[2024-01-24 12:22:34,069] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:34,071] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:34,071] [INFO] DQC Reference Directory: /var/lib/cwl/stg077bd309-6a33-4bae-b9c9-951d74cf58e1/dqc_reference
[2024-01-24 12:22:35,360] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:35,361] [INFO] Task started: Prodigal
[2024-01-24 12:22:35,361] [INFO] Running command: gunzip -c /var/lib/cwl/stgbb2d8dc0-c7dd-4ba7-9ad2-8099e591b35a/GCF_001561995.1_ASM156199v1_genomic.fna.gz | prodigal -d GCF_001561995.1_ASM156199v1_genomic.fna/cds.fna -a GCF_001561995.1_ASM156199v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:47,667] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:47,667] [INFO] Task started: HMMsearch
[2024-01-24 12:22:47,667] [INFO] Running command: hmmsearch --tblout GCF_001561995.1_ASM156199v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg077bd309-6a33-4bae-b9c9-951d74cf58e1/dqc_reference/reference_markers.hmm GCF_001561995.1_ASM156199v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:47,966] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:47,969] [INFO] Found 6/6 markers.
[2024-01-24 12:22:48,015] [INFO] Query marker FASTA was written to GCF_001561995.1_ASM156199v1_genomic.fna/markers.fasta
[2024-01-24 12:22:48,015] [INFO] Task started: Blastn
[2024-01-24 12:22:48,015] [INFO] Running command: blastn -query GCF_001561995.1_ASM156199v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg077bd309-6a33-4bae-b9c9-951d74cf58e1/dqc_reference/reference_markers.fasta -out GCF_001561995.1_ASM156199v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:48,755] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:48,758] [INFO] Selected 25 target genomes.
[2024-01-24 12:22:48,759] [INFO] Target genome list was writen to GCF_001561995.1_ASM156199v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:48,770] [INFO] Task started: fastANI
[2024-01-24 12:22:48,771] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb2d8dc0-c7dd-4ba7-9ad2-8099e591b35a/GCF_001561995.1_ASM156199v1_genomic.fna.gz --refList GCF_001561995.1_ASM156199v1_genomic.fna/target_genomes.txt --output GCF_001561995.1_ASM156199v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:07,499] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:07,499] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg077bd309-6a33-4bae-b9c9-951d74cf58e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:07,499] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg077bd309-6a33-4bae-b9c9-951d74cf58e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:07,510] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:07,510] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:07,510] [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 hongkongensis	strain=UST20140214-015B	GCA_001561995.1	1647556	1647556	type	True	100.0	1227	1230	95	conclusive
Pseudovibrio stylochi	strain=UST20140214-052	GCA_001562055.1	1807766	1807766	type	True	80.318	262	1230	95	below_threshold
Pseudovibrio japonicus	strain=KCTC 12861	GCA_014651595.1	366534	366534	type	True	77.7005	151	1230	95	below_threshold
Pseudovibrio brasiliensis	strain=Ab134	GCA_018282095.1	1898042	1898042	type	True	77.4776	188	1230	95	below_threshold
Pseudovibrio brasiliensis	strain=Ab134	GCA_001941685.1	1898042	1898042	type	True	77.4392	184	1230	95	below_threshold
Pseudovibrio denitrificans	strain=JCM 12308	GCA_001310815.1	258256	258256	type	True	77.4222	174	1230	95	below_threshold
Pseudovibrio ascidiaceicola	strain=DSM 16392	GCA_900114245.1	285279	285279	type	True	77.2565	179	1230	95	below_threshold
Pseudovibrio flavus	strain=RKSG542	GCA_009711345.1	2529854	2529854	type	True	77.061	150	1230	95	below_threshold
Roseibium sediminis	strain=KCTC 52373	GCA_008711325.1	1775174	1775174	type	True	76.9519	82	1230	95	below_threshold
Pseudovibrio exalbescens	strain=DSM 16456	GCA_000422785.1	197461	197461	type	True	76.9476	112	1230	95	below_threshold
Stappia taiwanensis	strain=DSM 23284	GCA_013868145.1	992267	992267	type	True	76.334	68	1230	95	below_threshold
Stappia taiwanensis	strain=CCM 7757	GCA_014635285.1	992267	992267	type	True	76.2886	70	1230	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:07,512] [INFO] DFAST Taxonomy check result was written to GCF_001561995.1_ASM156199v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:07,513] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:07,513] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:07,513] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg077bd309-6a33-4bae-b9c9-951d74cf58e1/dqc_reference/checkm_data
[2024-01-24 12:23:07,514] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:07,557] [INFO] Task started: CheckM
[2024-01-24 12:23:07,557] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001561995.1_ASM156199v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001561995.1_ASM156199v1_genomic.fna/checkm_input GCF_001561995.1_ASM156199v1_genomic.fna/checkm_result
[2024-01-24 12:23:44,994] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:44,995] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:45,020] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:45,020] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:45,021] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001561995.1_ASM156199v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:45,021] [INFO] Task started: Blastn
[2024-01-24 12:23:45,021] [INFO] Running command: blastn -query GCF_001561995.1_ASM156199v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg077bd309-6a33-4bae-b9c9-951d74cf58e1/dqc_reference/reference_markers_gtdb.fasta -out GCF_001561995.1_ASM156199v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:46,217] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:46,221] [INFO] Selected 21 target genomes.
[2024-01-24 12:23:46,222] [INFO] Target genome list was writen to GCF_001561995.1_ASM156199v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:46,254] [INFO] Task started: fastANI
[2024-01-24 12:23:46,254] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb2d8dc0-c7dd-4ba7-9ad2-8099e591b35a/GCF_001561995.1_ASM156199v1_genomic.fna.gz --refList GCF_001561995.1_ASM156199v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001561995.1_ASM156199v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:02,267] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:02,284] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:02,284] [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_001561995.1	s__Pseudovibrio hongkongensis	100.0	1227	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pseudovibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001562055.1	s__Pseudovibrio stylochi	80.3232	261	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pseudovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651595.1	s__Pseudovibrio japonicus	77.7149	150	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pseudovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001623075.1	s__Pseudovibrio sp001623075	77.5628	162	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pseudovibrio	95.0	96.77	96.77	0.91	0.91	2	-
GCF_018282095.1	s__Pseudovibrio brasiliensis	77.4796	187	1230	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	77.4248	173	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pseudovibrio	95.0	96.81	95.18	0.94	0.91	4	-
GCF_900114245.1	s__Pseudovibrio ascidiaceicola	77.2637	181	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pseudovibrio	95.0	96.13	95.42	0.93	0.92	3	-
GCA_001310715.1	s__Pseudovibrio sp001310715	77.1957	157	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pseudovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422785.1	s__Pseudovibrio exalbescens	76.9476	112	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pseudovibrio	95.0	99.33	98.67	0.98	0.97	3	-
GCF_014635285.1	s__Stappia taiwanensis	76.2886	70	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900185725.1	s__Stappia sp900185725	76.2173	59	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	98.18	97.99	0.94	0.94	3	-
GCF_900105595.1	s__Stappia sp900105595	76.0865	55	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001696535.1	s__Stappia indica	76.0301	59	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	97.23	96.79	0.94	0.94	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:02,286] [INFO] GTDB search result was written to GCF_001561995.1_ASM156199v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:02,286] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:02,290] [INFO] DFAST_QC result json was written to GCF_001561995.1_ASM156199v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:02,290] [INFO] DFAST_QC completed!
[2024-01-24 12:24:02,290] [INFO] Total running time: 0h1m28s