[2024-01-24 14:54:56,599] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:54:56,601] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:54:56,601] [INFO] DQC Reference Directory: /var/lib/cwl/stg83028684-559e-461b-9b96-8ed5d1a9e3ec/dqc_reference
[2024-01-24 14:54:58,002] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:54:58,003] [INFO] Task started: Prodigal
[2024-01-24 14:54:58,003] [INFO] Running command: gunzip -c /var/lib/cwl/stg41c15866-7445-47b5-9423-5b70b93adf6b/GCF_900187175.1_51342_A02_genomic.fna.gz | prodigal -d GCF_900187175.1_51342_A02_genomic.fna/cds.fna -a GCF_900187175.1_51342_A02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:19,940] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:19,941] [INFO] Task started: HMMsearch
[2024-01-24 14:55:19,941] [INFO] Running command: hmmsearch --tblout GCF_900187175.1_51342_A02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg83028684-559e-461b-9b96-8ed5d1a9e3ec/dqc_reference/reference_markers.hmm GCF_900187175.1_51342_A02_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:20,289] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:20,290] [INFO] Found 6/6 markers.
[2024-01-24 14:55:20,328] [INFO] Query marker FASTA was written to GCF_900187175.1_51342_A02_genomic.fna/markers.fasta
[2024-01-24 14:55:20,328] [INFO] Task started: Blastn
[2024-01-24 14:55:20,328] [INFO] Running command: blastn -query GCF_900187175.1_51342_A02_genomic.fna/markers.fasta -db /var/lib/cwl/stg83028684-559e-461b-9b96-8ed5d1a9e3ec/dqc_reference/reference_markers.fasta -out GCF_900187175.1_51342_A02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:20,949] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:20,952] [INFO] Selected 16 target genomes.
[2024-01-24 14:55:20,953] [INFO] Target genome list was writen to GCF_900187175.1_51342_A02_genomic.fna/target_genomes.txt
[2024-01-24 14:55:20,964] [INFO] Task started: fastANI
[2024-01-24 14:55:20,964] [INFO] Running command: fastANI --query /var/lib/cwl/stg41c15866-7445-47b5-9423-5b70b93adf6b/GCF_900187175.1_51342_A02_genomic.fna.gz --refList GCF_900187175.1_51342_A02_genomic.fna/target_genomes.txt --output GCF_900187175.1_51342_A02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:36,244] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:36,245] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg83028684-559e-461b-9b96-8ed5d1a9e3ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:36,245] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg83028684-559e-461b-9b96-8ed5d1a9e3ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:36,254] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:55:36,254] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:36,254] [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
Odoribacter splanchnicus	strain=NCTC10825	GCA_900187175.1	28118	28118	type	True	100.0	1463	1464	95	conclusive
Odoribacter splanchnicus	strain=DSM 220712	GCA_000190535.1	28118	28118	type	True	99.9952	1463	1464	95	conclusive
Culturomica massiliensis	strain=Marseille-P2698	GCA_900091655.1	1841857	1841857	type	True	78.1868	202	1464	95	below_threshold
Butyricimonas virosa	strain=DSM 23226	GCA_025148635.1	544645	544645	type	True	77.9588	109	1464	95	below_threshold
Odoribacter laneus	strain=YIT 12061	GCA_000243215.1	626933	626933	type	True	77.4863	164	1464	95	below_threshold
Butyricimonas virosa	strain=DSM 23226	GCA_000519105.1	544645	544645	type	True	76.9944	102	1464	95	below_threshold
Butyricimonas faecihominis	strain=JCM 18676	GCA_014647335.1	1472416	1472416	type	True	76.5814	102	1464	95	below_threshold
Butyricimonas faecihominis	strain=DSM 105721	GCA_014196975.1	1472416	1472416	type	True	76.4389	103	1464	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:36,256] [INFO] DFAST Taxonomy check result was written to GCF_900187175.1_51342_A02_genomic.fna/tc_result.tsv
[2024-01-24 14:55:36,257] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:36,257] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:36,258] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg83028684-559e-461b-9b96-8ed5d1a9e3ec/dqc_reference/checkm_data
[2024-01-24 14:55:36,259] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:36,312] [INFO] Task started: CheckM
[2024-01-24 14:55:36,312] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900187175.1_51342_A02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900187175.1_51342_A02_genomic.fna/checkm_input GCF_900187175.1_51342_A02_genomic.fna/checkm_result
[2024-01-24 14:56:35,948] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:35,949] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:35,971] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:35,972] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:35,972] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900187175.1_51342_A02_genomic.fna/markers.fasta)
[2024-01-24 14:56:35,973] [INFO] Task started: Blastn
[2024-01-24 14:56:35,973] [INFO] Running command: blastn -query GCF_900187175.1_51342_A02_genomic.fna/markers.fasta -db /var/lib/cwl/stg83028684-559e-461b-9b96-8ed5d1a9e3ec/dqc_reference/reference_markers_gtdb.fasta -out GCF_900187175.1_51342_A02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:36,781] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:36,785] [INFO] Selected 21 target genomes.
