[2024-01-24 14:06:30,225] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:30,226] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:30,227] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c04119a-71f4-4790-88be-7e3f9fec810a/dqc_reference
[2024-01-24 14:06:31,542] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:31,543] [INFO] Task started: Prodigal
[2024-01-24 14:06:31,543] [INFO] Running command: gunzip -c /var/lib/cwl/stg339b28a5-dc0b-4bad-baaa-3c674bf375b9/GCF_004361735.1_ASM436173v1_genomic.fna.gz | prodigal -d GCF_004361735.1_ASM436173v1_genomic.fna/cds.fna -a GCF_004361735.1_ASM436173v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:47,921] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:47,922] [INFO] Task started: HMMsearch
[2024-01-24 14:06:47,922] [INFO] Running command: hmmsearch --tblout GCF_004361735.1_ASM436173v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c04119a-71f4-4790-88be-7e3f9fec810a/dqc_reference/reference_markers.hmm GCF_004361735.1_ASM436173v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:48,174] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:48,175] [INFO] Found 6/6 markers.
[2024-01-24 14:06:48,216] [INFO] Query marker FASTA was written to GCF_004361735.1_ASM436173v1_genomic.fna/markers.fasta
[2024-01-24 14:06:48,217] [INFO] Task started: Blastn
[2024-01-24 14:06:48,217] [INFO] Running command: blastn -query GCF_004361735.1_ASM436173v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c04119a-71f4-4790-88be-7e3f9fec810a/dqc_reference/reference_markers.fasta -out GCF_004361735.1_ASM436173v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:49,070] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:49,074] [INFO] Selected 22 target genomes.
[2024-01-24 14:06:49,074] [INFO] Target genome list was writen to GCF_004361735.1_ASM436173v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:49,088] [INFO] Task started: fastANI
[2024-01-24 14:06:49,088] [INFO] Running command: fastANI --query /var/lib/cwl/stg339b28a5-dc0b-4bad-baaa-3c674bf375b9/GCF_004361735.1_ASM436173v1_genomic.fna.gz --refList GCF_004361735.1_ASM436173v1_genomic.fna/target_genomes.txt --output GCF_004361735.1_ASM436173v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:08,333] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:08,333] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c04119a-71f4-4790-88be-7e3f9fec810a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:08,334] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c04119a-71f4-4790-88be-7e3f9fec810a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:08,350] [INFO] Found 22 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:07:08,350] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:07:08,351] [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
Azoarcus indigens	strain=DSM 12121	GCA_004361735.1	29545	29545	type	True	100.0	1784	1785	95	conclusive
Azoarcus indigens	strain=VB32	GCA_012910835.1	29545	29545	type	True	99.9807	1733	1785	95	conclusive
Azoarcus rhizosphaerae	strain=CC-YHH848	GCA_004801305.1	2565932	2565932	type	True	81.6583	776	1785	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	81.1599	704	1785	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	80.9954	604	1785	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	80.8422	593	1785	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	80.7997	661	1785	95	below_threshold
Thauera linaloolentis	strain=47Lol = DSM 12138	GCA_000310205.1	76112	76112	type	True	80.7824	633	1785	95	below_threshold
Thauera chlorobenzoica	strain=3CB1	GCA_001922305.1	96773	96773	type	True	80.6451	583	1785	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	80.6199	590	1785	95	below_threshold
Thauera aromatica	strain=K172	GCA_003030465.1	59405	59405	type	True	80.584	569	1785	95	below_threshold
Thauera phenolivorans	strain=ZV1C	GCA_001696715.1	1792543	1792543	type	True	80.4754	596	1785	95	below_threshold
Azoarcus communis	strain=SWub3	GCA_003226565.1	41977	41977	type	True	79.6981	611	1785	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	79.6725	617	1785	95	below_threshold
Azoarcus communis	strain=SWub3	GCA_012910815.1	41977	41977	type	True	79.6312	613	1785	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	79.2977	565	1785	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	78.9314	529	1785	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	78.7381	488	1785	95	below_threshold
Nitrogeniibacter aestuarii	strain=H1-1-2A	GCA_017309585.1	2815343	2815343	type	True	78.1691	393	1785	95	below_threshold
Tepidimonas sediminis	strain=YIM 72259	GCA_007556605.1	2588941	2588941	type	True	76.8505	324	1785	95	below_threshold
Pseudoxanthomonas suwonensis	strain=DSM 17175	GCA_010093235.1	314722	314722	suspected-type	True	76.2579	285	1785	95	below_threshold
