[2024-01-24 14:19:17,213] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:17,215] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:17,215] [INFO] DQC Reference Directory: /var/lib/cwl/stgb73ec8b2-9354-4ed0-ae81-c01ad87e34aa/dqc_reference
[2024-01-24 14:19:21,124] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:21,125] [INFO] Task started: Prodigal
[2024-01-24 14:19:21,126] [INFO] Running command: gunzip -c /var/lib/cwl/stg5f90e19d-3142-4f56-8c4d-6bdc02c94a23/GCF_001310815.1_ASM131081v1_genomic.fna.gz | prodigal -d GCF_001310815.1_ASM131081v1_genomic.fna/cds.fna -a GCF_001310815.1_ASM131081v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:38,959] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:38,960] [INFO] Task started: HMMsearch
[2024-01-24 14:19:38,960] [INFO] Running command: hmmsearch --tblout GCF_001310815.1_ASM131081v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb73ec8b2-9354-4ed0-ae81-c01ad87e34aa/dqc_reference/reference_markers.hmm GCF_001310815.1_ASM131081v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:39,363] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:39,366] [INFO] Found 6/6 markers.
[2024-01-24 14:19:39,458] [INFO] Query marker FASTA was written to GCF_001310815.1_ASM131081v1_genomic.fna/markers.fasta
[2024-01-24 14:19:39,458] [INFO] Task started: Blastn
[2024-01-24 14:19:39,459] [INFO] Running command: blastn -query GCF_001310815.1_ASM131081v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb73ec8b2-9354-4ed0-ae81-c01ad87e34aa/dqc_reference/reference_markers.fasta -out GCF_001310815.1_ASM131081v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:42,424] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:42,428] [INFO] Selected 11 target genomes.
[2024-01-24 14:19:42,428] [INFO] Target genome list was writen to GCF_001310815.1_ASM131081v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:42,433] [INFO] Task started: fastANI
[2024-01-24 14:19:42,434] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f90e19d-3142-4f56-8c4d-6bdc02c94a23/GCF_001310815.1_ASM131081v1_genomic.fna.gz --refList GCF_001310815.1_ASM131081v1_genomic.fna/target_genomes.txt --output GCF_001310815.1_ASM131081v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:57,258] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:57,259] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb73ec8b2-9354-4ed0-ae81-c01ad87e34aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:57,259] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb73ec8b2-9354-4ed0-ae81-c01ad87e34aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:57,271] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:19:57,271] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:57,271] [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 denitrificans	strain=JCM 12308	GCA_001310815.1	258256	258256	type	True	100.0	1970	1974	95	conclusive
Pseudovibrio denitrificans	strain=DSM 17465	GCA_900116575.1	258256	258256	type	True	99.9702	1971	1974	95	conclusive
Pseudovibrio brasiliensis	strain=Ab134	GCA_018282095.1	1898042	1898042	type	True	93.9955	1739	1974	95	below_threshold
Pseudovibrio brasiliensis	strain=Ab134	GCA_001941685.1	1898042	1898042	type	True	93.9901	1746	1974	95	below_threshold
Pseudovibrio ascidiaceicola	strain=DSM 16392	GCA_900114245.1	285279	285279	type	True	86.0748	1544	1974	95	below_threshold
Pseudovibrio japonicus	strain=KCTC 12861	GCA_014651595.1	366534	366534	type	True	83.705	1135	1974	95	below_threshold
Pseudovibrio flavus	strain=RKSG542	GCA_009711345.1	2529854	2529854	type	True	78.0836	303	1974	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	75.9302	68	1974	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:57,273] [INFO] DFAST Taxonomy check result was written to GCF_001310815.1_ASM131081v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:57,274] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:57,274] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:57,275] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb73ec8b2-9354-4ed0-ae81-c01ad87e34aa/dqc_reference/checkm_data
[2024-01-24 14:19:57,276] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:57,339] [INFO] Task started: CheckM
[2024-01-24 14:19:57,339] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001310815.1_ASM131081v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001310815.1_ASM131081v1_genomic.fna/checkm_input GCF_001310815.1_ASM131081v1_genomic.fna/checkm_result
[2024-01-24 14:20:59,455] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:59,457] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:59,478] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:59,479] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:59,479] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001310815.1_ASM131081v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:59,479] [INFO] Task started: Blastn
[2024-01-24 14:20:59,480] [INFO] Running command: blastn -query GCF_001310815.1_ASM131081v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb73ec8b2-9354-4ed0-ae81-c01ad87e34aa/dqc_reference/reference_markers_gtdb.fasta -out GCF_001310815.1_ASM131081v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:01,141] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:01,146] [INFO] Selected 7 target genomes.
[2024-01-24 14:21:01,146] [INFO] Target genome list was writen to GCF_001310815.1_ASM131081v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:01,153] [INFO] Task started: fastANI
[2024-01-24 14:21:01,154] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f90e19d-3142-4f56-8c4d-6bdc02c94a23/GCF_001310815.1_ASM131081v1_genomic.fna.gz --refList GCF_001310815.1_ASM131081v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001310815.1_ASM131081v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:11,850] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:11,857] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:11,858] [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_001310815.1	s__Pseudovibrio denitrificans	100.0	1970	1974	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pseudovibrio	95.0	96.81	95.18	0.94	0.91	4	conclusive
GCF_018282095.1	s__Pseudovibrio brasiliensis	94.0034	1738	1974	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pseudovibrio	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900114245.1	s__Pseudovibrio ascidiaceicola	86.0817	1542	1974	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pseudovibrio	95.0	96.13	95.42	0.93	0.92	3	-
GCF_900143565.1	s__Pseudovibrio sp900143565	86.0373	1531	1974	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	85.8725	1419	1974	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pseudovibrio	95.0	96.77	96.77	0.91	0.91	2	-
GCF_014651595.1	s__Pseudovibrio japonicus	83.6968	1136	1974	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pseudovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001310715.1	s__Pseudovibrio sp001310715	83.6187	1017	1974	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 14:21:11,859] [INFO] GTDB search result was written to GCF_001310815.1_ASM131081v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:11,860] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:11,865] [INFO] DFAST_QC result json was written to GCF_001310815.1_ASM131081v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:11,865] [INFO] DFAST_QC completed!
[2024-01-24 14:21:11,866] [INFO] Total running time: 0h1m55s