[2024-01-24 13:31:11,849] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:11,851] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:11,851] [INFO] DQC Reference Directory: /var/lib/cwl/stg875366d0-d7a5-4060-aa2f-ca416acd56ff/dqc_reference
[2024-01-24 13:31:13,018] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:13,019] [INFO] Task started: Prodigal
[2024-01-24 13:31:13,019] [INFO] Running command: gunzip -c /var/lib/cwl/stg4f8e7413-52c1-4db3-aec0-8749126ce713/GCF_009711345.1_ASM971134v1_genomic.fna.gz | prodigal -d GCF_009711345.1_ASM971134v1_genomic.fna/cds.fna -a GCF_009711345.1_ASM971134v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:24,832] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:24,833] [INFO] Task started: HMMsearch
[2024-01-24 13:31:24,833] [INFO] Running command: hmmsearch --tblout GCF_009711345.1_ASM971134v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg875366d0-d7a5-4060-aa2f-ca416acd56ff/dqc_reference/reference_markers.hmm GCF_009711345.1_ASM971134v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:25,047] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:25,048] [INFO] Found 6/6 markers.
[2024-01-24 13:31:25,084] [INFO] Query marker FASTA was written to GCF_009711345.1_ASM971134v1_genomic.fna/markers.fasta
[2024-01-24 13:31:25,084] [INFO] Task started: Blastn
[2024-01-24 13:31:25,084] [INFO] Running command: blastn -query GCF_009711345.1_ASM971134v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg875366d0-d7a5-4060-aa2f-ca416acd56ff/dqc_reference/reference_markers.fasta -out GCF_009711345.1_ASM971134v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:25,776] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:25,779] [INFO] Selected 15 target genomes.
[2024-01-24 13:31:25,780] [INFO] Target genome list was writen to GCF_009711345.1_ASM971134v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:25,786] [INFO] Task started: fastANI
[2024-01-24 13:31:25,786] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f8e7413-52c1-4db3-aec0-8749126ce713/GCF_009711345.1_ASM971134v1_genomic.fna.gz --refList GCF_009711345.1_ASM971134v1_genomic.fna/target_genomes.txt --output GCF_009711345.1_ASM971134v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:31:38,393] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:38,393] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg875366d0-d7a5-4060-aa2f-ca416acd56ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:31:38,393] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg875366d0-d7a5-4060-aa2f-ca416acd56ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:31:38,403] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:31:38,403] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:31:38,404] [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 flavus	strain=RKSG542	GCA_009711345.1	2529854	2529854	type	True	100.0	1398	1403	95	conclusive
Pseudovibrio japonicus	strain=KCTC 12861	GCA_014651595.1	366534	366534	type	True	78.1827	234	1403	95	below_threshold
Pseudovibrio denitrificans	strain=DSM 17465	GCA_900116575.1	258256	258256	type	True	78.1287	297	1403	95	below_threshold
Pseudovibrio denitrificans	strain=JCM 12308	GCA_001310815.1	258256	258256	type	True	78.107	290	1403	95	below_threshold
Pseudovibrio brasiliensis	strain=Ab134	GCA_001941685.1	1898042	1898042	type	True	78.0934	286	1403	95	below_threshold
Pseudovibrio brasiliensis	strain=Ab134	GCA_018282095.1	1898042	1898042	type	True	78.032	293	1403	95	below_threshold
Pseudovibrio ascidiaceicola	strain=DSM 16392	GCA_900114245.1	285279	285279	type	True	77.7981	245	1403	95	below_threshold
Pseudovibrio axinellae	strain=Ad2	GCA_001623255.1	989403	989403	type	True	77.7383	184	1403	95	below_threshold
Pseudovibrio exalbescens	strain=DSM 16456	GCA_000422785.1	197461	197461	type	True	76.9216	184	1403	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	76.1013	64	1403	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:31:38,405] [INFO] DFAST Taxonomy check result was written to GCF_009711345.1_ASM971134v1_genomic.fna/tc_result.tsv
[2024-01-24 13:31:38,406] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:31:38,406] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:31:38,407] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg875366d0-d7a5-4060-aa2f-ca416acd56ff/dqc_reference/checkm_data
[2024-01-24 13:31:38,408] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:31:38,449] [INFO] Task started: CheckM
[2024-01-24 13:31:38,449] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009711345.1_ASM971134v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009711345.1_ASM971134v1_genomic.fna/checkm_input GCF_009711345.1_ASM971134v1_genomic.fna/checkm_result
[2024-01-24 13:32:16,075] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:16,076] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:16,101] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:16,102] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:16,102] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009711345.1_ASM971134v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:16,102] [INFO] Task started: Blastn
[2024-01-24 13:32:16,102] [INFO] Running command: blastn -query GCF_009711345.1_ASM971134v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg875366d0-d7a5-4060-aa2f-ca416acd56ff/dqc_reference/reference_markers_gtdb.fasta -out GCF_009711345.1_ASM971134v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:17,262] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:17,265] [INFO] Selected 13 target genomes.
[2024-01-24 13:32:17,266] [INFO] Target genome list was writen to GCF_009711345.1_ASM971134v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:17,277] [INFO] Task started: fastANI
[2024-01-24 13:32:17,278] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f8e7413-52c1-4db3-aec0-8749126ce713/GCF_009711345.1_ASM971134v1_genomic.fna.gz --refList GCF_009711345.1_ASM971134v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009711345.1_ASM971134v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:28,507] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:28,518] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:28,518] [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
GCA_009711345.1	s__Pseudovibrio sp009711345	100.0	1398	1403	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_014651595.1	s__Pseudovibrio japonicus	78.1827	234	1403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pseudovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001310815.1	s__Pseudovibrio denitrificans	78.107	290	1403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pseudovibrio	95.0	96.81	95.18	0.94	0.91	4	-
GCF_018282095.1	s__Pseudovibrio brasiliensis	78.032	293	1403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pseudovibrio	95.0	99.99	99.99	1.00	1.00	2	-
GCA_001310715.1	s__Pseudovibrio sp001310715	78.0049	230	1403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pseudovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114245.1	s__Pseudovibrio ascidiaceicola	77.7981	245	1403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pseudovibrio	95.0	96.13	95.42	0.93	0.92	3	-
GCF_001623075.1	s__Pseudovibrio sp001623075	77.7647	236	1403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pseudovibrio	95.0	96.77	96.77	0.91	0.91	2	-
GCF_900143565.1	s__Pseudovibrio sp900143565	77.7347	246	1403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pseudovibrio	95.0	96.56	96.48	0.91	0.89	8	-
GCF_900110875.1	s__Pseudovibrio axinellae	77.7145	188	1403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pseudovibrio	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000422785.1	s__Pseudovibrio exalbescens	76.9216	184	1403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pseudovibrio	95.0	99.33	98.67	0.98	0.97	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:28,520] [INFO] GTDB search result was written to GCF_009711345.1_ASM971134v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:28,521] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:28,524] [INFO] DFAST_QC result json was written to GCF_009711345.1_ASM971134v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:28,524] [INFO] DFAST_QC completed!
[2024-01-24 13:32:28,524] [INFO] Total running time: 0h1m17s