[2024-01-24 13:10:03,892] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:10:03,894] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:10:03,895] [INFO] DQC Reference Directory: /var/lib/cwl/stgba4d5072-8479-4139-bca8-e6d71b02f96e/dqc_reference
[2024-01-24 13:10:05,168] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:10:05,169] [INFO] Task started: Prodigal
[2024-01-24 13:10:05,169] [INFO] Running command: gunzip -c /var/lib/cwl/stgf11683a4-811b-4665-a19e-8e29404b4053/GCF_004793635.1_ASM479363v1_genomic.fna.gz | prodigal -d GCF_004793635.1_ASM479363v1_genomic.fna/cds.fna -a GCF_004793635.1_ASM479363v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:13,965] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:13,965] [INFO] Task started: HMMsearch
[2024-01-24 13:10:13,965] [INFO] Running command: hmmsearch --tblout GCF_004793635.1_ASM479363v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba4d5072-8479-4139-bca8-e6d71b02f96e/dqc_reference/reference_markers.hmm GCF_004793635.1_ASM479363v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:14,261] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:14,262] [INFO] Found 6/6 markers.
[2024-01-24 13:10:14,289] [INFO] Query marker FASTA was written to GCF_004793635.1_ASM479363v1_genomic.fna/markers.fasta
[2024-01-24 13:10:14,290] [INFO] Task started: Blastn
[2024-01-24 13:10:14,290] [INFO] Running command: blastn -query GCF_004793635.1_ASM479363v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba4d5072-8479-4139-bca8-e6d71b02f96e/dqc_reference/reference_markers.fasta -out GCF_004793635.1_ASM479363v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:15,251] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:15,254] [INFO] Selected 12 target genomes.
[2024-01-24 13:10:15,254] [INFO] Target genome list was writen to GCF_004793635.1_ASM479363v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:15,262] [INFO] Task started: fastANI
[2024-01-24 13:10:15,262] [INFO] Running command: fastANI --query /var/lib/cwl/stgf11683a4-811b-4665-a19e-8e29404b4053/GCF_004793635.1_ASM479363v1_genomic.fna.gz --refList GCF_004793635.1_ASM479363v1_genomic.fna/target_genomes.txt --output GCF_004793635.1_ASM479363v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:23,681] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:23,682] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba4d5072-8479-4139-bca8-e6d71b02f96e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:23,682] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba4d5072-8479-4139-bca8-e6d71b02f96e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:23,697] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:10:23,697] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:23,697] [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
Marinicauda pacifica	strain=P-1 km-3	GCA_004793635.1	1133559	1133559	type	True	100.0	1000	1000	95	conclusive
Marinicauda pacifica	strain=P-1 km-3	GCA_009806145.1	1133559	1133559	type	True	99.9967	992	1000	95	conclusive
Marinicauda pacifica	strain=CGMCC 1.11031	GCA_014636415.1	1133559	1133559	type	True	99.9967	996	1000	95	conclusive
Marinicauda algicola	strain=JCM 31718	GCA_004793685.1	2029849	2029849	type	True	80.3673	580	1000	95	below_threshold
Marinicauda algicola	strain=RMAR8-3	GCA_017161425.1	2029849	2029849	type	True	80.342	590	1000	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	78.678	402	1000	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	76.9949	98	1000	95	below_threshold
Brevundimonas halotolerans	strain=DSM 24448	GCA_014199165.1	69670	69670	type	True	76.941	106	1000	95	below_threshold
Brevundimonas halotolerans	strain=MCS24	GCA_003730275.1	69670	69670	type	True	76.8838	107	1000	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	76.5109	119	1000	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	76.5032	96	1000	95	below_threshold
Bradyrhizobium altum	strain=Pear77	GCA_020889705.1	1571202	1571202	type	True	76.3414	107	1000	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:23,699] [INFO] DFAST Taxonomy check result was written to GCF_004793635.1_ASM479363v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:23,699] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:23,699] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:23,700] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba4d5072-8479-4139-bca8-e6d71b02f96e/dqc_reference/checkm_data
[2024-01-24 13:10:23,701] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:23,731] [INFO] Task started: CheckM
[2024-01-24 13:10:23,732] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004793635.1_ASM479363v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004793635.1_ASM479363v1_genomic.fna/checkm_input GCF_004793635.1_ASM479363v1_genomic.fna/checkm_result
[2024-01-24 13:10:54,325] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:54,326] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:54,355] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:54,355] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:54,356] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004793635.1_ASM479363v1_genomic.fna/markers.fasta)
[2024-01-24 13:10:54,357] [INFO] Task started: Blastn
[2024-01-24 13:10:54,357] [INFO] Running command: blastn -query GCF_004793635.1_ASM479363v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba4d5072-8479-4139-bca8-e6d71b02f96e/dqc_reference/reference_markers_gtdb.fasta -out GCF_004793635.1_ASM479363v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:56,123] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:56,127] [INFO] Selected 13 target genomes.
[2024-01-24 13:10:56,127] [INFO] Target genome list was writen to GCF_004793635.1_ASM479363v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:56,148] [INFO] Task started: fastANI
[2024-01-24 13:10:56,148] [INFO] Running command: fastANI --query /var/lib/cwl/stgf11683a4-811b-4665-a19e-8e29404b4053/GCF_004793635.1_ASM479363v1_genomic.fna.gz --refList GCF_004793635.1_ASM479363v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004793635.1_ASM479363v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:04,562] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:04,577] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:04,577] [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_004793635.1	s__Marinicauda pacifica	100.0	1000	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Marinicauda	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCF_017161425.1	s__Marinicauda algicola	80.3529	591	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Marinicauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003122085.1	s__WD6-1 sp003122085	78.7069	401	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__WD6-1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007050995.1	s__Glycocaulis profundi	78.3751	376	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Glycocaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008630495.1	s__Oceanicaulis satelles	78.2506	329	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124675.1	s__Oceanicaulis sp016124675	78.0452	312	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152745.1	s__Oceanicaulis sp000152745	78.0376	345	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	98.46	98.38	0.90	0.88	7	-
GCF_000420265.1	s__Oceanicaulis alexandrii	77.9155	301	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	97.56	97.05	0.94	0.85	5	-
GCF_000744995.1	s__Glycocaulis sp000744995	77.7788	265	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Glycocaulis	95.0	98.48	98.48	0.95	0.95	2	-
GCF_003046365.1	s__Oceanicaulis sp003046365	77.7686	261	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	96.56	96.56	0.93	0.93	2	-
GCA_001657295.1	s__Oceanicaulis sp001657295	77.4791	289	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002783385.1	s__Hyphobacterium sp002783385	76.4199	108	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Hyphobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124325.1	s__Phenylobacterium sp016124325	76.2285	139	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:04,579] [INFO] GTDB search result was written to GCF_004793635.1_ASM479363v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:04,580] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:04,583] [INFO] DFAST_QC result json was written to GCF_004793635.1_ASM479363v1_genomic.fna/dqc_result.json
[2024-01-24 13:11:04,583] [INFO] DFAST_QC completed!
[2024-01-24 13:11:04,583] [INFO] Total running time: 0h1m1s