[2024-01-24 12:29:39,469] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:39,474] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:39,474] [INFO] DQC Reference Directory: /var/lib/cwl/stg3181be28-7e32-43e2-804f-4aa03700f614/dqc_reference
[2024-01-24 12:29:42,395] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:42,397] [INFO] Task started: Prodigal
[2024-01-24 12:29:42,397] [INFO] Running command: gunzip -c /var/lib/cwl/stgacda5e0c-f00b-45d8-80a7-ee11c2a01ad9/GCF_003634345.1_ASM363434v1_genomic.fna.gz | prodigal -d GCF_003634345.1_ASM363434v1_genomic.fna/cds.fna -a GCF_003634345.1_ASM363434v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:56,516] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:56,516] [INFO] Task started: HMMsearch
[2024-01-24 12:29:56,516] [INFO] Running command: hmmsearch --tblout GCF_003634345.1_ASM363434v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3181be28-7e32-43e2-804f-4aa03700f614/dqc_reference/reference_markers.hmm GCF_003634345.1_ASM363434v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:56,796] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:56,797] [INFO] Found 6/6 markers.
[2024-01-24 12:29:56,829] [INFO] Query marker FASTA was written to GCF_003634345.1_ASM363434v1_genomic.fna/markers.fasta
[2024-01-24 12:29:56,829] [INFO] Task started: Blastn
[2024-01-24 12:29:56,829] [INFO] Running command: blastn -query GCF_003634345.1_ASM363434v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3181be28-7e32-43e2-804f-4aa03700f614/dqc_reference/reference_markers.fasta -out GCF_003634345.1_ASM363434v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:57,418] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:57,422] [INFO] Selected 21 target genomes.
[2024-01-24 12:29:57,422] [INFO] Target genome list was writen to GCF_003634345.1_ASM363434v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:57,433] [INFO] Task started: fastANI
[2024-01-24 12:29:57,433] [INFO] Running command: fastANI --query /var/lib/cwl/stgacda5e0c-f00b-45d8-80a7-ee11c2a01ad9/GCF_003634345.1_ASM363434v1_genomic.fna.gz --refList GCF_003634345.1_ASM363434v1_genomic.fna/target_genomes.txt --output GCF_003634345.1_ASM363434v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:11,319] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:11,320] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3181be28-7e32-43e2-804f-4aa03700f614/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:11,320] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3181be28-7e32-43e2-804f-4aa03700f614/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:11,334] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:30:11,335] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:11,335] [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
Coprobacter fastidiosus	strain=NSB1	GCA_003634345.1	1099853	1099853	type	True	100.0	1128	1128	95	conclusive
Coprobacter fastidiosus	strain=NSB1	GCA_000473955.1	1099853	1099853	type	True	99.9705	1105	1128	95	conclusive
Coprobacter secundus subsp. similis	strain=2CBH44	GCA_015097275.1	2751153	1501392	type	True	77.8813	158	1128	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI 5482	GCA_022453665.1	818	818	type	True	77.329	55	1128	95	below_threshold
Barnesiella intestinihominis	strain=YIT 11860	GCA_000296465.1	487174	487174	type	True	77.2112	74	1128	95	below_threshold
Phocaeicola dorei	strain=DSM 17855	GCA_013009555.1	357276	357276	type	True	76.807	50	1128	95	below_threshold
Phocaeicola dorei	strain=DSM 17855	GCA_025146415.1	357276	357276	type	True	76.7818	52	1128	95	below_threshold
Parabacteroides pacaensis	strain=Marseille-P4001	GCA_900292045.1	2086575	2086575	type	True	76.5796	53	1128	95	below_threshold
Parabacteroides timonensis	strain=Marseille-P3236	GCA_900128505.1	1871013	1871013	type	True	76.2964	58	1128	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:11,337] [INFO] DFAST Taxonomy check result was written to GCF_003634345.1_ASM363434v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:11,337] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:11,338] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:11,338] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3181be28-7e32-43e2-804f-4aa03700f614/dqc_reference/checkm_data
[2024-01-24 12:30:11,339] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:11,376] [INFO] Task started: CheckM
[2024-01-24 12:30:11,376] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003634345.1_ASM363434v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003634345.1_ASM363434v1_genomic.fna/checkm_input GCF_003634345.1_ASM363434v1_genomic.fna/checkm_result
[2024-01-24 12:30:54,429] [INFO] Task succeeded: CheckM
[2024-01-24 12:30:54,431] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:30:54,450] [INFO] ===== Completeness check finished =====
[2024-01-24 12:30:54,451] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:30:54,451] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003634345.1_ASM363434v1_genomic.fna/markers.fasta)
[2024-01-24 12:30:54,451] [INFO] Task started: Blastn
[2024-01-24 12:30:54,452] [INFO] Running command: blastn -query GCF_003634345.1_ASM363434v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3181be28-7e32-43e2-804f-4aa03700f614/dqc_reference/reference_markers_gtdb.fasta -out GCF_003634345.1_ASM363434v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:55,229] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:55,233] [INFO] Selected 19 target genomes.
[2024-01-24 12:30:55,234] [INFO] Target genome list was writen to GCF_003634345.1_ASM363434v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:30:55,256] [INFO] Task started: fastANI
[2024-01-24 12:30:55,257] [INFO] Running command: fastANI --query /var/lib/cwl/stgacda5e0c-f00b-45d8-80a7-ee11c2a01ad9/GCF_003634345.1_ASM363434v1_genomic.fna.gz --refList GCF_003634345.1_ASM363434v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003634345.1_ASM363434v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:06,540] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:06,554] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:06,554] [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_003634345.1	s__Coprobacter fastidiosus	100.0	1128	1128	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Coprobacteraceae;g__Coprobacter	95.0	98.46	97.98	0.89	0.59	13	conclusive
GCA_900545915.1	s__Coprobacter sp900545915	93.3979	950	1128	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Coprobacteraceae;g__Coprobacter	95.0	97.49	96.20	0.84	0.83	3	-
GCA_000803105.1	s__Coprobacter secundus	77.8285	159	1128	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Coprobacteraceae;g__Coprobacter	95.0	97.96	96.86	0.90	0.85	6	-
GCA_019114445.1	s__Barnesiella excrementigallinarum	77.5007	70	1128	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Barnesiellaceae;g__Barnesiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000296465.1	s__Barnesiella intestinihominis	77.2834	72	1128	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Barnesiellaceae;g__Barnesiella	95.0	98.49	98.18	0.93	0.86	27	-
GCA_017467745.1	s__Gallibacteroides sp017467745	77.0945	65	1128	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__CHK158-818;g__Gallibacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000434215.1	s__UBA11471 sp000434215	76.7199	70	1128	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA11471;g__UBA11471	95.0	99.32	98.64	0.92	0.84	6	-
GCF_015550595.1	s__Parabacteroides sp900540715	76.1833	51	1128	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.96	99.96	0.98	0.97	3	-
GCA_900541965.1	s__Parabacteroides sp900541965	76.161	54	1128	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.98	99.95	0.94	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:06,557] [INFO] GTDB search result was written to GCF_003634345.1_ASM363434v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:06,558] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:06,567] [INFO] DFAST_QC result json was written to GCF_003634345.1_ASM363434v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:06,567] [INFO] DFAST_QC completed!
[2024-01-24 12:31:06,567] [INFO] Total running time: 0h1m27s