[2024-01-24 13:55:45,609] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:45,611] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:45,611] [INFO] DQC Reference Directory: /var/lib/cwl/stgf8f64005-3bce-46c8-9a28-64808141fec0/dqc_reference
[2024-01-24 13:55:46,904] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:46,905] [INFO] Task started: Prodigal
[2024-01-24 13:55:46,906] [INFO] Running command: gunzip -c /var/lib/cwl/stg252c00b5-e176-40e7-8b3d-0e28f5531366/GCF_021043325.1_ASM2104332v1_genomic.fna.gz | prodigal -d GCF_021043325.1_ASM2104332v1_genomic.fna/cds.fna -a GCF_021043325.1_ASM2104332v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:14,478] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:14,479] [INFO] Task started: HMMsearch
[2024-01-24 13:56:14,479] [INFO] Running command: hmmsearch --tblout GCF_021043325.1_ASM2104332v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf8f64005-3bce-46c8-9a28-64808141fec0/dqc_reference/reference_markers.hmm GCF_021043325.1_ASM2104332v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:14,850] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:14,852] [INFO] Found 6/6 markers.
[2024-01-24 13:56:14,913] [INFO] Query marker FASTA was written to GCF_021043325.1_ASM2104332v1_genomic.fna/markers.fasta
[2024-01-24 13:56:14,914] [INFO] Task started: Blastn
[2024-01-24 13:56:14,914] [INFO] Running command: blastn -query GCF_021043325.1_ASM2104332v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf8f64005-3bce-46c8-9a28-64808141fec0/dqc_reference/reference_markers.fasta -out GCF_021043325.1_ASM2104332v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:15,970] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:15,974] [INFO] Selected 19 target genomes.
[2024-01-24 13:56:15,975] [INFO] Target genome list was writen to GCF_021043325.1_ASM2104332v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:15,995] [INFO] Task started: fastANI
[2024-01-24 13:56:15,996] [INFO] Running command: fastANI --query /var/lib/cwl/stg252c00b5-e176-40e7-8b3d-0e28f5531366/GCF_021043325.1_ASM2104332v1_genomic.fna.gz --refList GCF_021043325.1_ASM2104332v1_genomic.fna/target_genomes.txt --output GCF_021043325.1_ASM2104332v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:39,490] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:39,491] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf8f64005-3bce-46c8-9a28-64808141fec0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:39,491] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf8f64005-3bce-46c8-9a28-64808141fec0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:39,508] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:56:39,508] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:39,509] [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
Ideonella azotifigens	strain=DSM 21438	GCA_006519715.1	513160	513160	type	True	99.4848	1424	2398	95	conclusive
Ideonella dechloratans	strain=CCUG 30977	GCA_008801845.1	36863	36863	type	True	81.8573	885	2398	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	81.854	909	2398	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	81.6578	911	2398	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	80.1663	721	2398	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	80.1031	740	2398	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	80.0819	717	2398	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000420125.1	316997	316997	type	True	80.0509	746	2398	95	below_threshold
Sphaerotilus montanus	strain=HS	GCA_013426955.1	522889	522889	type	True	79.9878	731	2398	95	below_threshold
Ideonella livida	strain=TBM-1	GCA_010499455.1	2707176	2707176	type	True	79.9708	817	2398	95	below_threshold
Sphaerotilus montanus	strain=DSM 21226	GCA_013410775.1	522889	522889	type	True	79.8985	764	2398	95	below_threshold
Mitsuaria chitinivorans	strain=HWN-4	GCA_002761755.1	2917965	2917965	type	True	79.652	811	2398	95	below_threshold
Pelomonas saccharophila	strain=DSM 654	GCA_004342485.1	304	304	type	True	79.6123	870	2398	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	79.4096	898	2398	95	below_threshold
Pelomonas puraquae	strain=CCUG 52769	GCA_002205845.1	431059	431059	type	True	79.3588	813	2398	95	below_threshold
Azohydromonas lata	strain=NBRC 102462	GCA_001571085.1	45677	45677	type	True	79.3445	861	2398	95	below_threshold
Aquabacterium soli	strain=SJQ9	GCA_003933735.1	2493092	2493092	type	True	79.2098	638	2398	95	below_threshold
Roseateles depolymerans	strain=DSM 11813	GCA_003387155.1	76731	76731	type	True	79.1335	731	2398	95	below_threshold
Roseateles terrae	strain=CECT 7247	GCA_014192155.1	431060	431060	type	True	78.9651	691	2398	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:39,511] [INFO] DFAST Taxonomy check result was written to GCF_021043325.1_ASM2104332v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:39,511] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:39,512] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:39,512] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf8f64005-3bce-46c8-9a28-64808141fec0/dqc_reference/checkm_data
