[2023-06-28 14:18:54,785] [INFO] DFAST_QC pipeline started.
[2023-06-28 14:18:54,787] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 14:18:54,787] [INFO] DQC Reference Directory: /var/lib/cwl/stg338a671d-6db4-4bd9-a761-f25ee3890f2e/dqc_reference
[2023-06-28 14:18:55,909] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 14:18:55,909] [INFO] Task started: Prodigal
[2023-06-28 14:18:55,909] [INFO] Running command: gunzip -c /var/lib/cwl/stgd3b6f633-d3ea-4d84-a65d-47eeb56eeba4/GCA_913777445.1_SP266_1_metabat2_genome_mining.36_genomic.fna.gz | prodigal -d GCA_913777445.1_SP266_1_metabat2_genome_mining.36_genomic.fna/cds.fna -a GCA_913777445.1_SP266_1_metabat2_genome_mining.36_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 14:19:01,928] [INFO] Task succeeded: Prodigal
[2023-06-28 14:19:01,928] [INFO] Task started: HMMsearch
[2023-06-28 14:19:01,928] [INFO] Running command: hmmsearch --tblout GCA_913777445.1_SP266_1_metabat2_genome_mining.36_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg338a671d-6db4-4bd9-a761-f25ee3890f2e/dqc_reference/reference_markers.hmm GCA_913777445.1_SP266_1_metabat2_genome_mining.36_genomic.fna/protein.faa > /dev/null
[2023-06-28 14:19:02,159] [INFO] Task succeeded: HMMsearch
[2023-06-28 14:19:02,160] [INFO] Found 6/6 markers.
[2023-06-28 14:19:02,191] [INFO] Query marker FASTA was written to GCA_913777445.1_SP266_1_metabat2_genome_mining.36_genomic.fna/markers.fasta
[2023-06-28 14:19:02,191] [INFO] Task started: Blastn
[2023-06-28 14:19:02,191] [INFO] Running command: blastn -query GCA_913777445.1_SP266_1_metabat2_genome_mining.36_genomic.fna/markers.fasta -db /var/lib/cwl/stg338a671d-6db4-4bd9-a761-f25ee3890f2e/dqc_reference/reference_markers.fasta -out GCA_913777445.1_SP266_1_metabat2_genome_mining.36_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 14:19:02,734] [INFO] Task succeeded: Blastn
[2023-06-28 14:19:02,740] [INFO] Selected 11 target genomes.
[2023-06-28 14:19:02,740] [INFO] Target genome list was writen to GCA_913777445.1_SP266_1_metabat2_genome_mining.36_genomic.fna/target_genomes.txt
[2023-06-28 14:19:02,743] [INFO] Task started: fastANI
[2023-06-28 14:19:02,743] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3b6f633-d3ea-4d84-a65d-47eeb56eeba4/GCA_913777445.1_SP266_1_metabat2_genome_mining.36_genomic.fna.gz --refList GCA_913777445.1_SP266_1_metabat2_genome_mining.36_genomic.fna/target_genomes.txt --output GCA_913777445.1_SP266_1_metabat2_genome_mining.36_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 14:19:10,938] [INFO] Task succeeded: fastANI
[2023-06-28 14:19:10,938] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg338a671d-6db4-4bd9-a761-f25ee3890f2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 14:19:10,939] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg338a671d-6db4-4bd9-a761-f25ee3890f2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 14:19:10,946] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 14:19:10,946] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 14:19:10,946] [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
Exiguobacterium enclense	strain=NIO-1109	GCA_001456895.1	1017277	1017277	type	True	93.739	838	874	95	below_threshold
Exiguobacterium enclense	strain=NIO-1109	GCA_900096925.1	1017277	1017277	type	True	93.739	838	874	95	below_threshold
Exiguobacterium indicum	strain=HHS 31	GCA_001939065.1	296995	296995	type	True	93.7134	843	874	95	below_threshold
Exiguobacterium acetylicum	strain=DSM 20416	GCA_000702605.1	41170	41170	suspected-type	True	92.2711	804	874	95	below_threshold
Exiguobacterium oxidotolerans	strain=JCM 12280	GCA_000702625.1	223958	223958	type	True	81.2085	502	874	95	below_threshold
Exiguobacterium undae	strain=DSM 14481	GCA_000620805.1	169177	169177	type	True	81.0592	514	874	95	below_threshold
Exiguobacterium artemiae	strain=9AN	GCA_025234645.1	340145	340145	type	True	80.9998	457	874	95	below_threshold
Exiguobacterium aestuarii	strain=TF_16	GCA_025234735.1	273527	273527	type	True	77.3252	119	874	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 14:19:10,948] [INFO] DFAST Taxonomy check result was written to GCA_913777445.1_SP266_1_metabat2_genome_mining.36_genomic.fna/tc_result.tsv
