[2024-01-24 14:30:31,209] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:31,213] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:31,213] [INFO] DQC Reference Directory: /var/lib/cwl/stg3052eded-487f-40c0-adbb-c0789ca9aefc/dqc_reference
[2024-01-24 14:30:33,801] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:33,802] [INFO] Task started: Prodigal
[2024-01-24 14:30:33,803] [INFO] Running command: gunzip -c /var/lib/cwl/stgdb82a66f-3f81-4900-8819-6e372d356fde/GCF_009910475.1_ASM991047v1_genomic.fna.gz | prodigal -d GCF_009910475.1_ASM991047v1_genomic.fna/cds.fna -a GCF_009910475.1_ASM991047v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:44,961] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:44,961] [INFO] Task started: HMMsearch
[2024-01-24 14:30:44,961] [INFO] Running command: hmmsearch --tblout GCF_009910475.1_ASM991047v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3052eded-487f-40c0-adbb-c0789ca9aefc/dqc_reference/reference_markers.hmm GCF_009910475.1_ASM991047v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:45,285] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:45,287] [INFO] Found 6/6 markers.
[2024-01-24 14:30:45,329] [INFO] Query marker FASTA was written to GCF_009910475.1_ASM991047v1_genomic.fna/markers.fasta
[2024-01-24 14:30:45,329] [INFO] Task started: Blastn
[2024-01-24 14:30:45,329] [INFO] Running command: blastn -query GCF_009910475.1_ASM991047v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3052eded-487f-40c0-adbb-c0789ca9aefc/dqc_reference/reference_markers.fasta -out GCF_009910475.1_ASM991047v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:46,287] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:46,290] [INFO] Selected 19 target genomes.
[2024-01-24 14:30:46,291] [INFO] Target genome list was writen to GCF_009910475.1_ASM991047v1_genomic.fna/target_genomes.txt
[2024-01-24 14:30:46,335] [INFO] Task started: fastANI
[2024-01-24 14:30:46,336] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb82a66f-3f81-4900-8819-6e372d356fde/GCF_009910475.1_ASM991047v1_genomic.fna.gz --refList GCF_009910475.1_ASM991047v1_genomic.fna/target_genomes.txt --output GCF_009910475.1_ASM991047v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:02,841] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:02,842] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3052eded-487f-40c0-adbb-c0789ca9aefc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:02,842] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3052eded-487f-40c0-adbb-c0789ca9aefc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:02,857] [INFO] Found 19 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:31:02,857] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:02,858] [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
Pyruvatibacter mobilis	strain=GYP-11	GCA_009910475.1	1712261	1712261	type	True	100.0	1094	1097	95	conclusive
Pyruvatibacter mobilis	strain=CGMCC 1.15125	GCA_014640905.1	1712261	1712261	type	True	99.9979	1097	1097	95	conclusive
Pyruvatibacter mobilis	strain=CGMCC 1.15125	GCA_012848855.1	1712261	1712261	type	True	99.9979	1097	1097	95	conclusive
Parvibaculum indicum	strain=DSM 25305	GCA_011762095.1	562969	562969	type	True	77.6335	272	1097	95	below_threshold
Blastochloris sulfoviridis	strain=DSM 729	GCA_008630065.1	50712	50712	type	True	77.3877	157	1097	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_014197785.1	34017	34017	type	True	77.3271	175	1097	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_003258835.1	34017	34017	type	True	77.3136	169	1097	95	below_threshold
Hyphomicrobium album	strain=XQ2	GCA_009708035.1	2665159	2665159	type	True	77.0696	98	1097	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	76.9995	153	1097	95	below_threshold
Parvibaculum sedimenti	strain=HXT-9	GCA_009184905.1	2608632	2608632	type	True	76.9861	199	1097	95	below_threshold
Xanthobacter agilis	strain=LMG 16336	GCA_021730435.1	47492	47492	type	True	76.9006	151	1097	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	76.8365	153	1097	95	below_threshold
Methylorubrum zatmanii	strain=LMG 6087	GCA_014845115.1	29429	29429	type	True	76.8301	137	1097	95	below_threshold
Parvularcula oceani	strain=JLT2013	GCA_000733125.1	1247963	1247963	type	True	76.7946	113	1097	95	below_threshold
Parvularcula marina	strain=SM1705	GCA_003399445.1	2292771	2292771	type	True	76.7756	66	1097	95	below_threshold
Parvularcula dongshanensis	strain=DSM 102850	GCA_014199615.1	1173995	1173995	type	True	76.5258	85	1097	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	76.5016	160	1097	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	76.1132	138	1097	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	76.0954	128	1097	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:02,859] [INFO] DFAST Taxonomy check result was written to GCF_009910475.1_ASM991047v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:02,860] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:02,860] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:02,860] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3052eded-487f-40c0-adbb-c0789ca9aefc/dqc_reference/checkm_data
[2024-01-24 14:31:02,861] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:02,898] [INFO] Task started: CheckM
