[2024-01-24 12:06:21,114] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:21,116] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:21,116] [INFO] DQC Reference Directory: /var/lib/cwl/stg13db4984-174a-4677-9dc1-64fa4cef4573/dqc_reference
[2024-01-24 12:06:22,301] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:22,302] [INFO] Task started: Prodigal
[2024-01-24 12:06:22,302] [INFO] Running command: gunzip -c /var/lib/cwl/stg6ef6c45a-dd5e-4eb0-a8b1-d712660b643d/GCF_001761385.1_ASM176138v1_genomic.fna.gz | prodigal -d GCF_001761385.1_ASM176138v1_genomic.fna/cds.fna -a GCF_001761385.1_ASM176138v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:40,509] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:40,509] [INFO] Task started: HMMsearch
[2024-01-24 12:06:40,509] [INFO] Running command: hmmsearch --tblout GCF_001761385.1_ASM176138v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg13db4984-174a-4677-9dc1-64fa4cef4573/dqc_reference/reference_markers.hmm GCF_001761385.1_ASM176138v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:40,781] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:40,783] [INFO] Found 6/6 markers.
[2024-01-24 12:06:40,822] [INFO] Query marker FASTA was written to GCF_001761385.1_ASM176138v1_genomic.fna/markers.fasta
[2024-01-24 12:06:40,822] [INFO] Task started: Blastn
[2024-01-24 12:06:40,822] [INFO] Running command: blastn -query GCF_001761385.1_ASM176138v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13db4984-174a-4677-9dc1-64fa4cef4573/dqc_reference/reference_markers.fasta -out GCF_001761385.1_ASM176138v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:41,668] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:41,672] [INFO] Selected 16 target genomes.
[2024-01-24 12:06:41,673] [INFO] Target genome list was writen to GCF_001761385.1_ASM176138v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:41,680] [INFO] Task started: fastANI
[2024-01-24 12:06:41,680] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ef6c45a-dd5e-4eb0-a8b1-d712660b643d/GCF_001761385.1_ASM176138v1_genomic.fna.gz --refList GCF_001761385.1_ASM176138v1_genomic.fna/target_genomes.txt --output GCF_001761385.1_ASM176138v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:58,812] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:58,813] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg13db4984-174a-4677-9dc1-64fa4cef4573/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:58,813] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg13db4984-174a-4677-9dc1-64fa4cef4573/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:58,827] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:06:58,828] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:58,828] [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
Hydrogenophaga crassostreae	strain=LPB0072	GCA_001761385.1	1763535	1763535	type	True	100.0	1647	1648	95	conclusive
Hydrogenophaga crassostreae	strain=LPB0072	GCA_001640105.1	1763535	1763535	type	True	99.9779	1623	1648	95	conclusive
Hydrogenophaga aromaticivorans	strain=D2P1	GCA_013387465.1	2610898	2610898	type	True	80.5079	771	1648	95	below_threshold
Hydrogenophaga taeniospiralis	strain=NBRC 102512	GCA_001592305.1	65656	65656	type	True	80.2581	737	1648	95	below_threshold
Hydrogenophaga pseudoflava	strain=NBRC 102511	GCA_001592285.1	47421	47421	type	True	79.8795	692	1648	95	below_threshold
Hydrogenophaga palleronii	strain=NBRC 102513	GCA_001571225.1	65655	65655	type	True	79.7462	599	1648	95	below_threshold
Hydrogenophaga flava	strain=NBRC 102514	GCA_001571145.1	65657	65657	type	True	79.643	701	1648	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.1893	527	1648	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	78.6235	340	1648	95	below_threshold
Curvibacter gracilis	strain=ATCC BAA-807	GCA_000518645.1	230310	230310	type	True	78.4163	453	1648	95	below_threshold
Simplicispira metamorpha	strain=DSM 1837	GCA_004341365.1	80881	80881	type	True	78.3613	359	1648	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	78.3404	441	1648	95	below_threshold
Simplicispira metamorpha	strain=NBRC 13960	GCA_003568725.1	80881	80881	type	True	78.2723	351	1648	95	below_threshold
Diaphorobacter caeni	strain=NR2-3-3-1	GCA_015354245.1	2784387	2784387	type	True	78.0448	312	1648	95	below_threshold
Variovorax guangxiensis	strain=DSM 27352	GCA_003952165.1	1775474	1775474	type	True	77.9384	380	1648	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	77.5293	385	1648	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:58,830] [INFO] DFAST Taxonomy check result was written to GCF_001761385.1_ASM176138v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:58,830] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:58,830] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:58,831] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg13db4984-174a-4677-9dc1-64fa4cef4573/dqc_reference/checkm_data
