF_022809355.1_ASM2280935v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:06:25,023] [INFO] Task succeeded: Blastn
[2024-01-25 18:06:25,027] [INFO] Selected 27 target genomes.
[2024-01-25 18:06:25,028] [INFO] Target genome list was writen to GCF_022809355.1_ASM2280935v1_genomic.fna/target_genomes.txt
[2024-01-25 18:06:25,045] [INFO] Task started: fastANI
[2024-01-25 18:06:25,046] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ce8ac23-9ada-411a-b6e4-050d9eeaaa9e/GCF_022809355.1_ASM2280935v1_genomic.fna.gz --refList GCF_022809355.1_ASM2280935v1_genomic.fna/target_genomes.txt --output GCF_022809355.1_ASM2280935v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:06:42,630] [INFO] Task succeeded: fastANI
[2024-01-25 18:06:42,630] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3039896e-a71f-4e27-a8f8-252281cca2fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:06:42,630] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3039896e-a71f-4e27-a8f8-252281cca2fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:06:42,642] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:06:42,642] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:06:42,642] [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
Phocaeicola coprophilus	strain=JCM 13818	GCA_001315785.1	387090	387090	type	True	81.9623	143	1384	95	below_threshold
Phocaeicola coprophilus	strain=DSM 18228	GCA_000157915.1	387090	387090	type	True	81.7883	151	1384	95	below_threshold
Bacteroides muris	strain=KH365_2	GCA_024704915.1	2937417	2937417	type	True	80.369	87	1384	95	below_threshold
Parabacteroides johnsonii	strain=DSM 18315	GCA_025151045.1	387661	387661	type	True	79.3075	213	1384	95	below_threshold
Parabacteroides johnsonii	strain=DSM 18315	GCA_000156495.1	387661	387661	type	True	79.1935	210	1384	95	below_threshold
Parabacteroides gordonii	strain=FDAARGOS_1522	GCA_020297465.1	574930	574930	type	True	78.9879	210	1384	95	below_threshold
Parabacteroides gordonii	strain=DSM 23371	GCA_000428565.1	574930	574930	type	True	78.981	208	1384	95	below_threshold
Parabacteroides gordonii	strain=MS-1	GCA_000969825.1	574930	574930	type	True	78.9725	212	1384	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_025146565.1	28111	28111	type	True	78.5576	85	1384	95	below_threshold
Parabacteroides merdae	strain=NCTC13052	GCA_900445495.1	46503	46503	type	True	78.4483	211	1384	95	below_threshold
Parabacteroides merdae	strain=ATCC 43184	GCA_025151215.1	46503	46503	type	True	78.4156	208	1384	95	below_threshold
Parabacteroides merdae	strain=ATCC 43184	GCA_000154105.1	46503	46503	type	True	78.3871	211	1384	95	below_threshold
Parabacteroides goldsteinii	strain=DSM 19448	GCA_000969835.1	328812	328812	type	True	78.0508	219	1384	95	below_threshold
Parabacteroides distasonis	strain=NCTC11152	GCA_900445525.1	823	823	type	True	78.0138	162	1384	95	below_threshold
Parabacteroides acidifaciens	strain=426-9	GCA_003363715.1	2290935	2290935	type	True	77.958	205	1384	95	below_threshold
Parabacteroides faecis	strain=DSM 102983	GCA_014199665.1	1217282	1217282	type	True	77.9539	218	1384	95	below_threshold
Parabacteroides faecis	strain=JCM 18682	GCA_014647375.1	1217282	1217282	type	True	77.9532	212	1384	95	below_threshold
Parabacteroides acidifaciens	strain=426_9	GCA_014385205.1	2290935	2290935	type	True	77.9522	207	1384	95	below_threshold
Parabacteroides timonensis	strain=Marseille-P3236	GCA_900128505.1	1871013	1871013	type	True	77.5979	214	1384	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:06:42,645] [INFO] DFAST Taxonomy check result was written to GCF_022809355.1_ASM2280935v1_genomic.fna/tc_result.tsv
[2024-01-25 18:06:42,645] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:06:42,646] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:06:42,646] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3039896e-a71f-4e27-a8f8-252281cca2fd/dqc_reference/checkm_data
[2024-01-25 18:06:42,647] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:06:42,690] [INFO] Task started: CheckM
[2024-01-25 18:06:42,690] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022809355.1_ASM2280935v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022809355.1_ASM2280935v1_genomic.fna/checkm_input GCF_022809355.1_ASM2280935v1_genomic.fna/checkm_result
[2024-01-25 18:07:32,692] [INFO] Task succeeded: CheckM
[2024-01-25 18:07:32,693] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:07:32,711] [INFO] ===== Completeness check finished =====
[2024-01-25 18:07:32,712] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:07:32,712] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022809355.1_ASM2280935v1_genomic.fna/markers.fasta)
[2024-01-25 18:07:32,713] [INFO] Task started: Blastn
[2024-01-25 18:07:32,713] [INFO] Running command: blastn -query GCF_022809355.1_ASM2280935v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3039896e-a71f-4e27-a8f8-252281cca2fd/dqc_reference/reference_markers_gtdb.fasta -out GCF_022809355.1_ASM2280935v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:07:33,636] [INFO] Task succeeded: Blastn
[2024-01-25 18:07:33,641] [INFO] Selected 26 target genomes.
