[2023-06-19 13:14:20,885] [INFO] DFAST_QC pipeline started.
[2023-06-19 13:14:20,888] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 13:14:20,888] [INFO] DQC Reference Directory: /var/lib/cwl/stgf69cb8aa-4b61-4a5a-9aef-2b211a3c0543/dqc_reference
[2023-06-19 13:14:22,272] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 13:14:22,273] [INFO] Task started: Prodigal
[2023-06-19 13:14:22,273] [INFO] Running command: gunzip -c /var/lib/cwl/stgd94b6ae9-4b12-40e8-87e3-dbc5f050d864/GCA_013373445.1_ASM1337344v1_genomic.fna.gz | prodigal -d GCA_013373445.1_ASM1337344v1_genomic.fna/cds.fna -a GCA_013373445.1_ASM1337344v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 13:14:32,494] [INFO] Task succeeded: Prodigal
[2023-06-19 13:14:32,495] [INFO] Task started: HMMsearch
[2023-06-19 13:14:32,495] [INFO] Running command: hmmsearch --tblout GCA_013373445.1_ASM1337344v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf69cb8aa-4b61-4a5a-9aef-2b211a3c0543/dqc_reference/reference_markers.hmm GCA_013373445.1_ASM1337344v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 13:14:32,778] [INFO] Task succeeded: HMMsearch
[2023-06-19 13:14:32,780] [INFO] Found 6/6 markers.
[2023-06-19 13:14:32,812] [INFO] Query marker FASTA was written to GCA_013373445.1_ASM1337344v1_genomic.fna/markers.fasta
[2023-06-19 13:14:32,812] [INFO] Task started: Blastn
[2023-06-19 13:14:32,812] [INFO] Running command: blastn -query GCA_013373445.1_ASM1337344v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf69cb8aa-4b61-4a5a-9aef-2b211a3c0543/dqc_reference/reference_markers.fasta -out GCA_013373445.1_ASM1337344v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:14:33,516] [INFO] Task succeeded: Blastn
[2023-06-19 13:14:33,521] [INFO] Selected 21 target genomes.
[2023-06-19 13:14:33,522] [INFO] Target genome list was writen to GCA_013373445.1_ASM1337344v1_genomic.fna/target_genomes.txt
[2023-06-19 13:14:33,527] [INFO] Task started: fastANI
[2023-06-19 13:14:33,528] [INFO] Running command: fastANI --query /var/lib/cwl/stgd94b6ae9-4b12-40e8-87e3-dbc5f050d864/GCA_013373445.1_ASM1337344v1_genomic.fna.gz --refList GCA_013373445.1_ASM1337344v1_genomic.fna/target_genomes.txt --output GCA_013373445.1_ASM1337344v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 13:14:49,580] [INFO] Task succeeded: fastANI
[2023-06-19 13:14:49,580] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf69cb8aa-4b61-4a5a-9aef-2b211a3c0543/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 13:14:49,581] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf69cb8aa-4b61-4a5a-9aef-2b211a3c0543/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 13:14:49,597] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 13:14:49,597] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 13:14:49,597] [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
Roseibium limicola	strain=CAU 1637	GCA_017313085.1	2816037	2816037	type	True	77.1996	193	1120	95	below_threshold
Roseibium polysiphoniae	strain=KACC 19711	GCA_014842925.1	2571221	2571221	type	True	77.1853	216	1120	95	below_threshold
Roseibium alexandrii	strain=DFL-11	GCA_000158095.2	388408	388408	type	True	77.1805	135	1120	95	below_threshold
Roseibium marinum	strain=DSM 17023	GCA_002906165.1	281252	281252	type	True	76.995	149	1120	95	below_threshold
Roseibium suaedae	strain=DSM 22153	GCA_900142725.1	735517	735517	type	True	76.976	212	1120	95	below_threshold
Roseibium litorale	strain=4C16A	GCA_014842915.1	2803841	2803841	type	True	76.913	187	1120	95	below_threshold
Roseibium aggregatum	strain=IAM 12614	GCA_000168975.1	187304	187304	suspected-type	True	76.8464	156	1120	95	below_threshold
Roseibium sediminis	strain=KCTC 52373	GCA_008711325.1	1775174	1775174	type	True	76.7884	160	1120	95	below_threshold
Pannonibacter carbonis	strain=Q4.6	GCA_003012935.1	2067569	2067569	type	True	76.2042	130	1120	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	76.0753	68	1120	95	below_threshold
Rhizobium daejeonense	strain=L61	GCA_014280875.1	240521	240521	type	True	75.5932	55	1120	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 13:14:49,599] [INFO] DFAST Taxonomy check result was written to GCA_013373445.1_ASM1337344v1_genomic.fna/tc_result.tsv
[2023-06-19 13:14:49,600] [INFO] ===== Taxonomy check completed =====
[2023-06-19 13:14:49,600] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 13:14:49,600] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf69cb8aa-4b61-4a5a-9aef-2b211a3c0543/dqc_reference/checkm_data
[2023-06-19 13:14:49,602] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 13:14:49,643] [INFO] Task started: CheckM
