[2024-01-24 14:20:03,213] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:20:03,215] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:20:03,215] [INFO] DQC Reference Directory: /var/lib/cwl/stgb4ffe506-c7b7-48ee-a75a-ecd7a465de3a/dqc_reference
[2024-01-24 14:20:07,759] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:20:07,760] [INFO] Task started: Prodigal
[2024-01-24 14:20:07,760] [INFO] Running command: gunzip -c /var/lib/cwl/stgf1aa6889-09dc-4647-a16f-ada14c644853/GCF_008711285.1_ASM871128v1_genomic.fna.gz | prodigal -d GCF_008711285.1_ASM871128v1_genomic.fna/cds.fna -a GCF_008711285.1_ASM871128v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:22,740] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:22,741] [INFO] Task started: HMMsearch
[2024-01-24 14:20:22,741] [INFO] Running command: hmmsearch --tblout GCF_008711285.1_ASM871128v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb4ffe506-c7b7-48ee-a75a-ecd7a465de3a/dqc_reference/reference_markers.hmm GCF_008711285.1_ASM871128v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:23,113] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:23,114] [INFO] Found 6/6 markers.
[2024-01-24 14:20:23,171] [INFO] Query marker FASTA was written to GCF_008711285.1_ASM871128v1_genomic.fna/markers.fasta
[2024-01-24 14:20:23,172] [INFO] Task started: Blastn
[2024-01-24 14:20:23,172] [INFO] Running command: blastn -query GCF_008711285.1_ASM871128v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4ffe506-c7b7-48ee-a75a-ecd7a465de3a/dqc_reference/reference_markers.fasta -out GCF_008711285.1_ASM871128v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:24,297] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:24,301] [INFO] Selected 21 target genomes.
[2024-01-24 14:20:24,302] [INFO] Target genome list was writen to GCF_008711285.1_ASM871128v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:24,332] [INFO] Task started: fastANI
[2024-01-24 14:20:24,332] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1aa6889-09dc-4647-a16f-ada14c644853/GCF_008711285.1_ASM871128v1_genomic.fna.gz --refList GCF_008711285.1_ASM871128v1_genomic.fna/target_genomes.txt --output GCF_008711285.1_ASM871128v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:44,398] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:44,399] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb4ffe506-c7b7-48ee-a75a-ecd7a465de3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:44,400] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb4ffe506-c7b7-48ee-a75a-ecd7a465de3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:44,492] [INFO] Found 21 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:20:44,493] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:44,493] [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_008711285.1	1323746	1323746	type	True	100.0	1447	1453	95	conclusive
Roseibium aquae	strain=CGMCC 1.12426	GCA_014637575.1	1323746	1323746	type	True	99.9971	1433	1453	95	conclusive
Roseibium hamelinense	strain=NBRC 16783	GCA_009711505.1	150831	150831	type	True	78.5659	299	1453	95	below_threshold
Roseibium hamelinense	strain=ATCC BAA-252	GCA_007830545.1	150831	150831	type	True	78.4606	311	1453	95	below_threshold
Roseibium denhamense	strain=JCM 10543	GCA_009711415.1	76305	76305	type	True	78.1071	294	1453	95	below_threshold
Roseibium aestuarii	strain=SYSU M00256-3	GCA_008477545.1	2600299	2600299	type	True	77.9997	355	1453	95	below_threshold
Roseibium alexandrii	strain=DFL-11	GCA_000158095.2	388408	388408	type	True	77.9321	304	1453	95	below_threshold
Roseibium sediminis	strain=KCTC 52373	GCA_008711325.1	1775174	1775174	type	True	77.85	354	1453	95	below_threshold
Pannonibacter indicus	strain=DSM 23407	GCA_001418225.1	466044	466044	type	True	77.7829	285	1453	95	below_threshold
Roseibium litorale	strain=4C16A	GCA_014842915.1	2803841	2803841	type	True	77.7063	323	1453	95	below_threshold
Roseibium aggregatum	strain=IAM 12614	GCA_000168975.1	187304	187304	suspected-type	True	77.7011	378	1453	95	below_threshold
Pannonibacter phragmitetus	strain=NCTC13350	GCA_900454465.1	121719	121719	suspected-type	True	77.68	299	1453	95	below_threshold
Roseibium marinum	strain=DSM 17023	GCA_002906165.1	281252	281252	type	True	77.6745	381	1453	95	below_threshold
Pannonibacter phragmitetus	strain=DSM 14782	GCA_000382365.1	121719	121719	suspected-type	True	77.5375	295	1453	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	77.4318	247	1453	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	76.6605	129	1453	95	below_threshold
Rhizobium mongolense	strain=USDA 1844	GCA_007827505.1	57676	57676	type	True	76.6264	98	1453	95	below_threshold
Methylobacterium iners	strain=DSM 19015	GCA_022179305.1	418707	418707	type	True	76.2216	83	1453	95	below_threshold
