[2024-01-24 12:21:52,294] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:52,297] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:52,297] [INFO] DQC Reference Directory: /var/lib/cwl/stg3305cb11-3243-46dd-9d32-e2817778bce3/dqc_reference
[2024-01-24 12:21:53,546] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:53,547] [INFO] Task started: Prodigal
[2024-01-24 12:21:53,547] [INFO] Running command: gunzip -c /var/lib/cwl/stg40b04de2-effe-4683-a0dc-bec006864b5b/GCF_000025705.1_ASM2570v1_genomic.fna.gz | prodigal -d GCF_000025705.1_ASM2570v1_genomic.fna/cds.fna -a GCF_000025705.1_ASM2570v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:04,162] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:04,162] [INFO] Task started: HMMsearch
[2024-01-24 12:22:04,162] [INFO] Running command: hmmsearch --tblout GCF_000025705.1_ASM2570v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3305cb11-3243-46dd-9d32-e2817778bce3/dqc_reference/reference_markers.hmm GCF_000025705.1_ASM2570v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:04,465] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:04,467] [INFO] Found 6/6 markers.
[2024-01-24 12:22:04,496] [INFO] Query marker FASTA was written to GCF_000025705.1_ASM2570v1_genomic.fna/markers.fasta
[2024-01-24 12:22:04,496] [INFO] Task started: Blastn
[2024-01-24 12:22:04,496] [INFO] Running command: blastn -query GCF_000025705.1_ASM2570v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3305cb11-3243-46dd-9d32-e2817778bce3/dqc_reference/reference_markers.fasta -out GCF_000025705.1_ASM2570v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:05,390] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:05,393] [INFO] Selected 27 target genomes.
[2024-01-24 12:22:05,394] [INFO] Target genome list was writen to GCF_000025705.1_ASM2570v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:05,409] [INFO] Task started: fastANI
[2024-01-24 12:22:05,409] [INFO] Running command: fastANI --query /var/lib/cwl/stg40b04de2-effe-4683-a0dc-bec006864b5b/GCF_000025705.1_ASM2570v1_genomic.fna.gz --refList GCF_000025705.1_ASM2570v1_genomic.fna/target_genomes.txt --output GCF_000025705.1_ASM2570v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:24,736] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:24,737] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3305cb11-3243-46dd-9d32-e2817778bce3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:24,737] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3305cb11-3243-46dd-9d32-e2817778bce3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:24,757] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:22:24,757] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:22:24,758] [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
Ferrigenium kumadai	strain=An22	GCA_018324385.1	1682490	1682490	type	True	80.5928	410	1001	95	below_threshold
Ferriphaselus amnicola	strain=OYT1	GCA_000974685.2	1188319	1188319	type	True	78.6677	242	1001	95	below_threshold
Sulfurimicrobium lacus	strain=skT11	GCA_011764585.1	2715678	2715678	type	True	77.9076	198	1001	95	below_threshold
Thauera humireducens	strain=SgZ-1	GCA_001051995.2	1134435	1134435	type	True	77.5492	151	1001	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	77.4445	150	1001	95	below_threshold
Massilia agilis	strain=JCM 31605	GCA_024756255.1	1811226	1811226	type	True	77.4419	133	1001	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	77.4062	173	1001	95	below_threshold
Gallionella capsiferriformans	strain=ES-2	GCA_000145255.1	370405	370405	type	True	77.3752	151	1001	95	below_threshold
Pseudomethylobacillus aquaticus	strain=H-5	GCA_003730115.1	2676064	2676064	type	True	77.3295	95	1001	95	below_threshold
Chromobacterium violaceum	strain=ATCC 12472	GCA_000007705.1	536	536	type	True	77.2697	151	1001	95	below_threshold
Thauera propionica	strain=KNDSS-Mac4	GCA_002245655.1	2019431	2019431	type	True	77.2446	146	1001	95	below_threshold
Chromobacterium amazonense	strain=DSM 26508	GCA_001855565.1	1382803	1382803	type	True	77.1956	136	1001	95	below_threshold
Sulfuritortus calidifontis	strain=J1A	GCA_003967275.1	1914471	1914471	type	True	77.1951	161	1001	95	below_threshold
Cupriavidus oxalaticus	strain=Ox1	GCA_016894385.1	96344	96344	type	True	77.1868	153	1001	95	below_threshold
Sulfuritortus calidifontis	strain=DSM 103923	GCA_004346085.1	1914471	1914471	type	True	77.0129	159	1001	95	below_threshold
Aromatoleum tolulyticum	strain=ATCC 51758	GCA_900156155.1	34027	34027	type	True	76.9629	152	1001	95	below_threshold
Massilia terrae	strain=JCM 31606	GCA_024753145.1	1811224	1811224	type	True	76.9358	140	1001	95	below_threshold
Andreprevotia lacus	strain=DSM 23236	GCA_900176275.1	1121000	1121000	type	True	76.7643	107	1001	95	below_threshold
