[2023-06-30 00:10:04,705] [INFO] DFAST_QC pipeline started.
[2023-06-30 00:10:04,708] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 00:10:04,708] [INFO] DQC Reference Directory: /var/lib/cwl/stgdab779a4-7b0d-4633-b370-94ec4a6dd4e9/dqc_reference
[2023-06-30 00:10:06,256] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 00:10:06,262] [INFO] Task started: Prodigal
[2023-06-30 00:10:06,262] [INFO] Running command: gunzip -c /var/lib/cwl/stg6fc00925-699e-458f-8f41-04456f5924fc/GCA_024641965.1_ASM2464196v1_genomic.fna.gz | prodigal -d GCA_024641965.1_ASM2464196v1_genomic.fna/cds.fna -a GCA_024641965.1_ASM2464196v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 00:10:20,101] [INFO] Task succeeded: Prodigal
[2023-06-30 00:10:20,101] [INFO] Task started: HMMsearch
[2023-06-30 00:10:20,101] [INFO] Running command: hmmsearch --tblout GCA_024641965.1_ASM2464196v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdab779a4-7b0d-4633-b370-94ec4a6dd4e9/dqc_reference/reference_markers.hmm GCA_024641965.1_ASM2464196v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 00:10:20,429] [INFO] Task succeeded: HMMsearch
[2023-06-30 00:10:20,431] [INFO] Found 6/6 markers.
[2023-06-30 00:10:20,470] [INFO] Query marker FASTA was written to GCA_024641965.1_ASM2464196v1_genomic.fna/markers.fasta
[2023-06-30 00:10:20,470] [INFO] Task started: Blastn
[2023-06-30 00:10:20,470] [INFO] Running command: blastn -query GCA_024641965.1_ASM2464196v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdab779a4-7b0d-4633-b370-94ec4a6dd4e9/dqc_reference/reference_markers.fasta -out GCA_024641965.1_ASM2464196v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:10:21,521] [INFO] Task succeeded: Blastn
[2023-06-30 00:10:21,525] [INFO] Selected 19 target genomes.
[2023-06-30 00:10:21,526] [INFO] Target genome list was writen to GCA_024641965.1_ASM2464196v1_genomic.fna/target_genomes.txt
[2023-06-30 00:10:21,527] [INFO] Task started: fastANI
[2023-06-30 00:10:21,527] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fc00925-699e-458f-8f41-04456f5924fc/GCA_024641965.1_ASM2464196v1_genomic.fna.gz --refList GCA_024641965.1_ASM2464196v1_genomic.fna/target_genomes.txt --output GCA_024641965.1_ASM2464196v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 00:10:40,684] [INFO] Task succeeded: fastANI
[2023-06-30 00:10:40,684] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdab779a4-7b0d-4633-b370-94ec4a6dd4e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 00:10:40,685] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdab779a4-7b0d-4633-b370-94ec4a6dd4e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 00:10:40,703] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 00:10:40,703] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 00:10:40,704] [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
Rubrivivax benzoatilyticus	strain=JA2	GCA_000420125.1	316997	316997	type	True	80.3748	582	1311	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	80.2965	579	1311	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_016583525.1	28068	28068	suspected-type	True	80.2237	592	1311	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_004340905.1	28068	28068	suspected-type	True	80.1804	604	1311	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	79.7404	539	1311	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	79.7179	543	1311	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_003349825.1	215580	215580	type	True	79.6741	553	1311	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	79.4883	460	1311	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	79.4223	537	1311	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	79.3759	604	1311	95	below_threshold
Sphaerotilus natans	strain=ATCC 13338	GCA_900156335.1	34103	34103	type	True	79.3246	537	1311	95	below_threshold
Sphaerotilus natans subsp. natans	strain=DSM 6575	GCA_000689195.1	882627	34103	type	True	79.3235	527	1311	95	below_threshold
Azohydromonas aeria	strain=CFCC 13393	GCA_009760915.1	2590212	2590212	type	True	79.267	639	1311	95	below_threshold
Azohydromonas australica	strain=DSM 1124	GCA_000430725.1	364039	364039	type	True	79.2377	619	1311	95	below_threshold
Sphaerotilus montanus	strain=HS	GCA_013426955.1	522889	522889	type	True	79.1976	503	1311	95	below_threshold
Sphaerotilus hippei	strain=DSM 566	GCA_003201595.1	744406	744406	type	True	79.1278	502	1311	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	79.119	450	1311	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	78.8401	492	1311	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	78.6189	485	1311	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 00:10:40,710] [INFO] DFAST Taxonomy check result was written to GCA_024641965.1_ASM2464196v1_genomic.fna/tc_result.tsv
[2023-06-30 00:10:40,711] [INFO] ===== Taxonomy check completed =====
[2023-06-30 00:10:40,711] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 00:10:40,712] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdab779a4-7b0d-4633-b370-94ec4a6dd4e9/dqc_reference/checkm_data
[2023-06-30 00:10:40,713] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 00:10:40,765] [INFO] Task started: CheckM