[2024-01-24 14:31:02,898] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009910475.1_ASM991047v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009910475.1_ASM991047v1_genomic.fna/checkm_input GCF_009910475.1_ASM991047v1_genomic.fna/checkm_result
[2024-01-24 14:31:40,506] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:40,507] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:40,527] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:40,528] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:40,528] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009910475.1_ASM991047v1_genomic.fna/markers.fasta)
[2024-01-24 14:31:40,529] [INFO] Task started: Blastn
[2024-01-24 14:31:40,529] [INFO] Running command: blastn -query GCF_009910475.1_ASM991047v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3052eded-487f-40c0-adbb-c0789ca9aefc/dqc_reference/reference_markers_gtdb.fasta -out GCF_009910475.1_ASM991047v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:42,303] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:42,306] [INFO] Selected 24 target genomes.
[2024-01-24 14:31:42,306] [INFO] Target genome list was writen to GCF_009910475.1_ASM991047v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:42,325] [INFO] Task started: fastANI
[2024-01-24 14:31:42,325] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb82a66f-3f81-4900-8819-6e372d356fde/GCF_009910475.1_ASM991047v1_genomic.fna.gz --refList GCF_009910475.1_ASM991047v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009910475.1_ASM991047v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:00,075] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:00,094] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:00,094] [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_012848855.1	s__Pyruvatibacter mobilis	99.9979	1097	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__CGMCC-115125;g__Pyruvatibacter	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCF_000689395.1	s__Pyruvatibacter ectocarpi	79.1032	549	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__CGMCC-115125;g__Pyruvatibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002684405.1	s__Parvibaculum sp002684405	77.7607	214	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762095.1	s__Parvibaculum indicum	77.611	274	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008630065.1	s__Blastochloris sulfoviridis	77.3877	157	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Blastochloris	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258835.1	s__Rhodobium orientis	77.3136	169	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodobiaceae;g__Rhodobium	95.0	99.99	99.98	0.99	0.98	3	-
GCF_003966715.1	s__Blastochloris tepida	77.2285	168	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Blastochloris	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014843845.1	s__Mesorhizobium amorphae_A	77.1782	160	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0866	97.39	97.39	0.88	0.88	2	-
GCF_000192745.1	s__Polymorphum gilvum	77.1355	163	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Polymorphum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009708035.1	s__Hyphomicrobium_A sp009708035	77.0962	97	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003601975.1	s__Mesorhizobium waimense	76.9995	153	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009223885.1	s__Ancylobacter sp009223885	76.9848	189	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014692675.1	s__Roseibium aggregatum_C	76.9683	145	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903889655.1	s__Parvibaculum sp903889655	76.9582	178	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.81	99.81	0.91	0.91	2	-
GCF_016756535.1	s__Mesorhizobium sp016756535	76.9442	166	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014845115.1	s__Methylobacterium zatmanii	76.8463	136	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002841195.1	s__Parvibaculum sp002841195	76.7404	202	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016861165.1	s__BOKV01 sp016861165	76.5402	139	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__BOKV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240795.1	s__Phenylobacterium sp018240795	76.5172	134	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006385175.1	s__Emcibacter nanhaiensis	76.3475	76	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__Emcibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002383105.1	s__Methyloceanibacter sp002383105	76.3012	90	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloceanibacter	95.0	99.16	99.02	0.80	0.75	10	-
GCF_009848505.1	s__Roseomonas deserti_A	76.2649	102	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003105285.1	s__Methylosinus sp003105285	76.1965	65	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100085.1	s__Salipiger marinus	76.0603	131	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.13	98.13	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:00,096] [INFO] GTDB search result was written to GCF_009910475.1_ASM991047v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:00,097] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:00,102] [INFO] DFAST_QC result json was written to GCF_009910475.1_ASM991047v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:00,102] [INFO] DFAST_QC completed!
[2024-01-24 14:32:00,102] [INFO] Total running time: 0h1m29s