[2024-01-24 11:35:23,376] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:23,377] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:23,377] [INFO] DQC Reference Directory: /var/lib/cwl/stgc77c8e93-5d69-414b-82d1-d291e2c591b2/dqc_reference
[2024-01-24 11:35:26,239] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:26,241] [INFO] Task started: Prodigal
[2024-01-24 11:35:26,241] [INFO] Running command: gunzip -c /var/lib/cwl/stgf5ec16d5-bfd8-41ea-bae1-fd868b19cd81/GCF_014637575.1_ASM1463757v1_genomic.fna.gz | prodigal -d GCF_014637575.1_ASM1463757v1_genomic.fna/cds.fna -a GCF_014637575.1_ASM1463757v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:39,854] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:39,854] [INFO] Task started: HMMsearch
[2024-01-24 11:35:39,854] [INFO] Running command: hmmsearch --tblout GCF_014637575.1_ASM1463757v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc77c8e93-5d69-414b-82d1-d291e2c591b2/dqc_reference/reference_markers.hmm GCF_014637575.1_ASM1463757v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:40,204] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:40,205] [INFO] Found 6/6 markers.
[2024-01-24 11:35:40,311] [INFO] Query marker FASTA was written to GCF_014637575.1_ASM1463757v1_genomic.fna/markers.fasta
[2024-01-24 11:35:40,312] [INFO] Task started: Blastn
[2024-01-24 11:35:40,312] [INFO] Running command: blastn -query GCF_014637575.1_ASM1463757v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc77c8e93-5d69-414b-82d1-d291e2c591b2/dqc_reference/reference_markers.fasta -out GCF_014637575.1_ASM1463757v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:41,106] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:41,109] [INFO] Selected 21 target genomes.
[2024-01-24 11:35:41,110] [INFO] Target genome list was writen to GCF_014637575.1_ASM1463757v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:41,118] [INFO] Task started: fastANI
[2024-01-24 11:35:41,118] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5ec16d5-bfd8-41ea-bae1-fd868b19cd81/GCF_014637575.1_ASM1463757v1_genomic.fna.gz --refList GCF_014637575.1_ASM1463757v1_genomic.fna/target_genomes.txt --output GCF_014637575.1_ASM1463757v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:59,759] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:59,760] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc77c8e93-5d69-414b-82d1-d291e2c591b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:59,760] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc77c8e93-5d69-414b-82d1-d291e2c591b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:59,777] [INFO] Found 21 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:35:59,777] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:59,777] [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 aquae	strain=CGMCC 1.12426	GCA_014637575.1	1323746	1323746	type	True	100.0	1434	1436	95	conclusive
Roseibium aquae	strain=CGMCC 1.12426	GCA_008711285.1	1323746	1323746	type	True	99.9985	1434	1436	95	conclusive
Roseibium hamelinense	strain=NBRC 16783	GCA_009711505.1	150831	150831	type	True	78.4399	307	1436	95	below_threshold
Roseibium hamelinense	strain=ATCC BAA-252	GCA_007830545.1	150831	150831	type	True	78.3174	319	1436	95	below_threshold
Roseibium aestuarii	strain=SYSU M00256-3	GCA_008477545.1	2600299	2600299	type	True	78.1241	354	1436	95	below_threshold
Roseibium alexandrii	strain=DFL-11	GCA_000158095.2	388408	388408	type	True	77.9857	295	1436	95	below_threshold
Roseibium denhamense	strain=JCM 10543	GCA_009711415.1	76305	76305	type	True	77.9773	307	1436	95	below_threshold
Roseibium sediminis	strain=KCTC 52373	GCA_008711325.1	1775174	1775174	type	True	77.8526	347	1436	95	below_threshold
Roseibium aggregatum	strain=IAM 12614	GCA_000168975.1	187304	187304	suspected-type	True	77.847	360	1436	95	below_threshold
Roseibium litorale	strain=4C16A	GCA_014842915.1	2803841	2803841	type	True	77.7702	313	1436	95	below_threshold
Pannonibacter phragmitetus	strain=NCTC13350	GCA_900454465.1	121719	121719	suspected-type	True	77.7677	298	1436	95	below_threshold
Roseibium marinum	strain=DSM 17023	GCA_002906165.1	281252	281252	type	True	77.7286	378	1436	95	below_threshold
Pannonibacter indicus	strain=DSM 23407	GCA_001418225.1	466044	466044	type	True	77.7249	291	1436	95	below_threshold
Pannonibacter phragmitetus	strain=DSM 14782	GCA_000382365.1	121719	121719	suspected-type	True	77.587	292	1436	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	77.4838	254	1436	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	76.8017	123	1436	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	76.3565	131	1436	95	below_threshold
Rhizobium mongolense	strain=USDA 1844	GCA_007827505.1	57676	57676	type	True	76.3521	106	1436	95	below_threshold
Methylobacterium iners	strain=DSM 19015	GCA_022179305.1	418707	418707	type	True	76.2162	84	1436	95	below_threshold
Rhizobium mongolense	strain=USDA 1844	GCA_000419765.1	57676	57676	type	True	76.021	106	1436	95	below_threshold
