[2024-01-24 14:04:44,418] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:04:44,419] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:04:44,420] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f642559-ee2a-4014-a5d2-bde44230b169/dqc_reference
[2024-01-24 14:04:45,616] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:04:45,617] [INFO] Task started: Prodigal
[2024-01-24 14:04:45,618] [INFO] Running command: gunzip -c /var/lib/cwl/stgb4a02a14-1cb4-46a3-81d5-3e3ab99f9852/GCF_900187995.1_IMG-taxon_2724679806_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900187995.1_IMG-taxon_2724679806_annotated_assembly_genomic.fna/cds.fna -a GCF_900187995.1_IMG-taxon_2724679806_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:00,949] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:00,949] [INFO] Task started: HMMsearch
[2024-01-24 14:05:00,949] [INFO] Running command: hmmsearch --tblout GCF_900187995.1_IMG-taxon_2724679806_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f642559-ee2a-4014-a5d2-bde44230b169/dqc_reference/reference_markers.hmm GCF_900187995.1_IMG-taxon_2724679806_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:01,205] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:01,206] [INFO] Found 6/6 markers.
[2024-01-24 14:05:01,238] [INFO] Query marker FASTA was written to GCF_900187995.1_IMG-taxon_2724679806_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:05:01,238] [INFO] Task started: Blastn
[2024-01-24 14:05:01,239] [INFO] Running command: blastn -query GCF_900187995.1_IMG-taxon_2724679806_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f642559-ee2a-4014-a5d2-bde44230b169/dqc_reference/reference_markers.fasta -out GCF_900187995.1_IMG-taxon_2724679806_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:01,837] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:01,841] [INFO] Selected 12 target genomes.
[2024-01-24 14:05:01,841] [INFO] Target genome list was writen to GCF_900187995.1_IMG-taxon_2724679806_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:05:01,867] [INFO] Task started: fastANI
[2024-01-24 14:05:01,868] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4a02a14-1cb4-46a3-81d5-3e3ab99f9852/GCF_900187995.1_IMG-taxon_2724679806_annotated_assembly_genomic.fna.gz --refList GCF_900187995.1_IMG-taxon_2724679806_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900187995.1_IMG-taxon_2724679806_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:05:11,127] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:11,127] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f642559-ee2a-4014-a5d2-bde44230b169/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:05:11,128] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f642559-ee2a-4014-a5d2-bde44230b169/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:05:11,140] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:05:11,140] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:05:11,141] [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 jejuni	strain=DSM 26989	GCA_900187995.1	1177574	1177574	type	True	100.0	1168	1170	95	conclusive
Prevotella melaninogenica	strain=ATCC 25845	GCA_000144405.1	28132	28132	suspected-type	True	86.6089	803	1170	95	below_threshold
Prevotella melaninogenica	strain=FDAARGOS_1566	GCA_020735785.1	28132	28132	suspected-type	True	86.5474	793	1170	95	below_threshold
Prevotella scopos	strain=W2052	GCA_018127785.1	589437	589437	type	True	84.6279	729	1170	95	below_threshold
Prevotella scopos	strain=DSM 22613	GCA_900129535.1	589437	589437	type	True	84.6237	716	1170	95	below_threshold
Prevotella scopos	strain=W2052	GCA_001683355.1	589437	589437	type	True	84.5126	750	1170	95	below_threshold
Prevotella vespertina	strain=A2879	GCA_009728485.1	2608404	2608404	type	True	82.043	447	1170	95	below_threshold
Prevotella fusca	strain=W1435	GCA_018128145.1	589436	589436	type	True	81.7395	616	1170	95	below_threshold
Prevotella fusca	strain=W1435	GCA_001262015.1	589436	589436	type	True	81.7383	621	1170	95	below_threshold
Prevotella veroralis	strain=DSM 19559	GCA_000377625.1	28137	28137	type	True	80.9263	390	1170	95	below_threshold
Prevotella veroralis	strain=JCM 6290	GCA_000613325.1	28137	28137	type	True	80.9027	379	1170	95	below_threshold
Prevotella herbatica	strain=WR041	GCA_017347605.1	2801997	2801997	type	True	77.8819	78	1170	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:05:11,142] [INFO] DFAST Taxonomy check result was written to GCF_900187995.1_IMG-taxon_2724679806_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:05:11,143] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:05:11,143] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:05:11,143] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f642559-ee2a-4014-a5d2-bde44230b169/dqc_reference/checkm_data
[2024-01-24 14:05:11,144] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:05:11,180] [INFO] Task started: CheckM
[2024-01-24 14:05:11,180] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900187995.1_IMG-taxon_2724679806_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900187995.1_IMG-taxon_2724679806_annotated_assembly_genomic.fna/checkm_input GCF_900187995.1_IMG-taxon_2724679806_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:05:58,810] [INFO] Task succeeded: CheckM
[2024-01-24 14:05:58,811] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:05:58,837] [INFO] ===== Completeness check finished =====
[2024-01-24 14:05:58,837] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:05:58,838] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900187995.1_IMG-taxon_2724679806_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:05:58,838] [INFO] Task started: Blastn
[2024-01-24 14:05:58,838] [INFO] Running command: blastn -query GCF_900187995.1_IMG-taxon_2724679806_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f642559-ee2a-4014-a5d2-bde44230b169/dqc_reference/reference_markers_gtdb.fasta -out GCF_900187995.1_IMG-taxon_2724679806_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:59,683] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:59,686] [INFO] Selected 9 target genomes.
[2024-01-24 14:05:59,686] [INFO] Target genome list was writen to GCF_900187995.1_IMG-taxon_2724679806_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:05:59,711] [INFO] Task started: fastANI
[2024-01-24 14:05:59,711] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4a02a14-1cb4-46a3-81d5-3e3ab99f9852/GCF_900187995.1_IMG-taxon_2724679806_annotated_assembly_genomic.fna.gz --refList GCF_900187995.1_IMG-taxon_2724679806_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900187995.1_IMG-taxon_2724679806_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:08,341] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:08,349] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:08,350] [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_900187995.1	s__Prevotella jejuni	100.0	1168	1170	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.22	96.57	0.92	0.88	7	conclusive
GCF_000144405.1	s__Prevotella melaninogenica	86.5989	804	1170	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.46	95.36	0.87	0.78	36	-
GCF_018127965.1	s__Prevotella melaninogenica_B	86.3266	801	1170	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.77	95.72	0.91	0.89	4	-
GCF_018127925.1	s__Prevotella melaninogenica_C	86.0708	786	1170	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003609775.1	s__Prevotella melaninogenica_A	84.9147	782	1170	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018127785.1	s__Prevotella scopos	84.6628	727	1170	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.98	99.97	1.00	1.00	4	-
GCF_018128065.1	s__Prevotella sp000467895	83.9977	731	1170	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.71	96.42	0.91	0.83	4	-
GCF_000257925.1	s__Prevotella sp000257925	82.1607	424	1170	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.40	96.99	0.92	0.83	10	-
GCF_000377625.1	s__Prevotella veroralis	80.9694	386	1170	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.76	96.65	0.91	0.86	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:08,352] [INFO] GTDB search result was written to GCF_900187995.1_IMG-taxon_2724679806_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:08,352] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:08,356] [INFO] DFAST_QC result json was written to GCF_900187995.1_IMG-taxon_2724679806_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:06:08,356] [INFO] DFAST_QC completed!
[2024-01-24 14:06:08,356] [INFO] Total running time: 0h1m24s