[2023-06-29 14:27:03,860] [INFO] DFAST_QC pipeline started.
[2023-06-29 14:27:03,862] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 14:27:03,862] [INFO] DQC Reference Directory: /var/lib/cwl/stgf9eaf7a9-7294-4e75-a02d-86ecfedbdbfd/dqc_reference
[2023-06-29 14:27:05,362] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 14:27:05,363] [INFO] Task started: Prodigal
[2023-06-29 14:27:05,363] [INFO] Running command: gunzip -c /var/lib/cwl/stgd553aff6-91af-4072-bd9b-bd94949b7bd5/GCA_021767665.1_ASM2176766v1_genomic.fna.gz | prodigal -d GCA_021767665.1_ASM2176766v1_genomic.fna/cds.fna -a GCA_021767665.1_ASM2176766v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 14:27:11,496] [INFO] Task succeeded: Prodigal
[2023-06-29 14:27:11,496] [INFO] Task started: HMMsearch
[2023-06-29 14:27:11,497] [INFO] Running command: hmmsearch --tblout GCA_021767665.1_ASM2176766v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf9eaf7a9-7294-4e75-a02d-86ecfedbdbfd/dqc_reference/reference_markers.hmm GCA_021767665.1_ASM2176766v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 14:27:11,732] [INFO] Task succeeded: HMMsearch
[2023-06-29 14:27:11,733] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd553aff6-91af-4072-bd9b-bd94949b7bd5/GCA_021767665.1_ASM2176766v1_genomic.fna.gz]
[2023-06-29 14:27:11,758] [INFO] Query marker FASTA was written to GCA_021767665.1_ASM2176766v1_genomic.fna/markers.fasta
[2023-06-29 14:27:11,758] [INFO] Task started: Blastn
[2023-06-29 14:27:11,759] [INFO] Running command: blastn -query GCA_021767665.1_ASM2176766v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9eaf7a9-7294-4e75-a02d-86ecfedbdbfd/dqc_reference/reference_markers.fasta -out GCA_021767665.1_ASM2176766v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:27:12,444] [INFO] Task succeeded: Blastn
[2023-06-29 14:27:12,448] [INFO] Selected 27 target genomes.
[2023-06-29 14:27:12,448] [INFO] Target genome list was writen to GCA_021767665.1_ASM2176766v1_genomic.fna/target_genomes.txt
[2023-06-29 14:27:12,449] [INFO] Task started: fastANI
[2023-06-29 14:27:12,450] [INFO] Running command: fastANI --query /var/lib/cwl/stgd553aff6-91af-4072-bd9b-bd94949b7bd5/GCA_021767665.1_ASM2176766v1_genomic.fna.gz --refList GCA_021767665.1_ASM2176766v1_genomic.fna/target_genomes.txt --output GCA_021767665.1_ASM2176766v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 14:27:29,916] [INFO] Task succeeded: fastANI
[2023-06-29 14:27:29,916] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf9eaf7a9-7294-4e75-a02d-86ecfedbdbfd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 14:27:29,916] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf9eaf7a9-7294-4e75-a02d-86ecfedbdbfd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 14:27:29,925] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 14:27:29,926] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 14:27:29,926] [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
Ketobacter alkanivorans	strain=GI5	GCA_002863865.1	1917421	1917421	type	True	77.431	139	572	95	below_threshold
Alcanivorax venustensis	strain=ISO4	GCA_015356855.1	172371	172371	type	True	76.851	56	572	95	below_threshold
Alcanivorax profundimaris	strain=ST75FaO-1	GCA_015265435.1	2735259	2735259	type	True	76.82	67	572	95	below_threshold
Alcanivorax gelatiniphagus	strain=MEBiC 08158	GCA_005938655.1	1194167	1194167	type	True	76.5485	67	572	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 14:27:29,929] [INFO] DFAST Taxonomy check result was written to GCA_021767665.1_ASM2176766v1_genomic.fna/tc_result.tsv
[2023-06-29 14:27:29,930] [INFO] ===== Taxonomy check completed =====
[2023-06-29 14:27:29,930] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 14:27:29,930] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf9eaf7a9-7294-4e75-a02d-86ecfedbdbfd/dqc_reference/checkm_data
[2023-06-29 14:27:29,932] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 14:27:29,961] [INFO] Task started: CheckM
[2023-06-29 14:27:29,961] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021767665.1_ASM2176766v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021767665.1_ASM2176766v1_genomic.fna/checkm_input GCA_021767665.1_ASM2176766v1_genomic.fna/checkm_result
[2023-06-29 14:27:54,472] [INFO] Task succeeded: CheckM
[2023-06-29 14:27:54,473] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 31.02%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 14:27:54,495] [INFO] ===== Completeness check finished =====
[2023-06-29 14:27:54,495] [INFO] ===== Start GTDB Search =====
[2023-06-29 14:27:54,495] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021767665.1_ASM2176766v1_genomic.fna/markers.fasta)
[2023-06-29 14:27:54,496] [INFO] Task started: Blastn
[2023-06-29 14:27:54,496] [INFO] Running command: blastn -query GCA_021767665.1_ASM2176766v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9eaf7a9-7294-4e75-a02d-86ecfedbdbfd/dqc_reference/reference_markers_gtdb.fasta -out GCA_021767665.1_ASM2176766v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:27:55,481] [INFO] Task succeeded: Blastn
[2023-06-29 14:27:55,486] [INFO] Selected 14 target genomes.
[2023-06-29 14:27:55,486] [INFO] Target genome list was writen to GCA_021767665.1_ASM2176766v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 14:27:55,491] [INFO] Task started: fastANI
[2023-06-29 14:27:55,491] [INFO] Running command: fastANI --query /var/lib/cwl/stgd553aff6-91af-4072-bd9b-bd94949b7bd5/GCA_021767665.1_ASM2176766v1_genomic.fna.gz --refList GCA_021767665.1_ASM2176766v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021767665.1_ASM2176766v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 14:28:04,796] [INFO] Task succeeded: fastANI
[2023-06-29 14:28:04,808] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 14:28:04,808] [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_002701845.1	s__Ketobacter sp002701845	99.3768	550	572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ketobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003671495.1	s__Ketobacter sp003671495	78.3656	254	572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ketobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002708905.1	s__Ketobacter sp002708905	77.7217	190	572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ketobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002471665.1	s__Ketobacter sp002471665	77.6771	225	572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ketobacter	95.0	99.82	99.43	0.96	0.93	14	-
GCF_002863865.1	s__Ketobacter alkanivorans	77.431	139	572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ketobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013178375.1	s__Ch67 sp013178375	77.0868	126	572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ch67	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015356855.1	s__Alcanivorax venustensis	76.851	56	572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.73	95.38	0.91	0.87	46	-
GCF_005938655.1	s__Alcanivorax gelatiniphagus	76.5485	67	572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.53	98.53	0.93	0.93	3	-
--------------------------------------------------------------------------------
[2023-06-29 14:28:04,810] [INFO] GTDB search result was written to GCA_021767665.1_ASM2176766v1_genomic.fna/result_gtdb.tsv
[2023-06-29 14:28:04,811] [INFO] ===== GTDB Search completed =====
[2023-06-29 14:28:04,813] [INFO] DFAST_QC result json was written to GCA_021767665.1_ASM2176766v1_genomic.fna/dqc_result.json
[2023-06-29 14:28:04,813] [INFO] DFAST_QC completed!
[2023-06-29 14:28:04,813] [INFO] Total running time: 0h1m1s