[2024-01-24 13:36:43,110] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:43,112] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:43,112] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa389b6f-ff90-44b7-99f7-3c43349427b0/dqc_reference
[2024-01-24 13:36:44,354] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:44,355] [INFO] Task started: Prodigal
[2024-01-24 13:36:44,355] [INFO] Running command: gunzip -c /var/lib/cwl/stg793e67c0-37d4-48da-84d9-293f127f4e14/GCF_014145335.1_ASM1414533v1_genomic.fna.gz | prodigal -d GCF_014145335.1_ASM1414533v1_genomic.fna/cds.fna -a GCF_014145335.1_ASM1414533v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:53,593] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:53,594] [INFO] Task started: HMMsearch
[2024-01-24 13:36:53,594] [INFO] Running command: hmmsearch --tblout GCF_014145335.1_ASM1414533v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa389b6f-ff90-44b7-99f7-3c43349427b0/dqc_reference/reference_markers.hmm GCF_014145335.1_ASM1414533v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:53,869] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:53,871] [INFO] Found 6/6 markers.
[2024-01-24 13:36:53,902] [INFO] Query marker FASTA was written to GCF_014145335.1_ASM1414533v1_genomic.fna/markers.fasta
[2024-01-24 13:36:53,903] [INFO] Task started: Blastn
[2024-01-24 13:36:53,903] [INFO] Running command: blastn -query GCF_014145335.1_ASM1414533v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa389b6f-ff90-44b7-99f7-3c43349427b0/dqc_reference/reference_markers.fasta -out GCF_014145335.1_ASM1414533v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:55,023] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:55,025] [INFO] Selected 18 target genomes.
[2024-01-24 13:36:55,026] [INFO] Target genome list was writen to GCF_014145335.1_ASM1414533v1_genomic.fna/target_genomes.txt
[2024-01-24 13:36:55,050] [INFO] Task started: fastANI
[2024-01-24 13:36:55,050] [INFO] Running command: fastANI --query /var/lib/cwl/stg793e67c0-37d4-48da-84d9-293f127f4e14/GCF_014145335.1_ASM1414533v1_genomic.fna.gz --refList GCF_014145335.1_ASM1414533v1_genomic.fna/target_genomes.txt --output GCF_014145335.1_ASM1414533v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:12,848] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:12,849] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa389b6f-ff90-44b7-99f7-3c43349427b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:12,849] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa389b6f-ff90-44b7-99f7-3c43349427b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:12,863] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:37:12,863] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:37:12,864] [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
Sphaerotilus natans subsp. natans	strain=DSM 6575	GCA_000689195.1	882627	34103	type	True	80.7275	554	1099	95	below_threshold
Sphaerotilus natans	strain=ATCC 13338	GCA_900156335.1	34103	34103	type	True	80.6961	583	1099	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	80.6278	548	1099	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_003349825.1	215580	215580	type	True	80.5833	549	1099	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	80.5832	550	1099	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	80.5132	551	1099	95	below_threshold
Sphaerotilus hippei	strain=DSM 566	GCA_003201595.1	744406	744406	type	True	80.4693	558	1099	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	80.3471	538	1099	95	below_threshold
Azohydromonas australica	strain=DSM 1124	GCA_000430725.1	364039	364039	type	True	80.2519	589	1099	95	below_threshold
Ideonella azotifigens	strain=DSM 21438	GCA_006519715.1	513160	513160	type	True	80.1657	431	1099	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	80.1145	589	1099	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	80.1107	516	1099	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_016583525.1	28068	28068	suspected-type	True	79.8502	609	1099	95	below_threshold
Rhizobacter gummiphilus	strain=NBRC 109400	GCA_002762215.1	946333	946333	type	True	79.6719	530	1099	95	below_threshold
Mitsuaria chitinivorans	strain=HWN-4	GCA_002761755.1	2917965	2917965	type	True	79.643	526	1099	95	below_threshold
Aquabacterium soli	strain=SJQ9	GCA_003933735.1	2493092	2493092	type	True	79.5077	493	1099	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	79.1283	501	1099	95	below_threshold
Roseateles terrae	strain=CECT 7247	GCA_014192155.1	431060	431060	type	True	78.8755	404	1099	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:12,865] [INFO] DFAST Taxonomy check result was written to GCF_014145335.1_ASM1414533v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:12,866] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:12,866] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:12,866] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa389b6f-ff90-44b7-99f7-3c43349427b0/dqc_reference/checkm_data
[2024-01-24 13:37:12,868] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:12,908] [INFO] Task started: CheckM
[2024-01-24 13:37:12,908] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014145335.1_ASM1414533v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014145335.1_ASM1414533v1_genomic.fna/checkm_input GCF_014145335.1_ASM1414533v1_genomic.fna/checkm_result
[2024-01-24 13:38:08,485] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:08,486] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:08,507] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:08,507] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:08,507] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014145335.1_ASM1414533v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:08,508] [INFO] Task started: Blastn
[2024-01-24 13:38:08,508] [INFO] Running command: blastn -query GCF_014145335.1_ASM1414533v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa389b6f-ff90-44b7-99f7-3c43349427b0/dqc_reference/reference_markers_gtdb.fasta -out GCF_014145335.1_ASM1414533v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:10,721] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:10,726] [INFO] Selected 22 target genomes.
