[2024-01-24 13:32:13,920] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:13,922] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:13,923] [INFO] DQC Reference Directory: /var/lib/cwl/stg700a9a49-e58e-4f5b-8b10-6d0ce1a3f65d/dqc_reference
[2024-01-24 13:32:15,215] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:15,216] [INFO] Task started: Prodigal
[2024-01-24 13:32:15,216] [INFO] Running command: gunzip -c /var/lib/cwl/stgb77cc7e8-0b9f-4777-b029-d51defa23ccb/GCF_004360145.1_ASM436014v1_genomic.fna.gz | prodigal -d GCF_004360145.1_ASM436014v1_genomic.fna/cds.fna -a GCF_004360145.1_ASM436014v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:25,048] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:25,048] [INFO] Task started: HMMsearch
[2024-01-24 13:32:25,048] [INFO] Running command: hmmsearch --tblout GCF_004360145.1_ASM436014v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg700a9a49-e58e-4f5b-8b10-6d0ce1a3f65d/dqc_reference/reference_markers.hmm GCF_004360145.1_ASM436014v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:25,312] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:25,314] [INFO] Found 6/6 markers.
[2024-01-24 13:32:25,347] [INFO] Query marker FASTA was written to GCF_004360145.1_ASM436014v1_genomic.fna/markers.fasta
[2024-01-24 13:32:25,348] [INFO] Task started: Blastn
[2024-01-24 13:32:25,348] [INFO] Running command: blastn -query GCF_004360145.1_ASM436014v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg700a9a49-e58e-4f5b-8b10-6d0ce1a3f65d/dqc_reference/reference_markers.fasta -out GCF_004360145.1_ASM436014v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:26,232] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:26,236] [INFO] Selected 16 target genomes.
[2024-01-24 13:32:26,236] [INFO] Target genome list was writen to GCF_004360145.1_ASM436014v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:26,249] [INFO] Task started: fastANI
[2024-01-24 13:32:26,250] [INFO] Running command: fastANI --query /var/lib/cwl/stgb77cc7e8-0b9f-4777-b029-d51defa23ccb/GCF_004360145.1_ASM436014v1_genomic.fna.gz --refList GCF_004360145.1_ASM436014v1_genomic.fna/target_genomes.txt --output GCF_004360145.1_ASM436014v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:37,714] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:37,714] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg700a9a49-e58e-4f5b-8b10-6d0ce1a3f65d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:37,715] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg700a9a49-e58e-4f5b-8b10-6d0ce1a3f65d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:37,728] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:37,728] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:37,728] [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
Aliiroseovarius marinus	strain=A6024	GCA_004360145.1	2500159	2500159	type	True	100.0	1028	1030	95	conclusive
Aliiroseovarius pelagivivens	strain=CECT 8811	GCA_900302485.1	1639690	1639690	type	True	86.306	876	1030	95	below_threshold
Aliiroseovarius halocynthiae	strain=MA1-10	GCA_007004645.1	985055	985055	type	True	84.4333	769	1030	95	below_threshold
Aliiroseovarius zhejiangensis	strain=KCTC 42443	GCA_014656375.1	1632025	1632025	type	True	80.0555	585	1030	95	below_threshold
Aliiroseovarius crassostreae	strain=CV919-312	GCA_001307765.1	154981	154981	type	True	79.7597	457	1030	95	below_threshold
Aliiroseovarius crassostreae	strain=DSM 16950	GCA_900116725.1	154981	154981	type	True	79.702	460	1030	95	below_threshold
Aliiroseovarius sediminilitoris	strain=DSM 29439	GCA_900109955.1	1173584	1173584	type	True	79.45	540	1030	95	below_threshold
Falsiruegeria litorea	strain=CECT 7639	GCA_900172225.1	1280831	1280831	type	True	78.2192	339	1030	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	77.8919	222	1030	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	77.6214	202	1030	95	below_threshold
Paracoccus limosus	strain=JCM 17370	GCA_009711185.1	913252	913252	type	True	77.4449	222	1030	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.2408	284	1030	95	below_threshold
Pseudophaeobacter leonis	strain=306	GCA_002087335.1	1144477	1144477	type	True	77.2379	229	1030	95	below_threshold
Paracoccus laeviglucosivorans	strain=DSM 100094	GCA_900182695.1	1197861	1197861	type	True	77.217	191	1030	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	76.9568	234	1030	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	76.9567	234	1030	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:37,730] [INFO] DFAST Taxonomy check result was written to GCF_004360145.1_ASM436014v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:37,730] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:37,731] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:37,731] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg700a9a49-e58e-4f5b-8b10-6d0ce1a3f65d/dqc_reference/checkm_data
[2024-01-24 13:32:37,732] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:37,778] [INFO] Task started: CheckM
[2024-01-24 13:32:37,780] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004360145.1_ASM436014v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004360145.1_ASM436014v1_genomic.fna/checkm_input GCF_004360145.1_ASM436014v1_genomic.fna/checkm_result
[2024-01-24 13:33:12,951] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:12,953] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:12,974] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:12,975] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:12,975] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004360145.1_ASM436014v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:12,975] [INFO] Task started: Blastn
[2024-01-24 13:33:12,976] [INFO] Running command: blastn -query GCF_004360145.1_ASM436014v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg700a9a49-e58e-4f5b-8b10-6d0ce1a3f65d/dqc_reference/reference_markers_gtdb.fasta -out GCF_004360145.1_ASM436014v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:14,950] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:14,955] [INFO] Selected 10 target genomes.
[2024-01-24 13:33:14,955] [INFO] Target genome list was writen to GCF_004360145.1_ASM436014v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:14,964] [INFO] Task started: fastANI
[2024-01-24 13:33:14,964] [INFO] Running command: fastANI --query /var/lib/cwl/stgb77cc7e8-0b9f-4777-b029-d51defa23ccb/GCF_004360145.1_ASM436014v1_genomic.fna.gz --refList GCF_004360145.1_ASM436014v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004360145.1_ASM436014v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:23,401] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:23,411] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:23,411] [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_004360145.1	s__Aliiroseovarius marinus	100.0	1028	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_010500215.1	s__Aliiroseovarius sp010500215	88.9581	874	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900302485.1	s__Aliiroseovarius pelagivivens	86.3169	875	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007004645.1	s__Aliiroseovarius halocynthiae	84.4333	769	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656375.1	s__Aliiroseovarius zhejiangensis	80.046	586	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001307765.1	s__Aliiroseovarius crassostreae	79.7419	457	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	96.06	95.64	0.88	0.84	18	-
GCF_900109955.1	s__Aliiroseovarius sediminilitoris	79.45	540	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002367285.1	s__Aliiroseovarius sp002367285	78.0391	345	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013868135.1	s__Paracoccus sp013868135	77.2193	205	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900182695.1	s__Paracoccus laeviglucosivorans	77.2148	192	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:23,412] [INFO] GTDB search result was written to GCF_004360145.1_ASM436014v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:23,413] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:23,416] [INFO] DFAST_QC result json was written to GCF_004360145.1_ASM436014v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:23,416] [INFO] DFAST_QC completed!
[2024-01-24 13:33:23,417] [INFO] Total running time: 0h1m9s