[2023-06-30 00:10:40,765] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024641965.1_ASM2464196v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024641965.1_ASM2464196v1_genomic.fna/checkm_input GCA_024641965.1_ASM2464196v1_genomic.fna/checkm_result
[2023-06-30 00:11:32,917] [INFO] Task succeeded: CheckM
[2023-06-30 00:11:32,918] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.85%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 00:11:32,943] [INFO] ===== Completeness check finished =====
[2023-06-30 00:11:32,943] [INFO] ===== Start GTDB Search =====
[2023-06-30 00:11:32,944] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024641965.1_ASM2464196v1_genomic.fna/markers.fasta)
[2023-06-30 00:11:32,944] [INFO] Task started: Blastn
[2023-06-30 00:11:32,944] [INFO] Running command: blastn -query GCA_024641965.1_ASM2464196v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdab779a4-7b0d-4633-b370-94ec4a6dd4e9/dqc_reference/reference_markers_gtdb.fasta -out GCA_024641965.1_ASM2464196v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:11:34,986] [INFO] Task succeeded: Blastn
[2023-06-30 00:11:34,991] [INFO] Selected 25 target genomes.
[2023-06-30 00:11:34,991] [INFO] Target genome list was writen to GCA_024641965.1_ASM2464196v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 00:11:34,996] [INFO] Task started: fastANI
[2023-06-30 00:11:34,996] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fc00925-699e-458f-8f41-04456f5924fc/GCA_024641965.1_ASM2464196v1_genomic.fna.gz --refList GCA_024641965.1_ASM2464196v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024641965.1_ASM2464196v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 00:12:00,161] [INFO] Task succeeded: fastANI
[2023-06-30 00:12:00,189] [INFO] Found 25 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 00:12:00,189] [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_017302505.1	s__Rubrivivax sp017302505	83.5415	690	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018261815.1	s__Rubrivivax sp018261815	83.1988	725	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302495.1	s__Rubrivivax sp017302495	82.1009	650	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240325.1	s__Rubrivivax sp018240325	81.7914	697	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017983795.1	s__Piscinibacter sp017983795	80.7322	649	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	97.66	96.21	0.89	0.79	4	-
GCA_016719535.1	s__Rubrivivax sp016719535	80.5495	747	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016707445.1	s__Rubrivivax sp016707445	80.4187	674	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	99.23	99.17	0.94	0.91	3	-
GCF_004011805.1	s__Piscinibacter defluvii	80.3974	723	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001725505.1	s__Rubrivivax sp001725505	80.3203	560	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000190375.1	s__Rubrivivax benzoatilyticus	80.2975	579	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	99.67	98.73	0.98	0.95	5	-
GCF_002198735.1	s__Aquabacterium_A sp002198735	80.2274	732	1311	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_017992055.1	s__Aquabacterium_A sp017992055	80.2007	700	1311	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_011391855.1	s__Rubrivivax sp011391855	80.0152	471	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716535.1	s__Rubrivivax sp016716535	79.9789	689	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018971105.1	s__Rubrivivax sp018971105	79.9125	530	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016223165.1	s__Rubrivivax sp016223165	79.8441	741	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014873965.1	s__VBDL01 sp014873965	79.8056	604	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__VBDL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724995.1	s__Rubrivivax sp001724995	79.8047	571	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213205.1	s__Aquabacterium_A sp016213205	79.7677	655	1311	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_013266755.1	s__Aquabacterium_A terrae	79.7264	717	1311	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_004217215.1	s__Rivibacter subsaxonicus	79.6746	534	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rivibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001293525.1	s__Ideonella_A sakaiensis	79.6224	626	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000244995.1	s__Aquabacterium_A sp000244995	79.5662	629	1311	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_005884255.1	s__VBDL01 sp005884255	79.5551	385	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__VBDL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903830565.1	s__CAIKUF01 sp903830565	79.4068	531	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAIKUF01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 00:12:00,191] [INFO] GTDB search result was written to GCA_024641965.1_ASM2464196v1_genomic.fna/result_gtdb.tsv
[2023-06-30 00:12:00,192] [INFO] ===== GTDB Search completed =====
[2023-06-30 00:12:00,197] [INFO] DFAST_QC result json was written to GCA_024641965.1_ASM2464196v1_genomic.fna/dqc_result.json
[2023-06-30 00:12:00,197] [INFO] DFAST_QC completed!
[2023-06-30 00:12:00,197] [INFO] Total running time: 0h1m55s