[2024-01-24 13:41:40,794] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:40,797] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:40,797] [INFO] DQC Reference Directory: /var/lib/cwl/stg6d43ed17-152a-42a1-98a5-cded97c6f74d/dqc_reference
[2024-01-24 13:41:42,273] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:42,274] [INFO] Task started: Prodigal
[2024-01-24 13:41:42,274] [INFO] Running command: gunzip -c /var/lib/cwl/stgd8001792-9a64-400b-bb72-297f0f984bde/GCF_003012935.1_ASM301293v1_genomic.fna.gz | prodigal -d GCF_003012935.1_ASM301293v1_genomic.fna/cds.fna -a GCF_003012935.1_ASM301293v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:56,945] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:56,945] [INFO] Task started: HMMsearch
[2024-01-24 13:41:56,946] [INFO] Running command: hmmsearch --tblout GCF_003012935.1_ASM301293v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6d43ed17-152a-42a1-98a5-cded97c6f74d/dqc_reference/reference_markers.hmm GCF_003012935.1_ASM301293v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:57,239] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:57,241] [INFO] Found 6/6 markers.
[2024-01-24 13:41:57,281] [INFO] Query marker FASTA was written to GCF_003012935.1_ASM301293v1_genomic.fna/markers.fasta
[2024-01-24 13:41:57,282] [INFO] Task started: Blastn
[2024-01-24 13:41:57,282] [INFO] Running command: blastn -query GCF_003012935.1_ASM301293v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d43ed17-152a-42a1-98a5-cded97c6f74d/dqc_reference/reference_markers.fasta -out GCF_003012935.1_ASM301293v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:58,325] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:58,333] [INFO] Selected 14 target genomes.
[2024-01-24 13:41:58,334] [INFO] Target genome list was writen to GCF_003012935.1_ASM301293v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:58,347] [INFO] Task started: fastANI
[2024-01-24 13:41:58,348] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8001792-9a64-400b-bb72-297f0f984bde/GCF_003012935.1_ASM301293v1_genomic.fna.gz --refList GCF_003012935.1_ASM301293v1_genomic.fna/target_genomes.txt --output GCF_003012935.1_ASM301293v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:42:11,245] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:11,246] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6d43ed17-152a-42a1-98a5-cded97c6f74d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:42:11,246] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6d43ed17-152a-42a1-98a5-cded97c6f74d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:42:11,260] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:42:11,260] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:42:11,260] [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
Pannonibacter carbonis	strain=Q4.6	GCA_003012935.1	2067569	2067569	type	True	100.0	1573	1577	95	conclusive
Pannonibacter phragmitetus	strain=NCTC13350	GCA_900454465.1	121719	121719	suspected-type	True	81.1157	798	1577	95	below_threshold
Pannonibacter phragmitetus	strain=DSM 14782	GCA_000382365.1	121719	121719	suspected-type	True	81.0269	796	1577	95	below_threshold
Pannonibacter indicus	strain=DSM 23407	GCA_001418225.1	466044	466044	type	True	80.8578	766	1577	95	below_threshold
Pannonibacter indicus	strain=DSM 23407	GCA_001517385.1	466044	466044	type	True	80.846	769	1577	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	78.5513	440	1577	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	78.0062	361	1577	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	77.6628	366	1577	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	77.3585	286	1577	95	below_threshold
Ciceribacter thiooxidans	strain=F43B	GCA_014126615.1	1969821	1969821	type	True	77.3428	265	1577	95	below_threshold
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	77.2723	280	1577	95	below_threshold
Aureimonas mangrovi	strain=LMG 31693	GCA_014058705.1	2758041	2758041	type	True	77.2241	221	1577	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	76.9589	277	1577	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	76.9013	261	1577	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:42:11,262] [INFO] DFAST Taxonomy check result was written to GCF_003012935.1_ASM301293v1_genomic.fna/tc_result.tsv
[2024-01-24 13:42:11,263] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:42:11,263] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:42:11,263] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6d43ed17-152a-42a1-98a5-cded97c6f74d/dqc_reference/checkm_data
[2024-01-24 13:42:11,264] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:42:11,314] [INFO] Task started: CheckM
[2024-01-24 13:42:11,314] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003012935.1_ASM301293v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003012935.1_ASM301293v1_genomic.fna/checkm_input GCF_003012935.1_ASM301293v1_genomic.fna/checkm_result
[2024-01-24 13:42:58,627] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:58,629] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:58,652] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:58,652] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:58,652] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003012935.1_ASM301293v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:58,653] [INFO] Task started: Blastn
[2024-01-24 13:42:58,653] [INFO] Running command: blastn -query GCF_003012935.1_ASM301293v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d43ed17-152a-42a1-98a5-cded97c6f74d/dqc_reference/reference_markers_gtdb.fasta -out GCF_003012935.1_ASM301293v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:00,689] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:00,694] [INFO] Selected 9 target genomes.
[2024-01-24 13:43:00,694] [INFO] Target genome list was writen to GCF_003012935.1_ASM301293v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:43:00,723] [INFO] Task started: fastANI
[2024-01-24 13:43:00,723] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8001792-9a64-400b-bb72-297f0f984bde/GCF_003012935.1_ASM301293v1_genomic.fna.gz --refList GCF_003012935.1_ASM301293v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003012935.1_ASM301293v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:11,866] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:11,884] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:11,884] [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_003012935.1	s__Pannonibacter carbonis	100.0	1573	1577	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pannonibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009915765.1	s__Pannonibacter sp009915765	86.6373	1132	1577	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pannonibacter	95.0	98.76	98.76	0.96	0.96	2	-
GCF_000382365.1	s__Pannonibacter phragmitetus	81.0355	795	1577	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pannonibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001418225.1	s__Pannonibacter indicus	80.8736	764	1577	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pannonibacter	95.0	96.01	95.55	0.94	0.89	12	-
GCF_000192745.1	s__Polymorphum gilvum	79.9671	717	1577	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Polymorphum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002237595.1	s__Roseibium sp002237595	78.2353	470	1577	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018760785.1	s__Rhizobium_A sp018760785	77.5715	317	1577	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900465605.1	s__Allorhizobium sp900465605	77.375	287	1577	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	96.96	95.85	0.92	0.91	5	-
GCA_900470965.1	s__Rhizobium sp900470965	77.0973	253	1577	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:43:11,886] [INFO] GTDB search result was written to GCF_003012935.1_ASM301293v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:11,887] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:11,892] [INFO] DFAST_QC result json was written to GCF_003012935.1_ASM301293v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:11,892] [INFO] DFAST_QC completed!
[2024-01-24 13:43:11,892] [INFO] Total running time: 0h1m31s