[2023-06-19 13:14:49,643] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013373445.1_ASM1337344v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013373445.1_ASM1337344v1_genomic.fna/checkm_input GCA_013373445.1_ASM1337344v1_genomic.fna/checkm_result
[2023-06-19 13:15:24,695] [INFO] Task succeeded: CheckM
[2023-06-19 13:15:24,696] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 96.30%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 13:15:24,715] [INFO] ===== Completeness check finished =====
[2023-06-19 13:15:24,715] [INFO] ===== Start GTDB Search =====
[2023-06-19 13:15:24,716] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013373445.1_ASM1337344v1_genomic.fna/markers.fasta)
[2023-06-19 13:15:24,716] [INFO] Task started: Blastn
[2023-06-19 13:15:24,716] [INFO] Running command: blastn -query GCA_013373445.1_ASM1337344v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf69cb8aa-4b61-4a5a-9aef-2b211a3c0543/dqc_reference/reference_markers_gtdb.fasta -out GCA_013373445.1_ASM1337344v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:15:25,833] [INFO] Task succeeded: Blastn
[2023-06-19 13:15:25,838] [INFO] Selected 22 target genomes.
[2023-06-19 13:15:25,838] [INFO] Target genome list was writen to GCA_013373445.1_ASM1337344v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 13:15:25,852] [INFO] Task started: fastANI
[2023-06-19 13:15:25,853] [INFO] Running command: fastANI --query /var/lib/cwl/stgd94b6ae9-4b12-40e8-87e3-dbc5f050d864/GCA_013373445.1_ASM1337344v1_genomic.fna.gz --refList GCA_013373445.1_ASM1337344v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013373445.1_ASM1337344v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 13:15:42,716] [INFO] Task succeeded: fastANI
[2023-06-19 13:15:42,737] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 13:15:42,737] [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_013373445.1	s__Roseibium sp013373445	100.0	1108	1120	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017313085.1	s__Roseibium sp017313085	77.1849	194	1120	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014842925.1	s__Roseibium polysiphoniae	77.1732	217	1120	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	96.20	96.20	0.93	0.93	2	-
GCF_007830545.1	s__Roseibium hamelinense	77.1102	109	1120	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002237595.1	s__Roseibium sp002237595	77.0828	173	1120	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009650605.1	s__Roseibium sp009650605	77.0114	205	1120	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002906165.1	s__Roseibium marinum	76.995	149	1120	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001890945.1	s__Roseibium sp001890945	76.8617	134	1120	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	95.65	95.54	0.93	0.91	4	-
GCF_000148725.1	s__Roseibium sp000148725	76.8567	129	1120	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006517275.1	s__Roseibium sp006517275	76.8564	137	1120	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003075075.1	s__Roseibium sp003075075	76.8281	159	1120	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014692675.1	s__Roseibium aggregatum_C	76.8202	193	1120	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001999245.1	s__Roseibium aggregatum_A	76.7924	169	1120	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	97.61	96.85	0.93	0.89	16	-
GCF_008711325.1	s__Roseibium sediminis	76.7884	160	1120	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001404055.1	s__Roseibium album_A	76.578	123	1120	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000192745.1	s__Polymorphum gilvum	76.3387	112	1120	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Polymorphum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009826895.1	s__Hongsoonwoonella sp009826895	76.3009	75	1120	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Hongsoonwoonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003012935.1	s__Pannonibacter carbonis	76.2042	130	1120	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pannonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002709505.1	s__Stappia sp002709505	75.6062	69	1120	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 13:15:42,739] [INFO] GTDB search result was written to GCA_013373445.1_ASM1337344v1_genomic.fna/result_gtdb.tsv
[2023-06-19 13:15:42,740] [INFO] ===== GTDB Search completed =====
[2023-06-19 13:15:42,744] [INFO] DFAST_QC result json was written to GCA_013373445.1_ASM1337344v1_genomic.fna/dqc_result.json
[2023-06-19 13:15:42,744] [INFO] DFAST_QC completed!
[2023-06-19 13:15:42,744] [INFO] Total running time: 0h1m22s