[2023-06-28 05:38:32,958] [INFO] DFAST_QC pipeline started.
[2023-06-28 05:38:32,961] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 05:38:32,962] [INFO] DQC Reference Directory: /var/lib/cwl/stg99da2f6a-95d6-450c-a857-1e393975ff49/dqc_reference
[2023-06-28 05:38:34,239] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 05:38:34,241] [INFO] Task started: Prodigal
[2023-06-28 05:38:34,241] [INFO] Running command: gunzip -c /var/lib/cwl/stge26c9d44-9da9-4896-a65b-5f550aec1fad/GCA_944322095.1_BRZ_LB_bin49_genomic.fna.gz | prodigal -d GCA_944322095.1_BRZ_LB_bin49_genomic.fna/cds.fna -a GCA_944322095.1_BRZ_LB_bin49_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 05:38:48,904] [INFO] Task succeeded: Prodigal
[2023-06-28 05:38:48,904] [INFO] Task started: HMMsearch
[2023-06-28 05:38:48,904] [INFO] Running command: hmmsearch --tblout GCA_944322095.1_BRZ_LB_bin49_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg99da2f6a-95d6-450c-a857-1e393975ff49/dqc_reference/reference_markers.hmm GCA_944322095.1_BRZ_LB_bin49_genomic.fna/protein.faa > /dev/null
[2023-06-28 05:38:49,124] [INFO] Task succeeded: HMMsearch
[2023-06-28 05:38:49,126] [INFO] Found 6/6 markers.
[2023-06-28 05:38:49,151] [INFO] Query marker FASTA was written to GCA_944322095.1_BRZ_LB_bin49_genomic.fna/markers.fasta
[2023-06-28 05:38:49,151] [INFO] Task started: Blastn
[2023-06-28 05:38:49,151] [INFO] Running command: blastn -query GCA_944322095.1_BRZ_LB_bin49_genomic.fna/markers.fasta -db /var/lib/cwl/stg99da2f6a-95d6-450c-a857-1e393975ff49/dqc_reference/reference_markers.fasta -out GCA_944322095.1_BRZ_LB_bin49_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 05:38:49,850] [INFO] Task succeeded: Blastn
[2023-06-28 05:38:49,855] [INFO] Selected 33 target genomes.
[2023-06-28 05:38:49,856] [INFO] Target genome list was writen to GCA_944322095.1_BRZ_LB_bin49_genomic.fna/target_genomes.txt
[2023-06-28 05:38:49,858] [INFO] Task started: fastANI
[2023-06-28 05:38:49,858] [INFO] Running command: fastANI --query /var/lib/cwl/stge26c9d44-9da9-4896-a65b-5f550aec1fad/GCA_944322095.1_BRZ_LB_bin49_genomic.fna.gz --refList GCA_944322095.1_BRZ_LB_bin49_genomic.fna/target_genomes.txt --output GCA_944322095.1_BRZ_LB_bin49_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 05:39:07,462] [INFO] Task succeeded: fastANI
[2023-06-28 05:39:07,462] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg99da2f6a-95d6-450c-a857-1e393975ff49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 05:39:07,463] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg99da2f6a-95d6-450c-a857-1e393975ff49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 05:39:07,475] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 05:39:07,475] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 05:39:07,476] [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
Prevotellamassilia timonensis	strain=Marseille-P2831	GCA_900106785.1	1852370	1852370	type	True	76.9903	98	765	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.2443	57	765	95	below_threshold
Sodaliphilus pleomorphus	strain=Oil-RF-744-WCA-WT-10	GCA_009696565.1	2606626	2606626	type	True	76.2075	64	765	95	below_threshold
Paraprevotella clara	strain=YIT 11840	GCA_000233955.1	454154	454154	type	True	76.1901	52	765	95	below_threshold
Pseudoprevotella muciniphila	strain=E39	GCA_003265305.2	2133944	2133944	type	True	76.0405	52	765	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_025145845.1	328814	328814	suspected-type	True	76.0078	52	765	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	75.8124	59	765	95	below_threshold
Prevotella baroniae	strain=JCM 13447	GCA_000613565.1	305719	305719	type	True	75.6269	68	765	95	below_threshold
Prevotella baroniae	strain=DSM 16972	GCA_000426585.1	305719	305719	type	True	75.6137	71	765	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 05:39:07,478] [INFO] DFAST Taxonomy check result was written to GCA_944322095.1_BRZ_LB_bin49_genomic.fna/tc_result.tsv
[2023-06-28 05:39:07,478] [INFO] ===== Taxonomy check completed =====
[2023-06-28 05:39:07,478] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 05:39:07,478] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg99da2f6a-95d6-450c-a857-1e393975ff49/dqc_reference/checkm_data
[2023-06-28 05:39:07,479] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 05:39:07,505] [INFO] Task started: CheckM
[2023-06-28 05:39:07,506] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944322095.1_BRZ_LB_bin49_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944322095.1_BRZ_LB_bin49_genomic.fna/checkm_input GCA_944322095.1_BRZ_LB_bin49_genomic.fna/checkm_result
[2023-06-28 05:39:49,408] [INFO] Task succeeded: CheckM
[2023-06-28 05:39:49,410] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 05:39:49,430] [INFO] ===== Completeness check finished =====
[2023-06-28 05:39:49,430] [INFO] ===== Start GTDB Search =====
[2023-06-28 05:39:49,430] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944322095.1_BRZ_LB_bin49_genomic.fna/markers.fasta)
[2023-06-28 05:39:49,431] [INFO] Task started: Blastn
[2023-06-28 05:39:49,431] [INFO] Running command: blastn -query GCA_944322095.1_BRZ_LB_bin49_genomic.fna/markers.fasta -db /var/lib/cwl/stg99da2f6a-95d6-450c-a857-1e393975ff49/dqc_reference/reference_markers_gtdb.fasta -out GCA_944322095.1_BRZ_LB_bin49_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 05:39:50,364] [INFO] Task succeeded: Blastn
[2023-06-28 05:39:50,369] [INFO] Selected 21 target genomes.
