[2024-01-24 15:11:09,507] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:11:09,510] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:11:09,510] [INFO] DQC Reference Directory: /var/lib/cwl/stg36e3d527-aa29-46aa-b47a-3c77daaa437f/dqc_reference
[2024-01-24 15:11:10,776] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:11:10,777] [INFO] Task started: Prodigal
[2024-01-24 15:11:10,778] [INFO] Running command: gunzip -c /var/lib/cwl/stga806ddbc-e2a7-4fc8-ab73-50038dedcc72/GCF_013415485.1_ASM1341548v1_genomic.fna.gz | prodigal -d GCF_013415485.1_ASM1341548v1_genomic.fna/cds.fna -a GCF_013415485.1_ASM1341548v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:11:25,333] [INFO] Task succeeded: Prodigal
[2024-01-24 15:11:25,334] [INFO] Task started: HMMsearch
[2024-01-24 15:11:25,334] [INFO] Running command: hmmsearch --tblout GCF_013415485.1_ASM1341548v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg36e3d527-aa29-46aa-b47a-3c77daaa437f/dqc_reference/reference_markers.hmm GCF_013415485.1_ASM1341548v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:11:25,640] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:11:25,641] [INFO] Found 6/6 markers.
[2024-01-24 15:11:25,687] [INFO] Query marker FASTA was written to GCF_013415485.1_ASM1341548v1_genomic.fna/markers.fasta
[2024-01-24 15:11:25,687] [INFO] Task started: Blastn
[2024-01-24 15:11:25,688] [INFO] Running command: blastn -query GCF_013415485.1_ASM1341548v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36e3d527-aa29-46aa-b47a-3c77daaa437f/dqc_reference/reference_markers.fasta -out GCF_013415485.1_ASM1341548v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:26,836] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:26,840] [INFO] Selected 27 target genomes.
[2024-01-24 15:11:26,841] [INFO] Target genome list was writen to GCF_013415485.1_ASM1341548v1_genomic.fna/target_genomes.txt
[2024-01-24 15:11:26,852] [INFO] Task started: fastANI
[2024-01-24 15:11:26,852] [INFO] Running command: fastANI --query /var/lib/cwl/stga806ddbc-e2a7-4fc8-ab73-50038dedcc72/GCF_013415485.1_ASM1341548v1_genomic.fna.gz --refList GCF_013415485.1_ASM1341548v1_genomic.fna/target_genomes.txt --output GCF_013415485.1_ASM1341548v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:47,435] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:47,436] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg36e3d527-aa29-46aa-b47a-3c77daaa437f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:47,437] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg36e3d527-aa29-46aa-b47a-3c77daaa437f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:47,467] [INFO] Found 27 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:11:47,467] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:47,468] [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
Rhabdonatronobacter sediminivivens	strain=IM2376	GCA_013415485.1	2743469	2743469	type	True	100.0	1275	1281	95	conclusive
Alkalilacustris brevis	strain=34079	GCA_003350345.1	2026338	2026338	type	True	78.5754	454	1281	95	below_threshold
Rhodobaca barguzinensis	strain=alga05	GCA_001870665.2	441209	441209	suspected-type	True	78.3813	382	1281	95	below_threshold
Rhodobaca barguzinensis	strain=DSM 19920	GCA_004365885.1	441209	441209	suspected-type	True	78.299	383	1281	95	below_threshold
Rhodobaca bogoriensis	strain=DSM 18756	GCA_004366635.1	119542	119542	suspected-type	True	78.2909	378	1281	95	below_threshold
Roseicitreum antarcticum	strain=ZS2-28	GCA_014681765.1	564137	564137	type	True	78.2895	429	1281	95	below_threshold
Roseicitreum antarcticum	strain=CGMCC 1.8894	GCA_900107025.1	564137	564137	type	True	78.2496	437	1281	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.1999	404	1281	95	below_threshold
Paracoccus binzhouensis	strain=wg1	GCA_016446475.1	2796149	2796149	type	True	78.1167	393	1281	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_004345735.1	35804	35804	type	True	78.0988	376	1281	95	below_threshold
Paracoccus siganidrum	strain=M26	GCA_003709565.1	1276757	1276757	type	True	78.0888	436	1281	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_016583705.1	35804	35804	type	True	78.0791	381	1281	95	below_threshold
Pararhodobacter marinus	strain=CIC4N-9	GCA_003122215.1	2184063	2184063	type	True	78.0491	450	1281	95	below_threshold
Paracoccus siganidrum	strain=DSM 26381	GCA_003594835.1	1276757	1276757	type	True	78.0466	429	1281	95	below_threshold
Rhodovulum visakhapatnamense	strain=JA181	GCA_004365965.1	364297	364297	type	True	78.0172	389	1281	95	below_threshold
Roseibaca ekhonensis	strain=CECT 7235	GCA_900499075.1	254356	254356	type	True	78.0012	369	1281	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	77.885	405	1281	95	below_threshold
Rhodobacter flagellatus	strain=SYSU G03088	GCA_008271465.1	2593021	2593021	type	True	77.8704	344	1281	95	below_threshold
Paracoccus fontiphilus	strain=MVW-1	GCA_017356265.1	1815556	1815556	type	True	77.786	329	1281	95	below_threshold
Allgaiera indica	strain=DSM 24802	GCA_900106675.1	765699	765699	type	True	77.7817	401	1281	95	below_threshold
Allgaiera indica	strain=CGMCC 1.10859	GCA_014653075.1	765699	765699	type	True	77.742	407	1281	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	77.7191	365	1281	95	below_threshold
