[2024-01-24 14:31:00,270] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:00,290] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:00,290] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d378ba0-d6e7-4882-ae13-20a9e6155876/dqc_reference
[2024-01-24 14:31:02,104] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:02,105] [INFO] Task started: Prodigal
[2024-01-24 14:31:02,105] [INFO] Running command: gunzip -c /var/lib/cwl/stg04c1a6b9-2ab8-4120-adae-5bd239520016/GCF_001623255.1_ASM162325v1_genomic.fna.gz | prodigal -d GCF_001623255.1_ASM162325v1_genomic.fna/cds.fna -a GCF_001623255.1_ASM162325v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:15,597] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:15,598] [INFO] Task started: HMMsearch
[2024-01-24 14:31:15,598] [INFO] Running command: hmmsearch --tblout GCF_001623255.1_ASM162325v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d378ba0-d6e7-4882-ae13-20a9e6155876/dqc_reference/reference_markers.hmm GCF_001623255.1_ASM162325v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:15,881] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:15,882] [INFO] Found 6/6 markers.
[2024-01-24 14:31:15,934] [INFO] Query marker FASTA was written to GCF_001623255.1_ASM162325v1_genomic.fna/markers.fasta
[2024-01-24 14:31:15,935] [INFO] Task started: Blastn
[2024-01-24 14:31:15,935] [INFO] Running command: blastn -query GCF_001623255.1_ASM162325v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d378ba0-d6e7-4882-ae13-20a9e6155876/dqc_reference/reference_markers.fasta -out GCF_001623255.1_ASM162325v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:16,499] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:16,503] [INFO] Selected 13 target genomes.
[2024-01-24 14:31:16,503] [INFO] Target genome list was writen to GCF_001623255.1_ASM162325v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:16,507] [INFO] Task started: fastANI
[2024-01-24 14:31:16,507] [INFO] Running command: fastANI --query /var/lib/cwl/stg04c1a6b9-2ab8-4120-adae-5bd239520016/GCF_001623255.1_ASM162325v1_genomic.fna.gz --refList GCF_001623255.1_ASM162325v1_genomic.fna/target_genomes.txt --output GCF_001623255.1_ASM162325v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:29,995] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:29,995] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d378ba0-d6e7-4882-ae13-20a9e6155876/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:29,995] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d378ba0-d6e7-4882-ae13-20a9e6155876/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:30,002] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:31:30,002] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:30,002] [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
Pseudovibrio axinellae	strain=Ad2	GCA_001623255.1	989403	989403	type	True	100.0	1644	1650	95	conclusive
Pseudovibrio axinellae	strain=DSM 24994	GCA_900110875.1	989403	989403	type	True	99.987	1639	1650	95	conclusive
Pseudovibrio ascidiaceicola	strain=DSM 16392	GCA_900114245.1	285279	285279	type	True	81.8446	916	1650	95	below_threshold
Pseudovibrio brasiliensis	strain=Ab134	GCA_001941685.1	1898042	1898042	type	True	81.3897	894	1650	95	below_threshold
Pseudovibrio denitrificans	strain=DSM 17465	GCA_900116575.1	258256	258256	type	True	81.2865	909	1650	95	below_threshold
Pseudovibrio brasiliensis	strain=Ab134	GCA_018282095.1	1898042	1898042	type	True	81.2808	915	1650	95	below_threshold
Pseudovibrio denitrificans	strain=JCM 12308	GCA_001310815.1	258256	258256	type	True	81.2163	896	1650	95	below_threshold
Pseudovibrio japonicus	strain=KCTC 12861	GCA_014651595.1	366534	366534	type	True	80.6583	785	1650	95	below_threshold
Pseudovibrio flavus	strain=RKSG542	GCA_009711345.1	2529854	2529854	type	True	77.8214	186	1650	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:30,004] [INFO] DFAST Taxonomy check result was written to GCF_001623255.1_ASM162325v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:30,004] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:30,005] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:30,005] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d378ba0-d6e7-4882-ae13-20a9e6155876/dqc_reference/checkm_data
[2024-01-24 14:31:30,006] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:30,056] [INFO] Task started: CheckM
[2024-01-24 14:31:30,056] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001623255.1_ASM162325v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001623255.1_ASM162325v1_genomic.fna/checkm_input GCF_001623255.1_ASM162325v1_genomic.fna/checkm_result
[2024-01-24 14:32:12,234] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:12,235] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:12,249] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:12,249] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:12,250] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001623255.1_ASM162325v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:12,250] [INFO] Task started: Blastn
[2024-01-24 14:32:12,250] [INFO] Running command: blastn -query GCF_001623255.1_ASM162325v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d378ba0-d6e7-4882-ae13-20a9e6155876/dqc_reference/reference_markers_gtdb.fasta -out GCF_001623255.1_ASM162325v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:13,057] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:13,060] [INFO] Selected 7 target genomes.
[2024-01-24 14:32:13,060] [INFO] Target genome list was writen to GCF_001623255.1_ASM162325v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:13,064] [INFO] Task started: fastANI
[2024-01-24 14:32:13,064] [INFO] Running command: fastANI --query /var/lib/cwl/stg04c1a6b9-2ab8-4120-adae-5bd239520016/GCF_001623255.1_ASM162325v1_genomic.fna.gz --refList GCF_001623255.1_ASM162325v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001623255.1_ASM162325v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:21,934] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:21,939] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:21,939] [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_900110875.1	s__Pseudovibrio axinellae	99.987	1639	1650	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pseudovibrio	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_900143565.1	s__Pseudovibrio sp900143565	82.0754	934	1650	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pseudovibrio	95.0	96.56	96.48	0.91	0.89	8	-
GCF_001623075.1	s__Pseudovibrio sp001623075	81.8857	945	1650	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pseudovibrio	95.0	96.77	96.77	0.91	0.91	2	-
GCF_900114245.1	s__Pseudovibrio ascidiaceicola	81.8446	916	1650	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pseudovibrio	95.0	96.13	95.42	0.93	0.92	3	-
GCF_018282095.1	s__Pseudovibrio brasiliensis	81.2845	915	1650	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pseudovibrio	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001310815.1	s__Pseudovibrio denitrificans	81.225	896	1650	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pseudovibrio	95.0	96.81	95.18	0.94	0.91	4	-
GCF_900104145.1	s__Pseudovibrio sp900104145	80.5389	770	1650	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pseudovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:21,941] [INFO] GTDB search result was written to GCF_001623255.1_ASM162325v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:21,941] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:21,943] [INFO] DFAST_QC result json was written to GCF_001623255.1_ASM162325v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:21,943] [INFO] DFAST_QC completed!
[2024-01-24 14:32:21,943] [INFO] Total running time: 0h1m22s