[2023-06-13 02:48:18,764] [INFO] DFAST_QC pipeline started.
[2023-06-13 02:48:18,767] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 02:48:18,767] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a0d1322-7eb9-4737-b4bd-0d9252f720f9/dqc_reference
[2023-06-13 02:48:20,056] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 02:48:20,057] [INFO] Task started: Prodigal
[2023-06-13 02:48:20,057] [INFO] Running command: gunzip -c /var/lib/cwl/stgaba4c635-e579-4a7d-ba49-5637f383267f/GCA_938045455.1_ERR589631_bin.19_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938045455.1_ERR589631_bin.19_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938045455.1_ERR589631_bin.19_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 02:48:34,825] [INFO] Task succeeded: Prodigal
[2023-06-13 02:48:34,826] [INFO] Task started: HMMsearch
[2023-06-13 02:48:34,826] [INFO] Running command: hmmsearch --tblout GCA_938045455.1_ERR589631_bin.19_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a0d1322-7eb9-4737-b4bd-0d9252f720f9/dqc_reference/reference_markers.hmm GCA_938045455.1_ERR589631_bin.19_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 02:48:35,054] [INFO] Task succeeded: HMMsearch
[2023-06-13 02:48:35,056] [INFO] Found 6/6 markers.
[2023-06-13 02:48:35,082] [INFO] Query marker FASTA was written to GCA_938045455.1_ERR589631_bin.19_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 02:48:35,082] [INFO] Task started: Blastn
[2023-06-13 02:48:35,083] [INFO] Running command: blastn -query GCA_938045455.1_ERR589631_bin.19_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a0d1322-7eb9-4737-b4bd-0d9252f720f9/dqc_reference/reference_markers.fasta -out GCA_938045455.1_ERR589631_bin.19_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 02:48:35,653] [INFO] Task succeeded: Blastn
[2023-06-13 02:48:35,657] [INFO] Selected 17 target genomes.
[2023-06-13 02:48:35,658] [INFO] Target genome list was writen to GCA_938045455.1_ERR589631_bin.19_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 02:48:35,659] [INFO] Task started: fastANI
[2023-06-13 02:48:35,660] [INFO] Running command: fastANI --query /var/lib/cwl/stgaba4c635-e579-4a7d-ba49-5637f383267f/GCA_938045455.1_ERR589631_bin.19_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938045455.1_ERR589631_bin.19_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938045455.1_ERR589631_bin.19_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 02:48:44,250] [INFO] Task succeeded: fastANI
[2023-06-13 02:48:44,251] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a0d1322-7eb9-4737-b4bd-0d9252f720f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 02:48:44,251] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a0d1322-7eb9-4737-b4bd-0d9252f720f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 02:48:44,260] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2023-06-13 02:48:44,260] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 02:48:44,260] [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
Prevotella oulorum	strain=JCM 14966	GCA_000613785.1	28136	28136	type	True	97.2783	649	727	95	conclusive
Prevotella oulorum	strain=ATCC 43324	GCA_900167385.1	28136	28136	type	True	97.21	671	727	95	conclusive
Prevotella maculosa	strain=DSM 19339	GCA_000382385.1	439703	439703	type	True	79.801	162	727	95	below_threshold
Prevotella maculosa	strain=JCM 15638	GCA_000613965.1	439703	439703	type	True	79.7367	160	727	95	below_threshold
Prevotella salivae	strain=DSM 15606	GCA_000185845.1	228604	228604	type	True	78.8893	138	727	95	below_threshold
Prevotella oris	strain=NCTC13071	GCA_900637655.1	28135	28135	type	True	78.7832	156	727	95	below_threshold
Prevotella oris	strain=DSM 18711	GCA_000377685.1	28135	28135	type	True	78.5865	160	727	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	77.3658	68	727	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	77.2521	86	727	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 02:48:44,262] [INFO] DFAST Taxonomy check result was written to GCA_938045455.1_ERR589631_bin.19_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 02:48:44,263] [INFO] ===== Taxonomy check completed =====
[2023-06-13 02:48:44,263] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 02:48:44,263] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a0d1322-7eb9-4737-b4bd-0d9252f720f9/dqc_reference/checkm_data
[2023-06-13 02:48:44,264] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 02:48:44,290] [INFO] Task started: CheckM
[2023-06-13 02:48:44,290] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938045455.1_ERR589631_bin.19_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938045455.1_ERR589631_bin.19_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938045455.1_ERR589631_bin.19_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 02:49:29,167] [INFO] Task succeeded: CheckM
[2023-06-13 02:49:29,168] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 02:49:29,189] [INFO] ===== Completeness check finished =====
[2023-06-13 02:49:29,190] [INFO] ===== Start GTDB Search =====
[2023-06-13 02:49:29,190] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938045455.1_ERR589631_bin.19_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 02:49:29,190] [INFO] Task started: Blastn
[2023-06-13 02:49:29,190] [INFO] Running command: blastn -query GCA_938045455.1_ERR589631_bin.19_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a0d1322-7eb9-4737-b4bd-0d9252f720f9/dqc_reference/reference_markers_gtdb.fasta -out GCA_938045455.1_ERR589631_bin.19_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 02:49:29,996] [INFO] Task succeeded: Blastn
[2023-06-13 02:49:30,001] [INFO] Selected 18 target genomes.
[2023-06-13 02:49:30,001] [INFO] Target genome list was writen to GCA_938045455.1_ERR589631_bin.19_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 02:49:30,008] [INFO] Task started: fastANI
[2023-06-13 02:49:30,008] [INFO] Running command: fastANI --query /var/lib/cwl/stgaba4c635-e579-4a7d-ba49-5637f383267f/GCA_938045455.1_ERR589631_bin.19_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938045455.1_ERR589631_bin.19_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938045455.1_ERR589631_bin.19_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 02:49:38,109] [INFO] Task succeeded: fastANI
[2023-06-13 02:49:38,120] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 02:49:38,121] [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_000613785.1	s__Prevotella oulorum	97.2524	650	727	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.00	96.91	0.92	0.84	5	conclusive
GCF_000599605.1	s__Prevotella sp000599605	92.0025	615	727	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.66	96.63	0.93	0.92	3	-
GCF_000382385.1	s__Prevotella maculosa	79.8307	161	727	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.13	97.00	0.93	0.87	4	-
GCF_000185845.1	s__Prevotella salivae	78.8769	139	727	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.60	96.70	0.94	0.87	27	-
GCF_900637655.1	s__Prevotella oris	78.7244	156	727	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.96	97.06	0.90	0.82	10	-
GCF_000184945.1	s__Prevotella buccae	77.2836	93	727	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.38	98.24	0.91	0.87	7	-
GCA_900199655.1	s__Prevotella sp900199655	77.01	68	727	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.91	99.91	0.98	0.98	2	-
GCA_000435635.1	s__Prevotella avicola	76.3336	50	727	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.53	97.19	0.88	0.87	5	-
GCA_900543975.1	s__Prevotella sp900543975	75.8779	52	727	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.48	97.34	0.84	0.79	5	-
--------------------------------------------------------------------------------
[2023-06-13 02:49:38,123] [INFO] GTDB search result was written to GCA_938045455.1_ERR589631_bin.19_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 02:49:38,123] [INFO] ===== GTDB Search completed =====
[2023-06-13 02:49:38,126] [INFO] DFAST_QC result json was written to GCA_938045455.1_ERR589631_bin.19_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 02:49:38,127] [INFO] DFAST_QC completed!
[2023-06-13 02:49:38,127] [INFO] Total running time: 0h1m19s