Paracoccus acridae	strain=CGMCC 1.15419	GCA_014642735.1	1795310	1795310	type	True	77.7114	339	1281	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	77.5987	372	1281	95	below_threshold
Cereibacter johrii	strain=JA192	GCA_001720585.1	445629	445629	type	True	77.4104	322	1281	95	below_threshold
Cereibacter johrii	strain=JA192	GCA_003046325.1	445629	445629	type	True	77.3664	347	1281	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	77.3206	355	1281	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:47,475] [INFO] DFAST Taxonomy check result was written to GCF_013415485.1_ASM1341548v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:47,476] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:47,477] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:47,477] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg36e3d527-aa29-46aa-b47a-3c77daaa437f/dqc_reference/checkm_data
[2024-01-24 15:11:47,479] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:47,522] [INFO] Task started: CheckM
[2024-01-24 15:11:47,522] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013415485.1_ASM1341548v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013415485.1_ASM1341548v1_genomic.fna/checkm_input GCF_013415485.1_ASM1341548v1_genomic.fna/checkm_result
[2024-01-24 15:12:37,166] [INFO] Task succeeded: CheckM
[2024-01-24 15:12:37,168] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:12:37,188] [INFO] ===== Completeness check finished =====
[2024-01-24 15:12:37,188] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:12:37,189] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013415485.1_ASM1341548v1_genomic.fna/markers.fasta)
[2024-01-24 15:12:37,189] [INFO] Task started: Blastn
[2024-01-24 15:12:37,189] [INFO] Running command: blastn -query GCF_013415485.1_ASM1341548v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36e3d527-aa29-46aa-b47a-3c77daaa437f/dqc_reference/reference_markers_gtdb.fasta -out GCF_013415485.1_ASM1341548v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:12:39,023] [INFO] Task succeeded: Blastn
[2024-01-24 15:12:39,026] [INFO] Selected 15 target genomes.
[2024-01-24 15:12:39,027] [INFO] Target genome list was writen to GCF_013415485.1_ASM1341548v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:12:39,060] [INFO] Task started: fastANI
[2024-01-24 15:12:39,061] [INFO] Running command: fastANI --query /var/lib/cwl/stga806ddbc-e2a7-4fc8-ab73-50038dedcc72/GCF_013415485.1_ASM1341548v1_genomic.fna.gz --refList GCF_013415485.1_ASM1341548v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013415485.1_ASM1341548v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:12:49,068] [INFO] Task succeeded: fastANI
[2024-01-24 15:12:49,084] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:12:49,084] [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
GCA_013415485.1	s__PUOA01 sp003567395	100.0	1275	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__PUOA01	95.0	98.54	98.26	0.95	0.89	5	conclusive
GCA_007121115.1	s__PUOA01 sp007121115	83.3181	612	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__PUOA01	95.0	99.30	99.15	0.84	0.78	4	-
GCA_007123625.1	s__PUOA01 sp007123625	81.6111	485	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__PUOA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003551925.1	s__PUOA01 sp003551925	81.1854	512	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__PUOA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003561595.1	s__Roseinatronobacter sp003561595	79.4439	456	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	98.99	98.90	0.87	0.78	5	-
GCA_007120685.1	s__Pararhodobacter sp007120685	79.4316	441	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	99.30	99.30	0.84	0.84	2	-
GCA_003564655.1	s__Roseinatronobacter sp003564655	79.3541	418	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007128135.1	s__Roseinatronobacter sp007128135	79.0726	472	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	99.53	99.53	0.93	0.93	2	-
GCA_007695345.1	s__Roseinatronobacter sp007695345	79.0185	452	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001314715.1	s__Pararhodobacter sp001314715	78.7133	453	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007134805.1	s__Roseinatronobacter sp007134805	78.421	333	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	99.08	99.08	0.63	0.63	2	-
GCA_007129775.1	s__Rhodobaculum sp007129775	78.285	330	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009908405.1	s__Roseinatronobacter sp009908405	78.2144	350	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008271465.1	s__Tabrizicola flagellata	77.89	342	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017356265.1	s__Paracoccus fontiphilus	77.7758	330	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:12:49,086] [INFO] GTDB search result was written to GCF_013415485.1_ASM1341548v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:12:49,087] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:12:49,091] [INFO] DFAST_QC result json was written to GCF_013415485.1_ASM1341548v1_genomic.fna/dqc_result.json
[2024-01-24 15:12:49,091] [INFO] DFAST_QC completed!
[2024-01-24 15:12:49,091] [INFO] Total running time: 0h1m40s