[2023-06-19 06:28:03,976] [INFO] DFAST_QC pipeline started.
[2023-06-19 06:28:03,979] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 06:28:03,979] [INFO] DQC Reference Directory: /var/lib/cwl/stg854cbed3-4bd5-4471-9b8d-6821bfde5c27/dqc_reference
[2023-06-19 06:28:05,161] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 06:28:05,162] [INFO] Task started: Prodigal
[2023-06-19 06:28:05,162] [INFO] Running command: gunzip -c /var/lib/cwl/stg1b4a3fe9-0fce-4bc2-be12-f0ab43bb1f88/GCA_018370385.1_ASM1837038v1_genomic.fna.gz | prodigal -d GCA_018370385.1_ASM1837038v1_genomic.fna/cds.fna -a GCA_018370385.1_ASM1837038v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 06:28:12,005] [INFO] Task succeeded: Prodigal
[2023-06-19 06:28:12,005] [INFO] Task started: HMMsearch
[2023-06-19 06:28:12,005] [INFO] Running command: hmmsearch --tblout GCA_018370385.1_ASM1837038v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg854cbed3-4bd5-4471-9b8d-6821bfde5c27/dqc_reference/reference_markers.hmm GCA_018370385.1_ASM1837038v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 06:28:12,188] [INFO] Task succeeded: HMMsearch
[2023-06-19 06:28:12,189] [INFO] Found 6/6 markers.
[2023-06-19 06:28:12,213] [INFO] Query marker FASTA was written to GCA_018370385.1_ASM1837038v1_genomic.fna/markers.fasta
[2023-06-19 06:28:12,213] [INFO] Task started: Blastn
[2023-06-19 06:28:12,213] [INFO] Running command: blastn -query GCA_018370385.1_ASM1837038v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg854cbed3-4bd5-4471-9b8d-6821bfde5c27/dqc_reference/reference_markers.fasta -out GCA_018370385.1_ASM1837038v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 06:28:12,901] [INFO] Task succeeded: Blastn
[2023-06-19 06:28:12,905] [INFO] Selected 7 target genomes.
[2023-06-19 06:28:12,905] [INFO] Target genome list was writen to GCA_018370385.1_ASM1837038v1_genomic.fna/target_genomes.txt
[2023-06-19 06:28:12,905] [INFO] Task started: fastANI
[2023-06-19 06:28:12,906] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b4a3fe9-0fce-4bc2-be12-f0ab43bb1f88/GCA_018370385.1_ASM1837038v1_genomic.fna.gz --refList GCA_018370385.1_ASM1837038v1_genomic.fna/target_genomes.txt --output GCA_018370385.1_ASM1837038v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 06:28:17,160] [INFO] Task succeeded: fastANI
[2023-06-19 06:28:17,161] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg854cbed3-4bd5-4471-9b8d-6821bfde5c27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 06:28:17,161] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg854cbed3-4bd5-4471-9b8d-6821bfde5c27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 06:28:17,169] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 06:28:17,169] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 06:28:17,169] [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
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	85.5882	562	805	95	below_threshold
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	84.4529	549	805	95	below_threshold
Faecalibacterium duncaniae	strain=JCM 31915	GCA_010509575.1	411483	411483	type	True	84.3306	564	805	95	below_threshold
Faecalibacterium prausnitzii	strain=ATCC 27768	GCA_003324185.1	853	853	suspected-type	True	83.9852	538	805	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	81.5949	397	805	95	below_threshold
Subdoligranulum variabile	strain=DSM 15176	GCA_025152575.1	214851	214851	type	True	78.8849	193	805	95	below_threshold
Fournierella massiliensis	strain=DSM 100451	GCA_004345265.1	1650663	1650663	type	True	78.1037	206	805	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 06:28:17,171] [INFO] DFAST Taxonomy check result was written to GCA_018370385.1_ASM1837038v1_genomic.fna/tc_result.tsv
[2023-06-19 06:28:17,172] [INFO] ===== Taxonomy check completed =====
[2023-06-19 06:28:17,172] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 06:28:17,172] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg854cbed3-4bd5-4471-9b8d-6821bfde5c27/dqc_reference/checkm_data
