[2024-01-24 12:31:04,549] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:04,551] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:04,551] [INFO] DQC Reference Directory: /var/lib/cwl/stga9a809c6-f161-484f-a586-37f92c5551b4/dqc_reference
[2024-01-24 12:31:05,729] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:05,730] [INFO] Task started: Prodigal
[2024-01-24 12:31:05,730] [INFO] Running command: gunzip -c /var/lib/cwl/stga32306fa-4f73-4804-aac9-a478d5339f1a/GCF_003143555.1_ASM314355v1_genomic.fna.gz | prodigal -d GCF_003143555.1_ASM314355v1_genomic.fna/cds.fna -a GCF_003143555.1_ASM314355v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:14,461] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:14,462] [INFO] Task started: HMMsearch
[2024-01-24 12:31:14,462] [INFO] Running command: hmmsearch --tblout GCF_003143555.1_ASM314355v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga9a809c6-f161-484f-a586-37f92c5551b4/dqc_reference/reference_markers.hmm GCF_003143555.1_ASM314355v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:14,708] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:14,709] [INFO] Found 6/6 markers.
[2024-01-24 12:31:14,740] [INFO] Query marker FASTA was written to GCF_003143555.1_ASM314355v1_genomic.fna/markers.fasta
[2024-01-24 12:31:14,740] [INFO] Task started: Blastn
[2024-01-24 12:31:14,741] [INFO] Running command: blastn -query GCF_003143555.1_ASM314355v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga9a809c6-f161-484f-a586-37f92c5551b4/dqc_reference/reference_markers.fasta -out GCF_003143555.1_ASM314355v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:15,474] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:15,479] [INFO] Selected 28 target genomes.
[2024-01-24 12:31:15,479] [INFO] Target genome list was writen to GCF_003143555.1_ASM314355v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:15,538] [INFO] Task started: fastANI
[2024-01-24 12:31:15,539] [INFO] Running command: fastANI --query /var/lib/cwl/stga32306fa-4f73-4804-aac9-a478d5339f1a/GCF_003143555.1_ASM314355v1_genomic.fna.gz --refList GCF_003143555.1_ASM314355v1_genomic.fna/target_genomes.txt --output GCF_003143555.1_ASM314355v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:33,009] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:33,010] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga9a809c6-f161-484f-a586-37f92c5551b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:33,010] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga9a809c6-f161-484f-a586-37f92c5551b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:33,024] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:33,024] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:33,025] [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
Saliniradius amylolyticus	strain=HMF8227	GCA_003143555.1	2183582	2183582	type	True	100.0	1070	1071	95	conclusive
Salinimonas lutimaris	strain=DPSR-4	GCA_005222225.1	914153	914153	type	True	78.5408	81	1071	95	below_threshold
Alteromonas lipolytica	strain=JW12	GCA_001758465.1	1856405	1856405	type	True	78.4832	78	1071	95	below_threshold
Lacimicrobium alkaliphilum	strain=CGMCC 1.12923	GCA_014640135.1	1526571	1526571	type	True	77.5137	133	1071	95	below_threshold
Lacimicrobium alkaliphilum	strain=X13M-12	GCA_002591895.1	1526571	1526571	type	True	77.4818	135	1071	95	below_threshold
Alteromonas alba	strain=190	GCA_002993365.1	2079529	2079529	type	True	77.4728	87	1071	95	below_threshold
Aestuariibacter halophilus	strain=JC2043	GCA_020687825.1	226011	226011	type	True	77.2589	110	1071	95	below_threshold
Bowmanella dokdonensis	strain=JCM 30855	GCA_017254865.1	751969	751969	type	True	77.1439	188	1071	95	below_threshold
Ferrimonas sediminicola	strain=IMCC35001	GCA_005116715.1	2569538	2569538	type	True	76.5113	61	1071	95	below_threshold
Ferrimonas marina	strain=DSM 16917	GCA_900129905.1	299255	299255	type	True	76.3337	63	1071	95	below_threshold
Ferrimonas sediminum	strain=DSM 23317	GCA_900100175.1	718193	718193	type	True	76.2916	62	1071	95	below_threshold
Ferrimonas marina	strain=NBRC 102583	GCA_001571125.1	299255	299255	type	True	76.1953	62	1071	95	below_threshold
Shewanella jiangmenensis	strain=JM162201	GCA_018596335.1	2837387	2837387	type	True	76.1832	53	1071	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:33,026] [INFO] DFAST Taxonomy check result was written to GCF_003143555.1_ASM314355v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:33,027] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:33,027] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:33,027] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga9a809c6-f161-484f-a586-37f92c5551b4/dqc_reference/checkm_data