Rhizobium mongolense	strain=USDA 1844	GCA_000419765.1	57676	57676	type	True	76.1859	99	1453	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	76.0712	136	1453	95	below_threshold
Methylobacterium longum	strain=DSM 23933	GCA_022179385.1	767694	767694	type	True	75.6674	101	1453	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:44,495] [INFO] DFAST Taxonomy check result was written to GCF_008711285.1_ASM871128v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:44,496] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:44,496] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:44,496] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb4ffe506-c7b7-48ee-a75a-ecd7a465de3a/dqc_reference/checkm_data
[2024-01-24 14:20:44,502] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:44,547] [INFO] Task started: CheckM
[2024-01-24 14:20:44,548] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008711285.1_ASM871128v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008711285.1_ASM871128v1_genomic.fna/checkm_input GCF_008711285.1_ASM871128v1_genomic.fna/checkm_result
[2024-01-24 14:21:34,663] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:34,665] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:34,687] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:34,688] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:34,688] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008711285.1_ASM871128v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:34,689] [INFO] Task started: Blastn
[2024-01-24 14:21:34,689] [INFO] Running command: blastn -query GCF_008711285.1_ASM871128v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4ffe506-c7b7-48ee-a75a-ecd7a465de3a/dqc_reference/reference_markers_gtdb.fasta -out GCF_008711285.1_ASM871128v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:37,210] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:37,215] [INFO] Selected 20 target genomes.
[2024-01-24 14:21:37,215] [INFO] Target genome list was writen to GCF_008711285.1_ASM871128v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:37,231] [INFO] Task started: fastANI
[2024-01-24 14:21:37,232] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1aa6889-09dc-4647-a16f-ada14c644853/GCF_008711285.1_ASM871128v1_genomic.fna.gz --refList GCF_008711285.1_ASM871128v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008711285.1_ASM871128v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:57,222] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:57,289] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:57,289] [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	100.0	1444	1453	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	78.4649	309	1453	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014692675.1	s__Roseibium aggregatum_C	78.0916	412	1453	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	78.046	401	1453	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	78.0056	336	1453	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Polymorphum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001999245.1	s__Roseibium aggregatum_A	77.9728	347	1453	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	97.61	96.85	0.93	0.89	16	-
GCF_000158095.2	s__Roseibium alexandrii	77.9231	304	1453	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	97.43	97.43	0.93	0.93	2	-
GCF_008711325.1	s__Roseibium sediminis	77.85	354	1453	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017309185.1	s__Roseibium aggregatum_B	77.8483	375	1453	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	77.8384	419	1453	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009915765.1	s__Pannonibacter sp009915765	77.7662	329	1453	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pannonibacter	95.0	98.76	98.76	0.96	0.96	2	-
GCF_003075075.1	s__Roseibium sp003075075	77.7428	396	1453	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	77.7309	357	1453	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000168975.1	s__Roseibium aggregatum	77.7191	375	1453	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	77.7165	322	1453	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	77.691	379	1453	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	77.6619	362	1453	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	77.5472	294	1453	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	77.529	347	1453	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	76.1457	100	1453	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 14:21:57,295] [INFO] GTDB search result was written to GCF_008711285.1_ASM871128v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:57,295] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:57,300] [INFO] DFAST_QC result json was written to GCF_008711285.1_ASM871128v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:57,300] [INFO] DFAST_QC completed!
[2024-01-24 14:21:57,300] [INFO] Total running time: 0h1m54s