[2023-06-19 06:28:17,173] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 06:28:17,198] [INFO] Task started: CheckM
[2023-06-19 06:28:17,198] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018370385.1_ASM1837038v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018370385.1_ASM1837038v1_genomic.fna/checkm_input GCA_018370385.1_ASM1837038v1_genomic.fna/checkm_result
[2023-06-19 06:28:41,250] [INFO] Task succeeded: CheckM
[2023-06-19 06:28:41,251] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 06:28:41,273] [INFO] ===== Completeness check finished =====
[2023-06-19 06:28:41,273] [INFO] ===== Start GTDB Search =====
[2023-06-19 06:28:41,274] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018370385.1_ASM1837038v1_genomic.fna/markers.fasta)
[2023-06-19 06:28:41,274] [INFO] Task started: Blastn
[2023-06-19 06:28:41,274] [INFO] Running command: blastn -query GCA_018370385.1_ASM1837038v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg854cbed3-4bd5-4471-9b8d-6821bfde5c27/dqc_reference/reference_markers_gtdb.fasta -out GCA_018370385.1_ASM1837038v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 06:28:42,465] [INFO] Task succeeded: Blastn
[2023-06-19 06:28:42,470] [INFO] Selected 12 target genomes.
[2023-06-19 06:28:42,470] [INFO] Target genome list was writen to GCA_018370385.1_ASM1837038v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 06:28:42,471] [INFO] Task started: fastANI
[2023-06-19 06:28:42,471] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b4a3fe9-0fce-4bc2-be12-f0ab43bb1f88/GCA_018370385.1_ASM1837038v1_genomic.fna.gz --refList GCA_018370385.1_ASM1837038v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018370385.1_ASM1837038v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 06:28:50,132] [INFO] Task succeeded: fastANI
[2023-06-19 06:28:50,144] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 06:28:50,144] [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_003293635.1	s__Faecalibacterium prausnitzii_G	96.4304	653	805	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.11	95.97	0.86	0.76	34	conclusive
GCA_900758465.1	s__Faecalibacterium sp900758465	91.2551	581	805	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.14	97.85	0.88	0.87	4	-
GCA_002313795.1	s__Faecalibacterium prausnitzii_L	86.4173	426	805	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.80	98.80	0.73	0.73	2	-
GCF_002549975.1	s__Faecalibacterium prausnitzii_H	85.5835	594	805	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.03	97.77	0.90	0.86	9	-
GCF_002550035.1	s__Faecalibacterium prausnitzii_E	85.3928	575	805	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.41	96.74	0.87	0.80	12	-
GCF_003287495.1	s__Faecalibacterium prausnitzii_I	84.9522	572	805	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.17	97.28	0.90	0.84	9	-
GCF_002549775.1	s__Faecalibacterium prausnitzii_F	84.6302	551	805	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.99	97.71	0.95	0.94	3	-
GCA_014858325.1	s__Faecalibacterium sp014858325	84.6099	379	805	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900539945.1	s__Faecalibacterium sp900539945	84.2023	527	805	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.71	98.00	0.92	0.86	4	-
GCF_003287405.1	s__Faecalibacterium prausnitzii_J	84.0465	527	805	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.32	96.98	0.87	0.83	5	-
GCA_900551435.1	s__Faecalibacterium sp900551435	83.5449	468	805	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.30	98.30	0.83	0.83	2	-
GCA_905215595.1	s__Faecalibacterium sp905215595	82.5779	376	805	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 06:28:50,147] [INFO] GTDB search result was written to GCA_018370385.1_ASM1837038v1_genomic.fna/result_gtdb.tsv
[2023-06-19 06:28:50,148] [INFO] ===== GTDB Search completed =====
[2023-06-19 06:28:50,152] [INFO] DFAST_QC result json was written to GCA_018370385.1_ASM1837038v1_genomic.fna/dqc_result.json
[2023-06-19 06:28:50,153] [INFO] DFAST_QC completed!
[2023-06-19 06:28:50,153] [INFO] Total running time: 0h0m46s