Pseudoxanthomonas jiangsuensis	strain=DSM 22398	GCA_010093185.1	619688	619688	type	True	75.9421	315	1785	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:08,352] [INFO] DFAST Taxonomy check result was written to GCF_004361735.1_ASM436173v1_genomic.fna/tc_result.tsv
[2024-01-24 14:07:08,353] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:08,353] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:08,353] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c04119a-71f4-4790-88be-7e3f9fec810a/dqc_reference/checkm_data
[2024-01-24 14:07:08,355] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:08,403] [INFO] Task started: CheckM
[2024-01-24 14:07:08,403] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004361735.1_ASM436173v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004361735.1_ASM436173v1_genomic.fna/checkm_input GCF_004361735.1_ASM436173v1_genomic.fna/checkm_result
[2024-01-24 14:07:58,680] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:58,681] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:58,702] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:58,702] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:58,702] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004361735.1_ASM436173v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:58,703] [INFO] Task started: Blastn
[2024-01-24 14:07:58,703] [INFO] Running command: blastn -query GCF_004361735.1_ASM436173v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c04119a-71f4-4790-88be-7e3f9fec810a/dqc_reference/reference_markers_gtdb.fasta -out GCF_004361735.1_ASM436173v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:08:00,462] [INFO] Task succeeded: Blastn
[2024-01-24 14:08:00,466] [INFO] Selected 17 target genomes.
[2024-01-24 14:08:00,466] [INFO] Target genome list was writen to GCF_004361735.1_ASM436173v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:08:00,480] [INFO] Task started: fastANI
[2024-01-24 14:08:00,481] [INFO] Running command: fastANI --query /var/lib/cwl/stg339b28a5-dc0b-4bad-baaa-3c674bf375b9/GCF_004361735.1_ASM436173v1_genomic.fna.gz --refList GCF_004361735.1_ASM436173v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004361735.1_ASM436173v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:18,299] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:18,313] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:08:18,313] [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_004361735.1	s__Azoarcus indigens	100.0	1784	1785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_012911025.1	s__Azoarcus sp012911025	93.8945	1491	1785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006496635.1	s__Azoarcus sp006496635	82.8613	954	1785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001682385.1	s__Azoarcus olearius	82.4497	921	1785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus	95.0	98.77	98.77	0.96	0.96	2	-
GCF_014489115.1	s__Thauera_A sp014489115	81.695	743	1785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004801305.1	s__Thauera_A rhizosphaerae	81.6162	780	1785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002354895.1	s__Thauera sp002354895	81.1816	739	1785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591165.1	s__Thauera butanivorans	81.1727	703	1785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000310205.1	s__Thauera linaloolentis	80.7557	636	1785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017302295.1	s__Thauera sp017302295	80.6609	599	1785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001696715.1	s__Thauera phenolivorans	80.4623	597	1785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	99.27	99.27	0.98	0.98	2	-
GCF_012910905.1	s__Aromatoleum toluvorans	79.9896	610	1785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003226565.1	s__Azoarcus_C communis	79.6882	613	1785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus_C	95.0	99.33	98.67	0.90	0.80	3	-
GCF_012911005.1	s__Aromatoleum toluolicum	79.6843	616	1785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003111645.1	s__Azoarcus_C communis_A	79.6255	602	1785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus_C	95.0	97.65	97.63	0.87	0.87	3	-
GCF_000510725.1	s__Pseudoxanthomonas sp000510725	76.3247	323	1785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.33	99.13	0.95	0.92	5	-
GCF_010093235.1	s__Pseudoxanthomonas suwonensis	76.2551	286	1785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:08:18,315] [INFO] GTDB search result was written to GCF_004361735.1_ASM436173v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:18,315] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:18,319] [INFO] DFAST_QC result json was written to GCF_004361735.1_ASM436173v1_genomic.fna/dqc_result.json
[2024-01-24 14:08:18,319] [INFO] DFAST_QC completed!
[2024-01-24 14:08:18,319] [INFO] Total running time: 0h1m48s