[2024-01-24 13:38:10,727] [INFO] Target genome list was writen to GCF_014145335.1_ASM1414533v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:10,767] [INFO] Task started: fastANI
[2024-01-24 13:38:10,767] [INFO] Running command: fastANI --query /var/lib/cwl/stg793e67c0-37d4-48da-84d9-293f127f4e14/GCF_014145335.1_ASM1414533v1_genomic.fna.gz --refList GCF_014145335.1_ASM1414533v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014145335.1_ASM1414533v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:32,702] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:32,728] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:32,728] [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_014145335.1	s__SJAQ100 sp014145335	100.0	1098	1099	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SJAQ100	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016735685.1	s__SJAQ100 sp016735685	91.6392	855	1099	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SJAQ100	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425905.1	s__Methylibium sp001425905	81.3684	639	1099	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Methylibium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826655.1	s__Methylibium sp902826655	81.1282	573	1099	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Methylibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217215.1	s__Rivibacter subsaxonicus	81.122	576	1099	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rivibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000015725.1	s__Methylibium petroleiphilum	81.0917	632	1099	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Methylibium	95.0	96.91	96.03	0.83	0.81	5	-
GCF_900156335.1	s__Sphaerotilus natans	80.6802	583	1099	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sphaerotilus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_018069875.1	s__Ideonella sp018069875	80.6417	614	1099	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	98.74	98.74	0.92	0.92	2	-
GCF_008329925.1	s__Sphaerotilus sulfidivorans	80.6162	572	1099	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sphaerotilus	95.0	99.98	99.98	1.00	1.00	2	-
GCF_018069755.1	s__Ideonella sp018069755	80.601	574	1099	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015476235.1	s__Schlegelella thermodepolymerans	80.5706	548	1099	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Schlegelella	95.0	99.89	99.68	0.98	0.95	4	-
GCA_017992055.1	s__Aquabacterium_A sp017992055	80.4755	626	1099	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004011805.1	s__Piscinibacter defluvii	80.4045	647	1099	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302505.1	s__Rubrivivax sp017302505	80.2287	467	1099	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001984095.1	s__KK5 sp001984095	80.2265	547	1099	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__KK5	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142965.1	s__Rhizobacter sp900142965	80.0243	571	1099	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016583785.1	s__Rubrivivax gelatinosus_B	79.8857	566	1099	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	99.02	99.02	0.92	0.92	2	-
GCA_019237615.1	s__Pelomonas sp019237615	79.8835	494	1099	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003550215.1	s__Pelomonas sp003550215	79.8523	558	1099	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113225.1	s__Mitsuaria sp900113225	79.6652	565	1099	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	98.36	98.28	0.95	0.95	4	-
GCF_002761755.1	s__Mitsuaria sp002761755	79.6466	526	1099	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240325.1	s__Rubrivivax sp018240325	79.6416	484	1099	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:32,730] [INFO] GTDB search result was written to GCF_014145335.1_ASM1414533v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:32,730] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:32,735] [INFO] DFAST_QC result json was written to GCF_014145335.1_ASM1414533v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:32,735] [INFO] DFAST_QC completed!
[2024-01-24 13:38:32,735] [INFO] Total running time: 0h1m50s