[2023-06-28 05:39:50,369] [INFO] Target genome list was writen to GCA_944322095.1_BRZ_LB_bin49_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 05:39:50,378] [INFO] Task started: fastANI
[2023-06-28 05:39:50,378] [INFO] Running command: fastANI --query /var/lib/cwl/stge26c9d44-9da9-4896-a65b-5f550aec1fad/GCA_944322095.1_BRZ_LB_bin49_genomic.fna.gz --refList GCA_944322095.1_BRZ_LB_bin49_genomic.fna/target_genomes_gtdb.txt --output GCA_944322095.1_BRZ_LB_bin49_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 05:39:58,690] [INFO] Task succeeded: fastANI
[2023-06-28 05:39:58,711] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 05:39:58,711] [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_900556465.1	s__Alloprevotella sp900556465	78.2265	151	765	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	77.9272	192	765	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	98.58	98.39	0.90	0.87	3	-
GCA_900772575.1	s__Alloprevotella sp900772575	77.8653	145	765	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004552195.1	s__Alloprevotella sp004552195	77.5142	127	765	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	77.5137	170	765	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	96.07	96.01	0.90	0.89	4	-
GCA_004552155.1	s__Alloprevotella sp004552155	77.4463	162	765	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018714085.1	s__Alloprevotella pullistercoris	77.4394	176	765	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900752815.1	s__Alloprevotella sp900752815	77.296	107	765	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	77.2871	157	765	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004557035.1	s__Alloprevotella sp004557035	77.2163	150	765	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	96.70	96.46	0.93	0.92	3	-
GCA_004562975.1	s__Alloprevotella sp004562975	77.207	102	765	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905216095.1	s__Alloprevotella sp905216095	77.1957	129	765	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000431275.1	s__Alloprevotella sp000431275	77.1488	160	765	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	98.27	97.96	0.89	0.88	3	-
GCA_004558535.1	s__Alloprevotella sp004558535	77.0907	136	765	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900128475.1	s__Bacteroides massiliensis	76.9479	117	765	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.63	97.57	0.90	0.85	6	-
GCF_002933955.1	s__Alloprevotella sp002933955	76.9393	80	765	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	99.18	98.84	0.78	0.72	4	-
GCA_900553285.1	s__Alloprevotella sp900553285	76.8637	83	765	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	76.7258	119	765	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	98.00	97.95	0.85	0.83	3	-
GCA_017547385.1	s__Alloprevotella sp017547385	76.6203	86	765	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	96.16	96.06	0.96	0.96	3	-
GCA_900541335.1	s__Alloprevotella sp900541335	76.0709	59	765	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	98.73	98.73	0.94	0.90	3	-
--------------------------------------------------------------------------------
[2023-06-28 05:39:58,720] [INFO] GTDB search result was written to GCA_944322095.1_BRZ_LB_bin49_genomic.fna/result_gtdb.tsv
[2023-06-28 05:39:58,721] [INFO] ===== GTDB Search completed =====
[2023-06-28 05:39:58,727] [INFO] DFAST_QC result json was written to GCA_944322095.1_BRZ_LB_bin49_genomic.fna/dqc_result.json
[2023-06-28 05:39:58,727] [INFO] DFAST_QC completed!
[2023-06-28 05:39:58,727] [INFO] Total running time: 0h1m26s