Massilia norwichensis	strain=LMG 28164	GCA_024753245.1	1442366	1442366	type	True	76.6874	144	1001	95	below_threshold
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	76.6385	147	1001	95	below_threshold
Paludibacterium purpuratum	strain=CECT 8976	GCA_004363805.1	1144873	1144873	type	True	76.5519	90	1001	95	below_threshold
Leeia aquatica	strain=IMCC25680	GCA_012641365.1	2725557	2725557	type	True	76.5175	95	1001	95	below_threshold
Paraburkholderia mimosarum	strain=NBRC 106338	GCA_000739815.1	312026	312026	type	True	76.5154	91	1001	95	below_threshold
Paraburkholderia mimosarum	strain=LMG 23256	GCA_902833725.1	312026	312026	type	True	76.4734	94	1001	95	below_threshold
Paraburkholderia mimosarum	strain=LMG 23256	GCA_000472825.1	312026	312026	type	True	76.2901	93	1001	95	below_threshold
Paraburkholderia sacchari	strain=LMG 19450	GCA_902833715.1	159450	159450	type	True	76.0497	94	1001	95	below_threshold
Paraburkholderia sacchari	strain=LMG 19450	GCA_000785435.2	159450	159450	type	True	75.8644	98	1001	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:24,762] [INFO] DFAST Taxonomy check result was written to GCF_000025705.1_ASM2570v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:24,763] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:24,763] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:24,763] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3305cb11-3243-46dd-9d32-e2817778bce3/dqc_reference/checkm_data
[2024-01-24 12:22:24,764] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:24,799] [INFO] Task started: CheckM
[2024-01-24 12:22:24,799] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000025705.1_ASM2570v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000025705.1_ASM2570v1_genomic.fna/checkm_input GCF_000025705.1_ASM2570v1_genomic.fna/checkm_result
[2024-01-24 12:23:00,681] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:00,682] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:00,963] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:00,963] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:00,964] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000025705.1_ASM2570v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:00,964] [INFO] Task started: Blastn
[2024-01-24 12:23:00,964] [INFO] Running command: blastn -query GCF_000025705.1_ASM2570v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3305cb11-3243-46dd-9d32-e2817778bce3/dqc_reference/reference_markers_gtdb.fasta -out GCF_000025705.1_ASM2570v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:02,848] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:02,852] [INFO] Selected 9 target genomes.
[2024-01-24 12:23:02,853] [INFO] Target genome list was writen to GCF_000025705.1_ASM2570v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:02,876] [INFO] Task started: fastANI
[2024-01-24 12:23:02,876] [INFO] Running command: fastANI --query /var/lib/cwl/stg40b04de2-effe-4683-a0dc-bec006864b5b/GCF_000025705.1_ASM2570v1_genomic.fna.gz --refList GCF_000025705.1_ASM2570v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000025705.1_ASM2570v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:08,839] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:08,848] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:08,848] [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_000025705.1	s__Sideroxydans lithotrophicus	100.0	1001	1001	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016208015.1	s__Sideroxydans sp016208015	82.8618	584	1001	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016214695.1	s__Sideroxydans sp016214695	82.8239	587	1001	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235045.1	s__Sideroxydans sp016235045	82.6626	599	1001	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003445795.1	s__Sideroxydans sp003445795	82.3608	531	1001	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018813765.1	s__Sideroxydans sp018813765	82.0829	564	1001	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	99.93	99.86	0.97	0.93	3	-
GCA_018820925.1	s__Sideroxydans sp018820925	81.9236	606	1001	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	99.99	99.99	0.96	0.96	2	-
GCA_011620315.1	s__Sideroxydans sp011620315	80.4328	410	1001	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297065.1	s__PALSA-1006 sp004297065	79.9078	398	1001	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__PALSA-1006	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:08,850] [INFO] GTDB search result was written to GCF_000025705.1_ASM2570v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:08,851] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:08,855] [INFO] DFAST_QC result json was written to GCF_000025705.1_ASM2570v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:08,856] [INFO] DFAST_QC completed!
[2024-01-24 12:23:08,856] [INFO] Total running time: 0h1m17s