Methylobacterium longum	strain=DSM 23933	GCA_022179385.1	767694	767694	type	True	75.7044	97	1436	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:59,779] [INFO] DFAST Taxonomy check result was written to GCF_014637575.1_ASM1463757v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:59,780] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:59,780] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:59,780] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc77c8e93-5d69-414b-82d1-d291e2c591b2/dqc_reference/checkm_data
[2024-01-24 11:35:59,781] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:59,821] [INFO] Task started: CheckM
[2024-01-24 11:35:59,821] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014637575.1_ASM1463757v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014637575.1_ASM1463757v1_genomic.fna/checkm_input GCF_014637575.1_ASM1463757v1_genomic.fna/checkm_result
[2024-01-24 11:36:43,536] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:43,537] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:43,558] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:43,558] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:43,559] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014637575.1_ASM1463757v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:43,559] [INFO] Task started: Blastn
[2024-01-24 11:36:43,559] [INFO] Running command: blastn -query GCF_014637575.1_ASM1463757v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc77c8e93-5d69-414b-82d1-d291e2c591b2/dqc_reference/reference_markers_gtdb.fasta -out GCF_014637575.1_ASM1463757v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:45,025] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:45,030] [INFO] Selected 20 target genomes.
[2024-01-24 11:36:45,031] [INFO] Target genome list was writen to GCF_014637575.1_ASM1463757v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:45,048] [INFO] Task started: fastANI
[2024-01-24 11:36:45,048] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5ec16d5-bfd8-41ea-bae1-fd868b19cd81/GCF_014637575.1_ASM1463757v1_genomic.fna.gz --refList GCF_014637575.1_ASM1463757v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014637575.1_ASM1463757v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:37:03,066] [INFO] Task succeeded: fastANI
[2024-01-24 11:37:03,083] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:37:03,084] [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_008711285.1	s__Roseibium aquae	99.9985	1434	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_007830545.1	s__Roseibium hamelinense	78.3295	318	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_017309185.1	s__Roseibium aggregatum_B	78.1047	362	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002237595.1	s__Roseibium sp002237595	78.0265	406	1436	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	78.0029	420	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000158095.2	s__Roseibium alexandrii	78.0	293	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	97.43	97.43	0.93	0.93	2	-
GCF_001999245.1	s__Roseibium aggregatum_A	77.8782	351	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	97.61	96.85	0.93	0.89	16	-
GCF_009915765.1	s__Pannonibacter sp009915765	77.8739	322	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pannonibacter	95.0	98.76	98.76	0.96	0.96	2	-
GCF_000192745.1	s__Polymorphum gilvum	77.8721	340	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Polymorphum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000168975.1	s__Roseibium aggregatum	77.8637	359	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008711325.1	s__Roseibium sediminis	77.8614	346	1436	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	77.8439	378	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008107695.1	s__Roseibium sp008107695	77.8219	349	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014842915.1	s__Roseibium litorale	77.7703	313	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008107755.1	s__Roseibium sp008107755	77.7301	368	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643215.1	s__Roseibium sp017643215	77.7172	435	1436	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	77.7123	380	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382365.1	s__Pannonibacter phragmitetus	77.587	292	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pannonibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001624695.1	s__Roseibium sp001624695	77.5831	347	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000419765.1	s__Rhizobium mongolense	75.9988	106	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	96.0481	99.21	97.63	0.93	0.80	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:37:03,086] [INFO] GTDB search result was written to GCF_014637575.1_ASM1463757v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:37:03,086] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:37:03,090] [INFO] DFAST_QC result json was written to GCF_014637575.1_ASM1463757v1_genomic.fna/dqc_result.json
[2024-01-24 11:37:03,091] [INFO] DFAST_QC completed!
[2024-01-24 11:37:03,091] [INFO] Total running time: 0h1m40s