[2024-01-25 18:07:33,641] [INFO] Target genome list was writen to GCF_022809355.1_ASM2280935v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:07:33,656] [INFO] Task started: fastANI
[2024-01-25 18:07:33,656] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ce8ac23-9ada-411a-b6e4-050d9eeaaa9e/GCF_022809355.1_ASM2280935v1_genomic.fna.gz --refList GCF_022809355.1_ASM2280935v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022809355.1_ASM2280935v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:07:52,485] [INFO] Task succeeded: fastANI
[2024-01-25 18:07:52,497] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:07:52,497] [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
GCA_000436495.1	s__Parabacteroides faecavium	96.6248	917	1384	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	96.87	96.42	0.81	0.77	5	conclusive
GCA_900548175.1	s__Parabacteroides sp900548175	86.8782	698	1384	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	96.23	96.23	0.78	0.78	2	-
GCF_000156495.1	s__Parabacteroides johnsonii	79.2375	208	1384	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.42	96.67	0.88	0.77	13	-
GCA_902362595.1	s__Phocaeicola merdigallinarum	79.1956	127	1384	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.33	96.40	0.87	0.80	6	-
GCF_000969825.1	s__Parabacteroides gordonii	78.9846	211	1384	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.64	96.69	0.92	0.81	6	-
GCA_900549585.1	s__Parabacteroides sp900549585	78.7963	195	1384	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.88	98.86	0.81	0.76	3	-
GCF_000154105.1	s__Parabacteroides merdae	78.4773	208	1384	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.97	97.44	0.89	0.77	85	-
GCF_003480915.1	s__Parabacteroides sp003480915	78.2244	216	1384	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.39	97.67	0.93	0.87	5	-
GCF_000969835.1	s__Parabacteroides goldsteinii	78.0496	218	1384	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.03	95.33	0.85	0.78	37	-
GCF_003363715.1	s__Parabacteroides acidifaciens	78.001	204	1384	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	77.9267	213	1384	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.52	97.91	0.91	0.84	9	-
GCF_900108035.1	s__Parabacteroides chinchillae	77.9032	162	1384	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	97.95	97.95	0.87	0.87	3	-
GCA_900552415.1	s__Parabacteroides intestinipullorum	77.7255	82	1384	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	97.21	97.01	0.88	0.87	3	-
GCA_900547435.1	s__Parabacteroides sp900547435	77.6363	210	1384	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	100.00	100.00	0.96	0.96	2	-
GCF_002159645.1	s__Parabacteroides sp002159645	77.6313	195	1384	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578895.1	s__Bacteroides sp910578895	77.6192	68	1384	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019118725.1	s__Parabacteroides intestinavium	77.6058	179	1384	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017937385.1	s__Parabacteroides sp017937385	77.2885	160	1384	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019114945.1	s__Parabacteroides intestinigallinarum	77.175	92	1384	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:07:52,498] [INFO] GTDB search result was written to GCF_022809355.1_ASM2280935v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:07:52,498] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:07:52,502] [INFO] DFAST_QC result json was written to GCF_022809355.1_ASM2280935v1_genomic.fna/dqc_result.json
[2024-01-25 18:07:52,502] [INFO] DFAST_QC completed!
[2024-01-25 18:07:52,502] [INFO] Total running time: 0h1m47s