[2023-06-28 14:19:10,949] [INFO] ===== Taxonomy check completed =====
[2023-06-28 14:19:10,949] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 14:19:10,949] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg338a671d-6db4-4bd9-a761-f25ee3890f2e/dqc_reference/checkm_data
[2023-06-28 14:19:10,950] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 14:19:10,981] [INFO] Task started: CheckM
[2023-06-28 14:19:10,982] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913777445.1_SP266_1_metabat2_genome_mining.36_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913777445.1_SP266_1_metabat2_genome_mining.36_genomic.fna/checkm_input GCA_913777445.1_SP266_1_metabat2_genome_mining.36_genomic.fna/checkm_result
[2023-06-28 14:19:34,451] [INFO] Task succeeded: CheckM
[2023-06-28 14:19:34,452] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 14:19:34,471] [INFO] ===== Completeness check finished =====
[2023-06-28 14:19:34,471] [INFO] ===== Start GTDB Search =====
[2023-06-28 14:19:34,472] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913777445.1_SP266_1_metabat2_genome_mining.36_genomic.fna/markers.fasta)
[2023-06-28 14:19:34,472] [INFO] Task started: Blastn
[2023-06-28 14:19:34,472] [INFO] Running command: blastn -query GCA_913777445.1_SP266_1_metabat2_genome_mining.36_genomic.fna/markers.fasta -db /var/lib/cwl/stg338a671d-6db4-4bd9-a761-f25ee3890f2e/dqc_reference/reference_markers_gtdb.fasta -out GCA_913777445.1_SP266_1_metabat2_genome_mining.36_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 14:19:35,189] [INFO] Task succeeded: Blastn
[2023-06-28 14:19:35,192] [INFO] Selected 10 target genomes.
[2023-06-28 14:19:35,192] [INFO] Target genome list was writen to GCA_913777445.1_SP266_1_metabat2_genome_mining.36_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 14:19:35,194] [INFO] Task started: fastANI
[2023-06-28 14:19:35,195] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3b6f633-d3ea-4d84-a65d-47eeb56eeba4/GCA_913777445.1_SP266_1_metabat2_genome_mining.36_genomic.fna.gz --refList GCA_913777445.1_SP266_1_metabat2_genome_mining.36_genomic.fna/target_genomes_gtdb.txt --output GCA_913777445.1_SP266_1_metabat2_genome_mining.36_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 14:19:41,758] [INFO] Task succeeded: fastANI
[2023-06-28 14:19:41,765] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 14:19:41,766] [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_001939065.1	s__Exiguobacterium_A indicum	93.7134	843	874	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium_A	95.0	96.62	95.33	0.92	0.89	22	-
GCF_000702605.1	s__Exiguobacterium_A acetylicum	92.2801	803	874	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium_A	95.0	97.66	95.06	0.95	0.91	10	-
GCF_001423965.1	s__Exiguobacterium_A sp001423965	91.3757	786	874	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium_A	95.0	97.21	96.36	0.96	0.93	17	-
GCF_001275385.1	s__Exiguobacterium_A sp001275385	89.9524	825	874	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000702625.1	s__Exiguobacterium_A oxidotolerans	81.2136	501	874	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium_A	95.0	95.91	95.68	0.90	0.87	15	-
GCF_000620805.1	s__Exiguobacterium_A undae	81.0462	515	874	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium_A	95.0	97.90	97.06	0.95	0.92	5	-
GCF_018618755.1	s__Exiguobacterium_A sp018618755	81.0087	506	874	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003339585.1	s__Exiguobacterium_A sp003339585	80.9957	508	874	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620865.1	s__Exiguobacterium_A sibiricum_A	80.9468	502	874	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001870785.1	s__Exiguobacterium_A sp001870785	80.7327	497	874	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 14:19:41,769] [INFO] GTDB search result was written to GCA_913777445.1_SP266_1_metabat2_genome_mining.36_genomic.fna/result_gtdb.tsv
[2023-06-28 14:19:41,769] [INFO] ===== GTDB Search completed =====
[2023-06-28 14:19:41,772] [INFO] DFAST_QC result json was written to GCA_913777445.1_SP266_1_metabat2_genome_mining.36_genomic.fna/dqc_result.json
[2023-06-28 14:19:41,772] [INFO] DFAST_QC completed!
[2023-06-28 14:19:41,772] [INFO] Total running time: 0h0m47s