[2024-01-24 13:56:39,514] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:39,581] [INFO] Task started: CheckM
[2024-01-24 13:56:39,581] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021043325.1_ASM2104332v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021043325.1_ASM2104332v1_genomic.fna/checkm_input GCF_021043325.1_ASM2104332v1_genomic.fna/checkm_result
[2024-01-24 13:59:06,899] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:06,900] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:06,921] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:06,922] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:06,922] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021043325.1_ASM2104332v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:06,923] [INFO] Task started: Blastn
[2024-01-24 13:59:06,923] [INFO] Running command: blastn -query GCF_021043325.1_ASM2104332v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf8f64005-3bce-46c8-9a28-64808141fec0/dqc_reference/reference_markers_gtdb.fasta -out GCF_021043325.1_ASM2104332v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:09,129] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:09,133] [INFO] Selected 22 target genomes.
[2024-01-24 13:59:09,133] [INFO] Target genome list was writen to GCF_021043325.1_ASM2104332v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:09,147] [INFO] Task started: fastANI
[2024-01-24 13:59:09,147] [INFO] Running command: fastANI --query /var/lib/cwl/stg252c00b5-e176-40e7-8b3d-0e28f5531366/GCF_021043325.1_ASM2104332v1_genomic.fna.gz --refList GCF_021043325.1_ASM2104332v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021043325.1_ASM2104332v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:35,028] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:35,049] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:59:35,049] [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_008801845.1	s__Ideonella dechloratans	81.8877	881	2398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000333615.1	s__Ideonella sp000333615	81.6888	785	2398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002255925.1	s__Ideonella sp002255925	81.562	839	2398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302485.1	s__Ideonella sp017302485	81.3864	575	2398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018069875.1	s__Ideonella sp018069875	81.2328	981	2398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	98.74	98.74	0.92	0.92	2	-
GCF_018069755.1	s__Ideonella sp018069755	81.1404	927	2398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016710065.1	s__Ideonella sp016710065	80.8802	812	2398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	99.07	99.00	0.95	0.93	3	-
GCA_018780145.1	s__Ideonella sp018780145	80.8268	898	2398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213265.1	s__Ideonella sp016213265	80.4894	796	2398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000190375.1	s__Rubrivivax benzoatilyticus	80.1811	719	2398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	99.67	98.73	0.98	0.95	5	-
GCF_000969605.1	s__Aquincola tertiaricarbonis	80.1048	979	2398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000019785.1	s__Leptothrix cholodnii	80.0923	793	2398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Leptothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000284255.1	s__Rubrivivax gelatinosus_A	79.9577	854	2398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	98.28	98.28	0.94	0.94	2	-
GCF_013410775.1	s__Sphaerotilus montanus	79.9021	763	2398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sphaerotilus	95.0	99.98	99.98	1.00	1.00	2	-
GCF_001598255.1	s__Mitsuaria chitosanitabida	79.7576	813	2398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	99.05	99.05	0.96	0.96	2	-
GCF_002761755.1	s__Mitsuaria sp002761755	79.6851	803	2398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342485.1	s__Pelomonas saccharophila	79.6268	866	2398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002205645.1	s__Mitsuaria aquatilis	79.5925	828	2398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213205.1	s__Aquabacterium_A sp016213205	79.4982	871	2398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002205125.1	s__Mitsuaria noduli	79.4504	847	2398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004210455.1	s__Mitsuaria sp004210455	79.4407	776	2398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963005.1	s__Pelomonas sp003963005	79.2878	747	2398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:35,051] [INFO] GTDB search result was written to GCF_021043325.1_ASM2104332v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:35,052] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:35,056] [INFO] DFAST_QC result json was written to GCF_021043325.1_ASM2104332v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:35,056] [INFO] DFAST_QC completed!
[2024-01-24 13:59:35,057] [INFO] Total running time: 0h3m49s