[2024-01-24 15:02:07,443] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:07,446] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:07,447] [INFO] DQC Reference Directory: /var/lib/cwl/stg9baa2b14-75cc-4a95-bdb9-d76821392c38/dqc_reference
[2024-01-24 15:02:09,602] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:09,604] [INFO] Task started: Prodigal
[2024-01-24 15:02:09,604] [INFO] Running command: gunzip -c /var/lib/cwl/stgf90ad960-b377-40b5-bd61-132bada972f0/GCF_002930615.1_ASM293061v1_genomic.fna.gz | prodigal -d GCF_002930615.1_ASM293061v1_genomic.fna/cds.fna -a GCF_002930615.1_ASM293061v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:21,897] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:21,898] [INFO] Task started: HMMsearch
[2024-01-24 15:02:21,898] [INFO] Running command: hmmsearch --tblout GCF_002930615.1_ASM293061v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9baa2b14-75cc-4a95-bdb9-d76821392c38/dqc_reference/reference_markers.hmm GCF_002930615.1_ASM293061v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:22,157] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:22,158] [INFO] Found 6/6 markers.
[2024-01-24 15:02:22,191] [INFO] Query marker FASTA was written to GCF_002930615.1_ASM293061v1_genomic.fna/markers.fasta
[2024-01-24 15:02:22,191] [INFO] Task started: Blastn
[2024-01-24 15:02:22,191] [INFO] Running command: blastn -query GCF_002930615.1_ASM293061v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9baa2b14-75cc-4a95-bdb9-d76821392c38/dqc_reference/reference_markers.fasta -out GCF_002930615.1_ASM293061v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:23,302] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:23,309] [INFO] Selected 15 target genomes.
[2024-01-24 15:02:23,310] [INFO] Target genome list was writen to GCF_002930615.1_ASM293061v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:23,316] [INFO] Task started: fastANI
[2024-01-24 15:02:23,316] [INFO] Running command: fastANI --query /var/lib/cwl/stgf90ad960-b377-40b5-bd61-132bada972f0/GCF_002930615.1_ASM293061v1_genomic.fna.gz --refList GCF_002930615.1_ASM293061v1_genomic.fna/target_genomes.txt --output GCF_002930615.1_ASM293061v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:38,952] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:38,953] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9baa2b14-75cc-4a95-bdb9-d76821392c38/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:38,953] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9baa2b14-75cc-4a95-bdb9-d76821392c38/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:38,965] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:02:38,965] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:02:38,966] [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
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_003349825.1	215580	215580	type	True	82.0384	697	1199	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	82.024	690	1199	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	81.9714	706	1199	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	80.2919	554	1199	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	80.2407	660	1199	95	below_threshold
Azohydromonas australica	strain=DSM 1124	GCA_000430725.1	364039	364039	type	True	80.1512	610	1199	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	80.0973	591	1199	95	below_threshold
Sphaerotilus hippei	strain=DSM 566	GCA_003201595.1	744406	744406	type	True	80.0833	527	1199	95	below_threshold
Azohydromonas lata	strain=NBRC 102462	GCA_001571085.1	45677	45677	type	True	79.9384	570	1199	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	79.8332	513	1199	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	79.6115	489	1199	95	below_threshold
Rhizobacter gummiphilus	strain=NBRC 109400	GCA_002762215.1	946333	946333	type	True	79.5937	593	1199	95	below_threshold
Aquabacterium commune	strain=DSM 11901	GCA_004362855.1	70586	70586	type	True	79.5713	479	1199	95	below_threshold
Mitsuaria chitinivorans	strain=HWN-4	GCA_002761755.1	2917965	2917965	type	True	79.3175	510	1199	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	79.3075	511	1199	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:38,967] [INFO] DFAST Taxonomy check result was written to GCF_002930615.1_ASM293061v1_genomic.fna/tc_result.tsv
[2024-01-24 15:02:38,968] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:38,968] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:38,968] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9baa2b14-75cc-4a95-bdb9-d76821392c38/dqc_reference/checkm_data
[2024-01-24 15:02:38,969] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:39,008] [INFO] Task started: CheckM
[2024-01-24 15:02:39,008] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002930615.1_ASM293061v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002930615.1_ASM293061v1_genomic.fna/checkm_input GCF_002930615.1_ASM293061v1_genomic.fna/checkm_result
[2024-01-24 15:04:02,744] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:02,745] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:02,762] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:02,762] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:02,763] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002930615.1_ASM293061v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:02,763] [INFO] Task started: Blastn
[2024-01-24 15:04:02,763] [INFO] Running command: blastn -query GCF_002930615.1_ASM293061v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9baa2b14-75cc-4a95-bdb9-d76821392c38/dqc_reference/reference_markers_gtdb.fasta -out GCF_002930615.1_ASM293061v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:05,039] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:05,043] [INFO] Selected 17 target genomes.
[2024-01-24 15:04:05,043] [INFO] Target genome list was writen to GCF_002930615.1_ASM293061v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:05,056] [INFO] Task started: fastANI
[2024-01-24 15:04:05,057] [INFO] Running command: fastANI --query /var/lib/cwl/stgf90ad960-b377-40b5-bd61-132bada972f0/GCF_002930615.1_ASM293061v1_genomic.fna.gz --refList GCF_002930615.1_ASM293061v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002930615.1_ASM293061v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:24,316] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:24,331] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:24,331] [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_002930615.1	s__Zhizhongheella caldifontis	100.0	1199	1199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Zhizhongheella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000381125.1	s__Caldimonas manganoxidans	83.1542	821	1199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caldimonas	95.0	98.73	98.73	0.91	0.91	2	-
GCF_015476235.1	s__Schlegelella thermodepolymerans	81.9868	706	1199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Schlegelella	95.0	99.89	99.68	0.98	0.95	4	-
GCF_004011805.1	s__Piscinibacter defluvii	81.0836	706	1199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006386545.1	s__Pseudorivibacter rhizosphaerae	80.9356	679	1199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudorivibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003569765.1	s__Aquabacterium_B tepidiphilum	80.9346	621	1199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017983795.1	s__Piscinibacter sp017983795	80.7288	626	1199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	97.66	96.21	0.89	0.79	4	-
GCA_003265685.1	s__Piscinibacter caeni	80.4487	666	1199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302485.1	s__Ideonella sp017302485	80.2825	423	1199	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	80.2627	611	1199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	98.74	98.74	0.92	0.92	2	-
GCA_001017435.1	s__Polyangium_A brachysporum	80.2357	661	1199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polyangium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017992055.1	s__Aquabacterium_A sp017992055	80.0688	644	1199	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_016213265.1	s__Ideonella sp016213265	79.9713	551	1199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001571085.1	s__Azohydromonas lata	79.9587	568	1199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Azohydromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000015725.1	s__Methylibium petroleiphilum	79.9376	586	1199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Methylibium	95.0	96.91	96.03	0.83	0.81	5	-
GCF_900113225.1	s__Mitsuaria sp900113225	79.4563	542	1199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	98.36	98.28	0.95	0.95	4	-
GCA_002205125.1	s__Mitsuaria noduli	79.1571	513	1199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:04:24,333] [INFO] GTDB search result was written to GCF_002930615.1_ASM293061v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:24,333] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:24,338] [INFO] DFAST_QC result json was written to GCF_002930615.1_ASM293061v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:24,338] [INFO] DFAST_QC completed!
[2024-01-24 15:04:24,339] [INFO] Total running time: 0h2m17s