[2023-06-12 22:44:14,456] [INFO] DFAST_QC pipeline started.
[2023-06-12 22:44:14,458] [INFO] DFAST_QC version: 0.5.7
[2023-06-12 22:44:14,458] [INFO] DQC Reference Directory: /var/lib/cwl/stg495e3e29-7fc1-46bd-9a18-26831633a0e7/dqc_reference
[2023-06-12 22:44:15,619] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-12 22:44:15,621] [INFO] Task started: Prodigal
[2023-06-12 22:44:15,622] [INFO] Running command: gunzip -c /var/lib/cwl/stge364a874-61b4-4f75-86b6-9257f09196b6/GCA_022772475.1_ASM2277247v1_genomic.fna.gz | prodigal -d GCA_022772475.1_ASM2277247v1_genomic.fna/cds.fna -a GCA_022772475.1_ASM2277247v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-12 22:44:30,179] [INFO] Task succeeded: Prodigal
[2023-06-12 22:44:30,179] [INFO] Task started: HMMsearch
[2023-06-12 22:44:30,179] [INFO] Running command: hmmsearch --tblout GCA_022772475.1_ASM2277247v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg495e3e29-7fc1-46bd-9a18-26831633a0e7/dqc_reference/reference_markers.hmm GCA_022772475.1_ASM2277247v1_genomic.fna/protein.faa > /dev/null
[2023-06-12 22:44:30,427] [INFO] Task succeeded: HMMsearch
[2023-06-12 22:44:30,429] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge364a874-61b4-4f75-86b6-9257f09196b6/GCA_022772475.1_ASM2277247v1_genomic.fna.gz]
[2023-06-12 22:44:30,455] [INFO] Query marker FASTA was written to GCA_022772475.1_ASM2277247v1_genomic.fna/markers.fasta
[2023-06-12 22:44:30,455] [INFO] Task started: Blastn
[2023-06-12 22:44:30,455] [INFO] Running command: blastn -query GCA_022772475.1_ASM2277247v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg495e3e29-7fc1-46bd-9a18-26831633a0e7/dqc_reference/reference_markers.fasta -out GCA_022772475.1_ASM2277247v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 22:44:31,062] [INFO] Task succeeded: Blastn
[2023-06-12 22:44:31,066] [INFO] Selected 27 target genomes.
[2023-06-12 22:44:31,067] [INFO] Target genome list was writen to GCA_022772475.1_ASM2277247v1_genomic.fna/target_genomes.txt
[2023-06-12 22:44:31,090] [INFO] Task started: fastANI
[2023-06-12 22:44:31,091] [INFO] Running command: fastANI --query /var/lib/cwl/stge364a874-61b4-4f75-86b6-9257f09196b6/GCA_022772475.1_ASM2277247v1_genomic.fna.gz --refList GCA_022772475.1_ASM2277247v1_genomic.fna/target_genomes.txt --output GCA_022772475.1_ASM2277247v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-12 22:44:46,017] [INFO] Task succeeded: fastANI
[2023-06-12 22:44:46,017] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg495e3e29-7fc1-46bd-9a18-26831633a0e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-12 22:44:46,018] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg495e3e29-7fc1-46bd-9a18-26831633a0e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-12 22:44:46,033] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-12 22:44:46,033] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-12 22:44:46,033] [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
Prevotellamassilia timonensis	strain=Marseille-P2831	GCA_900106785.1	1852370	1852370	type	True	77.0655	116	744	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.8186	58	744	95	below_threshold
Prevotella baroniae	strain=DSM 16972	GCA_000426585.1	305719	305719	type	True	76.8164	61	744	95	below_threshold
Prevotella baroniae	strain=JCM 13447	GCA_000613565.1	305719	305719	type	True	76.7857	65	744	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	76.6866	95	744	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	76.6659	102	744	95	below_threshold
Barnesiella viscericola	strain=C46, DSM 18177	GCA_000512915.1	397865	397865	type	True	76.6297	69	744	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000220215.1	52227	52227	type	True	76.6074	103	744	95	below_threshold
Alistipes provencensis	strain=Marseille-P2431	GCA_900083545.1	1816676	1816676	type	True	76.5636	57	744	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	76.5343	59	744	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_025145645.1	1288121	1288121	type	True	76.3685	66	744	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_000312145.1	1288121	1288121	type	True	76.366	65	744	95	below_threshold
Alistipes senegalensis	strain=FDAARGOS_1578	GCA_020735725.1	1288121	1288121	type	True	76.3605	65	744	95	below_threshold
Prevotella mizrahii	strain=LKV-178-WT-2A	GCA_009695775.1	2606637	2606637	type	True	75.8298	60	744	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-12 22:44:46,035] [INFO] DFAST Taxonomy check result was written to GCA_022772475.1_ASM2277247v1_genomic.fna/tc_result.tsv
[2023-06-12 22:44:46,036] [INFO] ===== Taxonomy check completed =====
[2023-06-12 22:44:46,036] [INFO] ===== Start completeness check using CheckM =====
[2023-06-12 22:44:46,037] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg495e3e29-7fc1-46bd-9a18-26831633a0e7/dqc_reference/checkm_data
[2023-06-12 22:44:46,038] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-12 22:44:46,070] [INFO] Task started: CheckM
[2023-06-12 22:44:46,070] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022772475.1_ASM2277247v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022772475.1_ASM2277247v1_genomic.fna/checkm_input GCA_022772475.1_ASM2277247v1_genomic.fna/checkm_result
[2023-06-12 22:45:28,682] [INFO] Task succeeded: CheckM
[2023-06-12 22:45:28,683] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-12 22:45:28,705] [INFO] ===== Completeness check finished =====
[2023-06-12 22:45:28,706] [INFO] ===== Start GTDB Search =====
[2023-06-12 22:45:28,706] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022772475.1_ASM2277247v1_genomic.fna/markers.fasta)
[2023-06-12 22:45:28,706] [INFO] Task started: Blastn
[2023-06-12 22:45:28,706] [INFO] Running command: blastn -query GCA_022772475.1_ASM2277247v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg495e3e29-7fc1-46bd-9a18-26831633a0e7/dqc_reference/reference_markers_gtdb.fasta -out GCA_022772475.1_ASM2277247v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 22:45:29,605] [INFO] Task succeeded: Blastn
[2023-06-12 22:45:29,610] [INFO] Selected 21 target genomes.