[2024-01-24 12:31:33,028] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:33,061] [INFO] Task started: CheckM
[2024-01-24 12:31:33,061] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003143555.1_ASM314355v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003143555.1_ASM314355v1_genomic.fna/checkm_input GCF_003143555.1_ASM314355v1_genomic.fna/checkm_result
[2024-01-24 12:32:03,984] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:03,986] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:04,010] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:04,010] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:04,011] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003143555.1_ASM314355v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:04,011] [INFO] Task started: Blastn
[2024-01-24 12:32:04,011] [INFO] Running command: blastn -query GCF_003143555.1_ASM314355v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga9a809c6-f161-484f-a586-37f92c5551b4/dqc_reference/reference_markers_gtdb.fasta -out GCF_003143555.1_ASM314355v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:05,275] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:05,279] [INFO] Selected 23 target genomes.
[2024-01-24 12:32:05,280] [INFO] Target genome list was writen to GCF_003143555.1_ASM314355v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:05,296] [INFO] Task started: fastANI
[2024-01-24 12:32:05,297] [INFO] Running command: fastANI --query /var/lib/cwl/stga32306fa-4f73-4804-aac9-a478d5339f1a/GCF_003143555.1_ASM314355v1_genomic.fna.gz --refList GCF_003143555.1_ASM314355v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003143555.1_ASM314355v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:21,494] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:21,519] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:21,519] [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_003143555.1	s__Saliniradius amylolyticus	100.0	1070	1071	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Saliniradius	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005222225.1	s__Alteromonas lutimaris	78.5655	81	1071	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584565.2	s__Alteromonas sp002729795	78.4926	71	1071	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.21	97.21	0.92	0.92	2	-
GCF_001466725.1	s__Lacimicrobium alkaliphilum_B	77.7959	184	1071	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Lacimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001660395.1	s__XY-R5 sp001660395	77.5853	80	1071	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__XY-R5	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002591895.1	s__Lacimicrobium alkaliphilum	77.4818	135	1071	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Lacimicrobium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002993365.1	s__Alteromonas alba	77.4377	88	1071	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002201535.1	s__Lacimicrobium sp002201535	77.3957	149	1071	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Lacimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018531185.1	s__Bowmanella sp018531185	77.3766	133	1071	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Bowmanella	95.0	96.11	96.11	0.88	0.88	2	-
GCF_002887595.1	s__Bowmanella denitrificans	77.3109	145	1071	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Bowmanella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019249245.1	s__Alteromonas lipotrueiana	77.3093	55	1071	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017254865.1	s__Bowmanella dokdonensis	77.1439	188	1071	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Bowmanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000243075.1	s__Oceanimonas sp000243075	77.1067	88	1071	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002339125.1	s__Alteromonas sp002335925	76.9644	79	1071	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.57	96.36	0.89	0.83	19	-
GCF_005116715.1	s__Ferrimonas sp005116715	76.48	62	1071	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100175.1	s__Ferrimonas sediminum	76.3397	65	1071	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:21,522] [INFO] GTDB search result was written to GCF_003143555.1_ASM314355v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:21,522] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:21,529] [INFO] DFAST_QC result json was written to GCF_003143555.1_ASM314355v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:21,529] [INFO] DFAST_QC completed!
[2024-01-24 12:32:21,530] [INFO] Total running time: 0h1m17s