[2023-06-05 03:27:52,938] [INFO] DFAST_QC pipeline started.
[2023-06-05 03:27:52,940] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 03:27:52,940] [INFO] DQC Reference Directory: /var/lib/cwl/stg03069a27-b8fd-431e-bbc8-24789b53a84b/dqc_reference
[2023-06-05 03:27:54,993] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 03:27:54,994] [INFO] Task started: Prodigal
[2023-06-05 03:27:54,995] [INFO] Running command: gunzip -c /var/lib/cwl/stg336dcf0f-bd8c-4355-b07d-a56a781ebb17/GCA_004563425.1_ASM456342v1_genomic.fna.gz | prodigal -d GCA_004563425.1_ASM456342v1_genomic.fna/cds.fna -a GCA_004563425.1_ASM456342v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 03:27:59,610] [INFO] Task succeeded: Prodigal
[2023-06-05 03:27:59,610] [INFO] Task started: HMMsearch
[2023-06-05 03:27:59,611] [INFO] Running command: hmmsearch --tblout GCA_004563425.1_ASM456342v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg03069a27-b8fd-431e-bbc8-24789b53a84b/dqc_reference/reference_markers.hmm GCA_004563425.1_ASM456342v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 03:27:59,842] [INFO] Task succeeded: HMMsearch
[2023-06-05 03:27:59,844] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg336dcf0f-bd8c-4355-b07d-a56a781ebb17/GCA_004563425.1_ASM456342v1_genomic.fna.gz]
[2023-06-05 03:27:59,865] [INFO] Query marker FASTA was written to GCA_004563425.1_ASM456342v1_genomic.fna/markers.fasta
[2023-06-05 03:27:59,866] [INFO] Task started: Blastn
[2023-06-05 03:27:59,866] [INFO] Running command: blastn -query GCA_004563425.1_ASM456342v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03069a27-b8fd-431e-bbc8-24789b53a84b/dqc_reference/reference_markers.fasta -out GCA_004563425.1_ASM456342v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 03:28:00,487] [INFO] Task succeeded: Blastn
[2023-06-05 03:28:00,491] [INFO] Selected 7 target genomes.
[2023-06-05 03:28:00,491] [INFO] Target genome list was writen to GCA_004563425.1_ASM456342v1_genomic.fna/target_genomes.txt
[2023-06-05 03:28:00,492] [INFO] Task started: fastANI
[2023-06-05 03:28:00,492] [INFO] Running command: fastANI --query /var/lib/cwl/stg336dcf0f-bd8c-4355-b07d-a56a781ebb17/GCA_004563425.1_ASM456342v1_genomic.fna.gz --refList GCA_004563425.1_ASM456342v1_genomic.fna/target_genomes.txt --output GCA_004563425.1_ASM456342v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 03:28:03,551] [INFO] Task succeeded: fastANI
[2023-06-05 03:28:03,552] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg03069a27-b8fd-431e-bbc8-24789b53a84b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 03:28:03,552] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg03069a27-b8fd-431e-bbc8-24789b53a84b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 03:28:03,558] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 03:28:03,558] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 03:28:03,558] [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
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	78.307	59	486	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 03:28:03,560] [INFO] DFAST Taxonomy check result was written to GCA_004563425.1_ASM456342v1_genomic.fna/tc_result.tsv
[2023-06-05 03:28:03,560] [INFO] ===== Taxonomy check completed =====
[2023-06-05 03:28:03,560] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 03:28:03,561] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg03069a27-b8fd-431e-bbc8-24789b53a84b/dqc_reference/checkm_data
[2023-06-05 03:28:03,562] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 03:28:03,585] [INFO] Task started: CheckM
[2023-06-05 03:28:03,586] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004563425.1_ASM456342v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004563425.1_ASM456342v1_genomic.fna/checkm_input GCA_004563425.1_ASM456342v1_genomic.fna/checkm_result
[2023-06-05 03:28:25,206] [INFO] Task succeeded: CheckM
[2023-06-05 03:28:25,208] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 23.11%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 03:28:25,233] [INFO] ===== Completeness check finished =====
[2023-06-05 03:28:25,233] [INFO] ===== Start GTDB Search =====
[2023-06-05 03:28:25,233] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004563425.1_ASM456342v1_genomic.fna/markers.fasta)
[2023-06-05 03:28:25,234] [INFO] Task started: Blastn
[2023-06-05 03:28:25,234] [INFO] Running command: blastn -query GCA_004563425.1_ASM456342v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03069a27-b8fd-431e-bbc8-24789b53a84b/dqc_reference/reference_markers_gtdb.fasta -out GCA_004563425.1_ASM456342v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 03:28:26,230] [INFO] Task succeeded: Blastn
[2023-06-05 03:28:26,235] [INFO] Selected 18 target genomes.
[2023-06-05 03:28:26,235] [INFO] Target genome list was writen to GCA_004563425.1_ASM456342v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 03:28:26,290] [INFO] Task started: fastANI
[2023-06-05 03:28:26,290] [INFO] Running command: fastANI --query /var/lib/cwl/stg336dcf0f-bd8c-4355-b07d-a56a781ebb17/GCA_004563425.1_ASM456342v1_genomic.fna.gz --refList GCA_004563425.1_ASM456342v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004563425.1_ASM456342v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 03:28:32,562] [INFO] Task succeeded: fastANI
[2023-06-05 03:28:32,579] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 03:28:32,579] [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_004556965.1	s__CAG-103 sp004556965	97.3094	269	486	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	98.49	98.32	0.91	0.88	6	conclusive
GCA_018265835.1	s__CAG-103 sp018265835	92.6036	229	486	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004557905.1	s__Ventricola sp004557905	84.1346	60	486	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Ventricola	95.0	98.75	98.68	0.87	0.86	3	-
GCA_017937505.1	s__Ventricola sp017937505	82.283	51	486	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Ventricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900317855.1	s__CAG-103 sp900317855	81.7833	165	486	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	97.11	95.56	0.88	0.84	11	-
GCA_902760845.1	s__CAG-103 sp902760845	81.2819	155	486	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000432375.1	s__CAG-103 sp000432375	80.999	173	486	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	98.15	97.87	0.87	0.82	10	-
GCA_900543625.1	s__CAG-103 sp900543625	80.7193	181	486	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	96.93	95.23	0.89	0.87	12	-
GCA_900757655.1	s__CAG-103 sp900757655	80.6217	160	486	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	96.74	95.66	0.88	0.82	7	-
GCA_002405995.1	s__ER4 sp002405995	77.8668	57	486	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	99.39	99.39	0.82	0.82	2	-
GCA_017429835.1	s__Faecousia sp017429835	77.8549	57	486	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544705.1	s__Faecousia sp900544705	77.5917	62	486	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	98.60	98.49	0.88	0.86	3	-
--------------------------------------------------------------------------------
[2023-06-05 03:28:32,582] [INFO] GTDB search result was written to GCA_004563425.1_ASM456342v1_genomic.fna/result_gtdb.tsv
[2023-06-05 03:28:32,582] [INFO] ===== GTDB Search completed =====
[2023-06-05 03:28:32,586] [INFO] DFAST_QC result json was written to GCA_004563425.1_ASM456342v1_genomic.fna/dqc_result.json
[2023-06-05 03:28:32,586] [INFO] DFAST_QC completed!
[2023-06-05 03:28:32,586] [INFO] Total running time: 0h0m40s