[2023-06-12 22:45:29,611] [INFO] Target genome list was writen to GCA_022772475.1_ASM2277247v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-12 22:45:29,618] [INFO] Task started: fastANI
[2023-06-12 22:45:29,618] [INFO] Running command: fastANI --query /var/lib/cwl/stge364a874-61b4-4f75-86b6-9257f09196b6/GCA_022772475.1_ASM2277247v1_genomic.fna.gz --refList GCA_022772475.1_ASM2277247v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022772475.1_ASM2277247v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-12 22:45:38,105] [INFO] Task succeeded: fastANI
[2023-06-12 22:45:38,127] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-12 22:45:38,128] [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_900772575.1	s__Alloprevotella sp900772575	78.9331	205	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004557185.1	s__Alloprevotella sp004557185	78.8361	242	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	98.58	98.39	0.90	0.87	3	-
GCA_004562975.1	s__Alloprevotella sp004562975	78.4873	138	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017933995.1	s__Alloprevotella sp017933995	78.2693	174	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900556465.1	s__Alloprevotella sp900556465	78.0843	161	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004555425.1	s__Alloprevotella sp004555425	78.0144	187	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	98.00	97.95	0.85	0.83	3	-
GCA_004552195.1	s__Alloprevotella sp004552195	77.8483	159	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004556745.1	s__Alloprevotella sp004556745	77.819	185	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	96.07	96.01	0.90	0.89	4	-
GCA_004558535.1	s__Alloprevotella sp004558535	77.76	158	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004552155.1	s__Alloprevotella sp004552155	77.7409	188	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002933955.1	s__Alloprevotella sp002933955	77.7144	87	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	99.18	98.84	0.78	0.72	4	-
GCA_905216095.1	s__Alloprevotella sp905216095	77.6372	168	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900539625.1	s__Alloprevotella sp900539625	77.5096	171	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	98.08	97.36	0.88	0.77	5	-
GCF_900128475.1	s__Bacteroides massiliensis	77.3202	127	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.63	97.57	0.90	0.85	6	-
GCA_002394305.1	s__UBA4372 sp002394305	77.0248	115	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	97.13	97.13	0.80	0.80	2	-
GCA_017547385.1	s__Alloprevotella sp017547385	76.9125	89	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	96.16	96.06	0.96	0.96	3	-
GCA_902763865.1	s__UBA4372 sp902763865	76.8867	117	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	98.22	98.22	0.85	0.84	3	-
GCA_017483665.1	s__UBA4372 sp017483665	76.8037	106	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541335.1	s__Alloprevotella sp900541335	76.6495	75	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	98.73	98.73	0.94	0.90	3	-
GCA_017464815.1	s__Phocaeicola_A sp017464815	76.4147	84	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900760455.1	s__Paraprevotella sp900760455	75.7926	74	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	96.69	96.51	0.74	0.73	3	-
--------------------------------------------------------------------------------
[2023-06-12 22:45:38,130] [INFO] GTDB search result was written to GCA_022772475.1_ASM2277247v1_genomic.fna/result_gtdb.tsv
[2023-06-12 22:45:38,130] [INFO] ===== GTDB Search completed =====
[2023-06-12 22:45:38,135] [INFO] DFAST_QC result json was written to GCA_022772475.1_ASM2277247v1_genomic.fna/dqc_result.json
[2023-06-12 22:45:38,135] [INFO] DFAST_QC completed!
[2023-06-12 22:45:38,135] [INFO] Total running time: 0h1m24s