[2024-01-24 13:17:11,282] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:11,284] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:11,284] [INFO] DQC Reference Directory: /var/lib/cwl/stg147cfd09-6912-431e-9bbd-e2b92e9b21ed/dqc_reference
[2024-01-24 13:17:12,510] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:12,529] [INFO] Task started: Prodigal
[2024-01-24 13:17:12,529] [INFO] Running command: gunzip -c /var/lib/cwl/stg01100c19-cd1b-4899-96b1-99186c809c5b/GCF_004346185.1_ASM434618v1_genomic.fna.gz | prodigal -d GCF_004346185.1_ASM434618v1_genomic.fna/cds.fna -a GCF_004346185.1_ASM434618v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:27,411] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:27,412] [INFO] Task started: HMMsearch
[2024-01-24 13:17:27,412] [INFO] Running command: hmmsearch --tblout GCF_004346185.1_ASM434618v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg147cfd09-6912-431e-9bbd-e2b92e9b21ed/dqc_reference/reference_markers.hmm GCF_004346185.1_ASM434618v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:27,696] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:27,698] [INFO] Found 6/6 markers.
[2024-01-24 13:17:27,745] [INFO] Query marker FASTA was written to GCF_004346185.1_ASM434618v1_genomic.fna/markers.fasta
[2024-01-24 13:17:27,746] [INFO] Task started: Blastn
[2024-01-24 13:17:27,746] [INFO] Running command: blastn -query GCF_004346185.1_ASM434618v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg147cfd09-6912-431e-9bbd-e2b92e9b21ed/dqc_reference/reference_markers.fasta -out GCF_004346185.1_ASM434618v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:28,598] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:28,602] [INFO] Selected 14 target genomes.
[2024-01-24 13:17:28,603] [INFO] Target genome list was writen to GCF_004346185.1_ASM434618v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:28,776] [INFO] Task started: fastANI
[2024-01-24 13:17:28,777] [INFO] Running command: fastANI --query /var/lib/cwl/stg01100c19-cd1b-4899-96b1-99186c809c5b/GCF_004346185.1_ASM434618v1_genomic.fna.gz --refList GCF_004346185.1_ASM434618v1_genomic.fna/target_genomes.txt --output GCF_004346185.1_ASM434618v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:42,282] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:42,283] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg147cfd09-6912-431e-9bbd-e2b92e9b21ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:42,284] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg147cfd09-6912-431e-9bbd-e2b92e9b21ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:42,298] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:17:42,298] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:17:42,299] [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
Azorhizobium doebereinerae	strain=UFLA1-100	GCA_000473085.1	281091	281091	type	True	80.1135	746	1693	95	below_threshold
Xanthobacter tagetidis	strain=ATCC 700314	GCA_003667445.1	60216	60216	type	True	79.9556	733	1693	95	below_threshold
Xanthobacter tagetidis	strain=DSM 11105	GCA_014206845.1	60216	60216	type	True	79.9426	731	1693	95	below_threshold
Xanthobacter oligotrophicus	strain=29k	GCA_008364685.1	2607286	2607286	type	True	79.7239	657	1693	95	below_threshold
Azorhizobium caulinodans	strain=ORS 571	GCA_000010525.1	7	7	type	True	79.6911	674	1693	95	below_threshold
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	79.596	727	1693	95	below_threshold
Xanthobacter aminoxidans	strain=ATCC BAA-299	GCA_023571765.1	186280	186280	type	True	79.4392	701	1693	95	below_threshold
Xanthobacter autotrophicus	strain=DSM 432	GCA_005871085.1	280	280	type	True	79.3293	641	1693	95	below_threshold
Azorhizobium oxalatiphilum	strain=CCM 7897	GCA_014635325.1	980631	980631	type	True	79.2451	675	1693	95	below_threshold
Xanthobacter agilis	strain=LMG 16336	GCA_021730435.1	47492	47492	type	True	78.8182	531	1693	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	78.3498	499	1693	95	below_threshold
Blastochloris sulfoviridis	strain=DSM 729	GCA_008630065.1	50712	50712	type	True	77.6655	388	1693	95	below_threshold
Blastochloris tepida	strain=GI	GCA_003966715.1	2233851	2233851	type	True	77.6606	391	1693	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	77.1464	418	1693	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:42,301] [INFO] DFAST Taxonomy check result was written to GCF_004346185.1_ASM434618v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:42,301] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:42,302] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:42,302] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg147cfd09-6912-431e-9bbd-e2b92e9b21ed/dqc_reference/checkm_data
[2024-01-24 13:17:42,303] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:42,358] [INFO] Task started: CheckM
[2024-01-24 13:17:42,358] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004346185.1_ASM434618v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004346185.1_ASM434618v1_genomic.fna/checkm_input GCF_004346185.1_ASM434618v1_genomic.fna/checkm_result
[2024-01-24 13:18:29,943] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:29,944] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:29,977] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:29,978] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:29,978] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004346185.1_ASM434618v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:29,979] [INFO] Task started: Blastn
[2024-01-24 13:18:29,979] [INFO] Running command: blastn -query GCF_004346185.1_ASM434618v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg147cfd09-6912-431e-9bbd-e2b92e9b21ed/dqc_reference/reference_markers_gtdb.fasta -out GCF_004346185.1_ASM434618v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:31,523] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:31,533] [INFO] Selected 13 target genomes.
[2024-01-24 13:18:31,534] [INFO] Target genome list was writen to GCF_004346185.1_ASM434618v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:31,621] [INFO] Task started: fastANI
[2024-01-24 13:18:31,621] [INFO] Running command: fastANI --query /var/lib/cwl/stg01100c19-cd1b-4899-96b1-99186c809c5b/GCF_004346185.1_ASM434618v1_genomic.fna.gz --refList GCF_004346185.1_ASM434618v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004346185.1_ASM434618v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:44,812] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:44,827] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:44,827] [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_004346185.1	s__Aquabacter spiritensis	100.0	1689	1693	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Aquabacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013911975.1	s__Aquabacter sp013911975	81.3271	841	1693	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Aquabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002279855.1	s__Aquabacter sp002279855	81.0741	634	1693	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Aquabacter	95.0	98.44	97.78	0.75	0.72	3	-
GCF_003993795.1	s__Aquabacter cavernae	80.9032	844	1693	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Aquabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017742835.1	s__Aquabacter sp017742835	80.4346	759	1693	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Aquabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002257205.1	s__NCEH01 sp002257205	80.2794	497	1693	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__NCEH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002304505.1	s__NCEH01 sp002304505	80.2003	717	1693	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__NCEH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473085.1	s__Azorhizobium doebereinerae	80.1022	747	1693	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Azorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003667445.1	s__Xanthobacter tagetidis	79.9799	731	1693	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000010525.1	s__Azorhizobium caulinodans	79.7125	672	1693	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Azorhizobium	95.0	97.54	97.54	0.94	0.94	2	-
GCF_008364685.1	s__Xanthobacter sp008364685	79.7043	657	1693	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017849325.1	s__Xanthobacter autotrophicus_B	79.3251	402	1693	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008630065.1	s__Blastochloris sulfoviridis	77.6814	386	1693	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Blastochloris	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:44,829] [INFO] GTDB search result was written to GCF_004346185.1_ASM434618v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:44,832] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:44,838] [INFO] DFAST_QC result json was written to GCF_004346185.1_ASM434618v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:44,838] [INFO] DFAST_QC completed!
[2024-01-24 13:18:44,839] [INFO] Total running time: 0h1m34s