[2024-01-24 11:26:24,057] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:24,062] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:24,062] [INFO] DQC Reference Directory: /var/lib/cwl/stg0586202b-1680-4a98-86a2-a886ac25f36e/dqc_reference
[2024-01-24 11:26:25,287] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:25,288] [INFO] Task started: Prodigal
[2024-01-24 11:26:25,288] [INFO] Running command: gunzip -c /var/lib/cwl/stgb7d40d43-0afb-4407-b196-cd2f7b2a6632/GCF_011761565.1_ASM1176156v1_genomic.fna.gz | prodigal -d GCF_011761565.1_ASM1176156v1_genomic.fna/cds.fna -a GCF_011761565.1_ASM1176156v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:38,787] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:38,788] [INFO] Task started: HMMsearch
[2024-01-24 11:26:38,788] [INFO] Running command: hmmsearch --tblout GCF_011761565.1_ASM1176156v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0586202b-1680-4a98-86a2-a886ac25f36e/dqc_reference/reference_markers.hmm GCF_011761565.1_ASM1176156v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:39,109] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:39,110] [INFO] Found 6/6 markers.
[2024-01-24 11:26:39,149] [INFO] Query marker FASTA was written to GCF_011761565.1_ASM1176156v1_genomic.fna/markers.fasta
[2024-01-24 11:26:39,149] [INFO] Task started: Blastn
[2024-01-24 11:26:39,150] [INFO] Running command: blastn -query GCF_011761565.1_ASM1176156v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0586202b-1680-4a98-86a2-a886ac25f36e/dqc_reference/reference_markers.fasta -out GCF_011761565.1_ASM1176156v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:40,067] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:40,070] [INFO] Selected 25 target genomes.
[2024-01-24 11:26:40,071] [INFO] Target genome list was writen to GCF_011761565.1_ASM1176156v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:40,080] [INFO] Task started: fastANI
[2024-01-24 11:26:40,080] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7d40d43-0afb-4407-b196-cd2f7b2a6632/GCF_011761565.1_ASM1176156v1_genomic.fna.gz --refList GCF_011761565.1_ASM1176156v1_genomic.fna/target_genomes.txt --output GCF_011761565.1_ASM1176156v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:03,521] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:03,521] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0586202b-1680-4a98-86a2-a886ac25f36e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:03,522] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0586202b-1680-4a98-86a2-a886ac25f36e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:03,540] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:03,541] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:03,541] [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
Rhizomicrobium palustre	strain=DSM 19867	GCA_011761565.1	189966	189966	type	True	100.0	1420	1421	95	conclusive
Rhizomicrobium electricum	strain=DSM 21034	GCA_011762045.1	480070	480070	type	True	79.0938	615	1421	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_003119195.2	1064539	1064539	type	True	76.7004	118	1421	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_000237365.1	1064539	1064539	type	True	76.5467	117	1421	95	below_threshold
Aestuariivirga litoralis	strain=KCTC 52945	GCA_003234965.1	2650924	2650924	type	True	76.5185	112	1421	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	76.5114	104	1421	95	below_threshold
Kaistia granuli	strain=Ko04	GCA_000380505.1	363259	363259	type	True	76.4953	99	1421	95	below_threshold
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	76.4725	105	1421	95	below_threshold
Parvibaculum lavamentivorans	strain=DS-1	GCA_000017565.1	256618	256618	type	True	76.4548	100	1421	95	below_threshold
Bradyrhizobium daqingense	strain=CGMCC 1.10947	GCA_007830205.1	993502	993502	type	True	76.4436	118	1421	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	76.4278	105	1421	95	below_threshold
Bradyrhizobium arachidis	strain=CCBAU 051107	GCA_015291705.1	858423	858423	type	True	76.4262	141	1421	95	below_threshold
Methyloligella halotolerans	strain=VKM B-2706	GCA_001708935.1	1177755	1177755	type	True	76.4163	87	1421	95	below_threshold
Bradyrhizobium arachidis	strain=LMG 26795	GCA_900116675.1	858423	858423	type	True	76.399	142	1421	95	below_threshold
Kaistia soli	strain=DSM 19436	GCA_900129325.1	446684	446684	type	True	76.3623	90	1421	95	below_threshold
Xanthobacter oligotrophicus	strain=29k	GCA_008364685.1	2607286	2607286	type	True	76.3553	97	1421	95	below_threshold
Bauldia litoralis	strain=ATCC 35022	GCA_900104485.1	665467	665467	type	True	76.3398	82	1421	95	below_threshold
Jiella pacifica	strain=40Bstr34	GCA_010500815.1	2696469	2696469	type	True	76.3098	97	1421	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	76.1642	120	1421	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	76.0049	111	1421	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	76.0027	107	1421	95	below_threshold
Methylobacterium dankookense	strain=SW08-7	GCA_902141855.1	560405	560405	type	True	75.9765	115	1421	95	below_threshold