[2024-01-24 12:06:58,832] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:58,878] [INFO] Task started: CheckM
[2024-01-24 12:06:58,878] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001761385.1_ASM176138v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001761385.1_ASM176138v1_genomic.fna/checkm_input GCF_001761385.1_ASM176138v1_genomic.fna/checkm_result
[2024-01-24 12:08:46,057] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:46,059] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:46,082] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:46,082] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:46,082] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001761385.1_ASM176138v1_genomic.fna/markers.fasta)
[2024-01-24 12:08:46,082] [INFO] Task started: Blastn
[2024-01-24 12:08:46,082] [INFO] Running command: blastn -query GCF_001761385.1_ASM176138v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13db4984-174a-4677-9dc1-64fa4cef4573/dqc_reference/reference_markers_gtdb.fasta -out GCF_001761385.1_ASM176138v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:47,707] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:47,715] [INFO] Selected 20 target genomes.
[2024-01-24 12:08:47,715] [INFO] Target genome list was writen to GCF_001761385.1_ASM176138v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:47,729] [INFO] Task started: fastANI
[2024-01-24 12:08:47,729] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ef6c45a-dd5e-4eb0-a8b1-d712660b643d/GCF_001761385.1_ASM176138v1_genomic.fna.gz --refList GCF_001761385.1_ASM176138v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001761385.1_ASM176138v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:09:04,573] [INFO] Task succeeded: fastANI
[2024-01-24 12:09:04,588] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:09:04,589] [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_001761385.1	s__Hydrogenophaga crassostreae	100.0	1648	1648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_004795855.1	s__Hydrogenophaga sp004795855	81.6821	872	1648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013387465.1	s__Hydrogenophaga aromaticivorans	80.5015	771	1648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	96.00	95.64	0.87	0.82	12	-
GCA_002842215.1	s__Hydrogenophaga sp002842215	80.3734	760	1648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001592305.1	s__Hydrogenophaga taeniospiralis	80.2791	734	1648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018780075.1	s__Hydrogenophaga sp018780075	80.1506	739	1648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002001205.1	s__Hydrogenophaga sp002001205	80.0782	737	1648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011391495.1	s__Hydrogenophaga sp011391495	79.9891	570	1648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390835.1	s__Hydrogenophaga sp011390835	79.8444	564	1648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001713375.1	s__Hydrogenophaga sp001713375	79.7396	633	1648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001571145.1	s__Hydrogenophaga flava	79.6286	703	1648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018333605.1	s__Hydrogenophaga sp018333605	79.4828	382	1648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009859475.1	s__Hydrogenophaga sp009859475	79.4299	561	1648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002127265.1	s__Hydrogenophaga sp002127265	79.2036	556	1648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011388215.1	s__Hydrogenophaga sp011388215	79.1923	526	1648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	99.06	99.06	0.95	0.95	2	-
GCA_013823485.1	s__Hydrogenophaga sp013823485	79.1512	429	1648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	98.29	98.29	0.80	0.80	2	-
GCF_004341365.1	s__Giesbergeria metamorpha	78.4287	363	1648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	99.27	98.54	0.92	0.85	3	-
GCA_009912175.1	s__Comamonas_F wautersii_A	77.791	272	1648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas_F	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185115.1	s__Polaromonas sp016185115	77.6581	285	1648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903960915.1	s__Rhodoferax sp903960915	77.5203	281	1648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.23	97.99	0.89	0.81	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:09:04,590] [INFO] GTDB search result was written to GCF_001761385.1_ASM176138v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:09:04,591] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:09:04,594] [INFO] DFAST_QC result json was written to GCF_001761385.1_ASM176138v1_genomic.fna/dqc_result.json
[2024-01-24 12:09:04,595] [INFO] DFAST_QC completed!
[2024-01-24 12:09:04,595] [INFO] Total running time: 0h2m43s