[2024-01-25 19:37:06,476] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:37:06,481] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:37:06,481] [INFO] DQC Reference Directory: /var/lib/cwl/stg9adb9727-0125-4102-993d-c96106a18e83/dqc_reference
[2024-01-25 19:37:07,624] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:37:07,624] [INFO] Task started: Prodigal
[2024-01-25 19:37:07,625] [INFO] Running command: gunzip -c /var/lib/cwl/stg6f187e59-5bcc-44ed-b6c0-5689dbe70ef9/GCF_000613485.1_ASM61348v1_genomic.fna.gz | prodigal -d GCF_000613485.1_ASM61348v1_genomic.fna/cds.fna -a GCF_000613485.1_ASM61348v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:37:24,299] [INFO] Task succeeded: Prodigal
[2024-01-25 19:37:24,299] [INFO] Task started: HMMsearch
[2024-01-25 19:37:24,299] [INFO] Running command: hmmsearch --tblout GCF_000613485.1_ASM61348v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9adb9727-0125-4102-993d-c96106a18e83/dqc_reference/reference_markers.hmm GCF_000613485.1_ASM61348v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:37:24,501] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:37:24,503] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6f187e59-5bcc-44ed-b6c0-5689dbe70ef9/GCF_000613485.1_ASM61348v1_genomic.fna.gz]
[2024-01-25 19:37:24,531] [INFO] Query marker FASTA was written to GCF_000613485.1_ASM61348v1_genomic.fna/markers.fasta
[2024-01-25 19:37:24,531] [INFO] Task started: Blastn
[2024-01-25 19:37:24,531] [INFO] Running command: blastn -query GCF_000613485.1_ASM61348v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9adb9727-0125-4102-993d-c96106a18e83/dqc_reference/reference_markers.fasta -out GCF_000613485.1_ASM61348v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:37:25,118] [INFO] Task succeeded: Blastn
[2024-01-25 19:37:25,121] [INFO] Selected 12 target genomes.
[2024-01-25 19:37:25,121] [INFO] Target genome list was writen to GCF_000613485.1_ASM61348v1_genomic.fna/target_genomes.txt
[2024-01-25 19:37:25,125] [INFO] Task started: fastANI
[2024-01-25 19:37:25,125] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f187e59-5bcc-44ed-b6c0-5689dbe70ef9/GCF_000613485.1_ASM61348v1_genomic.fna.gz --refList GCF_000613485.1_ASM61348v1_genomic.fna/target_genomes.txt --output GCF_000613485.1_ASM61348v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:37:34,440] [INFO] Task succeeded: fastANI
[2024-01-25 19:37:34,441] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9adb9727-0125-4102-993d-c96106a18e83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:37:34,441] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9adb9727-0125-4102-993d-c96106a18e83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:37:34,447] [INFO] Found 7 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 19:37:34,447] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:37:34,448] [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 loescheii	strain=JCM 12249	GCA_000613485.1	840	840	type	True	100.0	1139	1139	95	conclusive
Prevotella loescheii	strain=DSM 19665	GCA_000378085.1	840	840	type	True	99.9599	1137	1139	95	conclusive
Prevotella loescheii	strain=ATCC 15930	GCA_000698925.1	840	840	type	True	99.9425	1126	1139	95	conclusive
Prevotella shahii	strain=DSM 15611	GCA_003201715.1	228603	228603	type	True	82.0482	714	1139	95	below_threshold
Prevotella shahii	strain=JCM 12083	GCA_000613445.1	228603	228603	type	True	81.9667	697	1139	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	78.1724	103	1139	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.8235	66	1139	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:37:34,450] [INFO] DFAST Taxonomy check result was written to GCF_000613485.1_ASM61348v1_genomic.fna/tc_result.tsv
[2024-01-25 19:37:34,450] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:37:34,450] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:37:34,450] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9adb9727-0125-4102-993d-c96106a18e83/dqc_reference/checkm_data
[2024-01-25 19:37:34,451] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:37:34,486] [INFO] Task started: CheckM
[2024-01-25 19:37:34,486] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000613485.1_ASM61348v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000613485.1_ASM61348v1_genomic.fna/checkm_input GCF_000613485.1_ASM61348v1_genomic.fna/checkm_result
[2024-01-25 19:38:20,553] [INFO] Task succeeded: CheckM
[2024-01-25 19:38:20,554] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.31%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:38:20,577] [INFO] ===== Completeness check finished =====
[2024-01-25 19:38:20,577] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:38:20,579] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000613485.1_ASM61348v1_genomic.fna/markers.fasta)
[2024-01-25 19:38:20,579] [INFO] Task started: Blastn
[2024-01-25 19:38:20,579] [INFO] Running command: blastn -query GCF_000613485.1_ASM61348v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9adb9727-0125-4102-993d-c96106a18e83/dqc_reference/reference_markers_gtdb.fasta -out GCF_000613485.1_ASM61348v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:38:21,589] [INFO] Task succeeded: Blastn
[2024-01-25 19:38:21,593] [INFO] Selected 11 target genomes.
[2024-01-25 19:38:21,593] [INFO] Target genome list was writen to GCF_000613485.1_ASM61348v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:38:21,606] [INFO] Task started: fastANI
[2024-01-25 19:38:21,606] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f187e59-5bcc-44ed-b6c0-5689dbe70ef9/GCF_000613485.1_ASM61348v1_genomic.fna.gz --refList GCF_000613485.1_ASM61348v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000613485.1_ASM61348v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:38:29,750] [INFO] Task succeeded: fastANI
[2024-01-25 19:38:29,757] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:38:29,757] [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_000378085.1	s__Prevotella loescheii	99.9599	1137	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.09	95.73	0.96	0.93	5	conclusive
GCF_000312305.1	s__Prevotella conceptionensis	85.7968	849	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.86	95.59	0.91	0.86	4	-
GCF_000613445.1	s__Prevotella shahii	81.9584	698	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.54	98.05	0.93	0.90	5	-
GCA_905373605.1	s__Prevotella sp905373605	81.6659	560	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018127805.1	s__Prevotella sp018127805	80.9139	232	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000184945.1	s__Prevotella buccae	78.1629	104	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.38	98.24	0.91	0.87	7	-
GCF_000235885.1	s__Prevotella stercorea	76.8235	66	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.02	96.84	0.81	0.69	8	-
GCF_016899955.1	s__Prevotella sp900540415	76.557	65	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.44	98.08	0.94	0.91	6	-
GCA_900315095.1	s__Prevotella sp900315095	76.2347	60	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.59	96.16	0.90	0.86	18	-
GCA_017474515.1	s__Prevotella sp017474515	75.9992	60	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:38:29,758] [INFO] GTDB search result was written to GCF_000613485.1_ASM61348v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:38:29,758] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:38:29,761] [INFO] DFAST_QC result json was written to GCF_000613485.1_ASM61348v1_genomic.fna/dqc_result.json
[2024-01-25 19:38:29,761] [INFO] DFAST_QC completed!
[2024-01-25 19:38:29,761] [INFO] Total running time: 0h1m23s