[2024-01-24 14:56:36,785] [INFO] Target genome list was writen to GCF_900187175.1_51342_A02_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:36,807] [INFO] Task started: fastANI
[2024-01-24 14:56:36,807] [INFO] Running command: fastANI --query /var/lib/cwl/stg41c15866-7445-47b5-9423-5b70b93adf6b/GCF_900187175.1_51342_A02_genomic.fna.gz --refList GCF_900187175.1_51342_A02_genomic.fna/target_genomes_gtdb.txt --output GCF_900187175.1_51342_A02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:52,477] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:52,494] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:52,494] [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_000190535.1	s__Odoribacter splanchnicus	99.9952	1463	1464	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Odoribacter	95.0	98.99	98.34	0.85	0.73	51	conclusive
GCA_900548135.1	s__Odoribacter sp900548135	80.5393	264	1464	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Odoribacter	95.0	100.00	100.00	0.94	0.94	2	-
GCA_905204385.1	s__Odoribacter sp905204385	79.9631	213	1464	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Odoribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905215395.1	s__Odoribacter sp905215395	79.1028	328	1464	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Odoribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900762515.1	s__Odoribacter sp900762515	78.7592	328	1464	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Odoribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009935865.1	s__Odoribacter sp009935865	78.6563	249	1464	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Odoribacter	95.0	99.00	98.96	0.93	0.92	3	-
GCA_910578105.1	s__Odoribacter sp910578105	78.4855	264	1464	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Odoribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091655.1	s__Odoribacter massiliensis	78.1783	202	1464	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Odoribacter	95.0	99.35	99.12	0.95	0.91	6	-
GCA_900544025.1	s__Odoribacter sp900544025	77.6051	209	1464	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Odoribacter	95.0	98.76	97.68	0.87	0.80	4	-
GCA_905193145.1	s__Odoribacter sp905193145	77.6017	143	1464	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Odoribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541415.1	s__Odoribacter sp900541415	77.5085	229	1464	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Odoribacter	95.0	99.97	99.97	0.96	0.96	2	-
GCA_001487125.1	s__Gabonibacter massiliensis	77.1335	91	1464	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Gabonibacter	95.0	98.83	98.37	0.92	0.88	5	-
GCA_900759925.1	s__Butyricimonas sp900759925	76.4054	90	1464	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900543425.1	s__Gabonibacter sp900543425	76.151	93	1464	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Gabonibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:56:52,495] [INFO] GTDB search result was written to GCF_900187175.1_51342_A02_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:52,496] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:52,499] [INFO] DFAST_QC result json was written to GCF_900187175.1_51342_A02_genomic.fna/dqc_result.json
[2024-01-24 14:56:52,500] [INFO] DFAST_QC completed!
[2024-01-24 14:56:52,500] [INFO] Total running time: 0h1m56s