Methylobacterium symbioticum	strain=SB0023/3	GCA_902141845.1	2584084	2584084	type	True	75.9706	105	1421	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	75.8251	121	1421	95	below_threshold
Methylobacterium hispanicum	strain=DSM 16372	GCA_022179285.1	270350	270350	type	True	75.7459	91	1421	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:03,542] [INFO] DFAST Taxonomy check result was written to GCF_011761565.1_ASM1176156v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:03,543] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:03,543] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:03,544] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0586202b-1680-4a98-86a2-a886ac25f36e/dqc_reference/checkm_data
[2024-01-24 11:27:03,545] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:03,586] [INFO] Task started: CheckM
[2024-01-24 11:27:03,587] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011761565.1_ASM1176156v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011761565.1_ASM1176156v1_genomic.fna/checkm_input GCF_011761565.1_ASM1176156v1_genomic.fna/checkm_result
[2024-01-24 11:27:44,550] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:44,552] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:44,577] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:44,578] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:44,578] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011761565.1_ASM1176156v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:44,579] [INFO] Task started: Blastn
[2024-01-24 11:27:44,579] [INFO] Running command: blastn -query GCF_011761565.1_ASM1176156v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0586202b-1680-4a98-86a2-a886ac25f36e/dqc_reference/reference_markers_gtdb.fasta -out GCF_011761565.1_ASM1176156v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:46,152] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:46,155] [INFO] Selected 12 target genomes.
[2024-01-24 11:27:46,155] [INFO] Target genome list was writen to GCF_011761565.1_ASM1176156v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:46,164] [INFO] Task started: fastANI
[2024-01-24 11:27:46,164] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7d40d43-0afb-4407-b196-cd2f7b2a6632/GCF_011761565.1_ASM1176156v1_genomic.fna.gz --refList GCF_011761565.1_ASM1176156v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011761565.1_ASM1176156v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:55,392] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:55,404] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:55,404] [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_011761565.1	s__Rhizomicrobium palustre	100.0	1419	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micropepsales;f__Micropepsaceae;g__Rhizomicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013149165.1	s__Rhizomicrobium sp013149165	81.1801	796	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micropepsales;f__Micropepsaceae;g__Rhizomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015654635.1	s__Rhizomicrobium sp015654635	79.3994	559	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micropepsales;f__Micropepsaceae;g__Rhizomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762045.1	s__Rhizomicrobium electricum	79.0975	614	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micropepsales;f__Micropepsaceae;g__Rhizomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002307725.1	s__Rhizomicrobium sp002307725	78.7259	506	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micropepsales;f__Micropepsaceae;g__Rhizomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015654715.1	s__Rhizomicrobium sp015654715	77.8925	313	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micropepsales;f__Micropepsaceae;g__Rhizomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003158585.1	s__Rhizomicrobium sp003158585	77.4647	326	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micropepsales;f__Micropepsaceae;g__Rhizomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241025.1	s__Rhizomicrobium sp018241025	77.4401	230	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micropepsales;f__Micropepsaceae;g__Rhizomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019247845.1	s__Rhizomicrobium sp019247845	77.3142	226	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micropepsales;f__Micropepsaceae;g__Rhizomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015654705.1	s__Rhizomicrobium sp015654705	76.6848	171	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micropepsales;f__Micropepsaceae;g__Rhizomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002088275.1	s__Jiella sp002088275	75.781	94	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:55,406] [INFO] GTDB search result was written to GCF_011761565.1_ASM1176156v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:55,407] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:55,411] [INFO] DFAST_QC result json was written to GCF_011761565.1_ASM1176156v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:55,411] [INFO] DFAST_QC completed!
[2024-01-24 11:27:55,411] [INFO] Total running time: 0h1m31s