[2024-01-24 13:48:59,751] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:59,753] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:59,753] [INFO] DQC Reference Directory: /var/lib/cwl/stga4ec750d-b288-4839-94bc-8ab8ad0735c8/dqc_reference
[2024-01-24 13:49:01,093] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:01,093] [INFO] Task started: Prodigal
[2024-01-24 13:49:01,094] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a6201a7-2f8c-4a54-891f-e43f23f6506b/GCF_000255295.1_ASM25529v1_genomic.fna.gz | prodigal -d GCF_000255295.1_ASM25529v1_genomic.fna/cds.fna -a GCF_000255295.1_ASM25529v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:17,482] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:17,483] [INFO] Task started: HMMsearch
[2024-01-24 13:50:17,483] [INFO] Running command: hmmsearch --tblout GCF_000255295.1_ASM25529v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga4ec750d-b288-4839-94bc-8ab8ad0735c8/dqc_reference/reference_markers.hmm GCF_000255295.1_ASM25529v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:17,899] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:17,900] [INFO] Found 6/6 markers.
[2024-01-24 13:50:17,972] [INFO] Query marker FASTA was written to GCF_000255295.1_ASM25529v1_genomic.fna/markers.fasta
[2024-01-24 13:50:17,972] [INFO] Task started: Blastn
[2024-01-24 13:50:17,972] [INFO] Running command: blastn -query GCF_000255295.1_ASM25529v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga4ec750d-b288-4839-94bc-8ab8ad0735c8/dqc_reference/reference_markers.fasta -out GCF_000255295.1_ASM25529v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:18,735] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:18,738] [INFO] Selected 14 target genomes.
[2024-01-24 13:50:18,738] [INFO] Target genome list was writen to GCF_000255295.1_ASM25529v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:18,765] [INFO] Task started: fastANI
[2024-01-24 13:50:18,766] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a6201a7-2f8c-4a54-891f-e43f23f6506b/GCF_000255295.1_ASM25529v1_genomic.fna.gz --refList GCF_000255295.1_ASM25529v1_genomic.fna/target_genomes.txt --output GCF_000255295.1_ASM25529v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:51,102] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:51,103] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga4ec750d-b288-4839-94bc-8ab8ad0735c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:51,103] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga4ec750d-b288-4839-94bc-8ab8ad0735c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:51,117] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:51,117] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:51,117] [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
Corallococcus coralloides	strain=DSM 2259	GCA_000255295.1	184914	184914	type	True	100.0	3360	3360	95	conclusive
Corallococcus exiguus	strain=DSM 14696	GCA_009909105.1	83462	83462	type	True	94.5131	2951	3360	95	below_threshold
Corallococcus interemptor	strain=AB047A	GCA_003668875.1	2316720	2316720	type	True	93.0837	2644	3360	95	below_threshold
Corallococcus aberystwythensis	strain=AB050A	GCA_003612165.1	2316722	2316722	type	True	92.5956	2596	3360	95	below_threshold
Corallococcus carmarthensis	strain=CA043D	GCA_003611695.1	2316728	2316728	type	True	92.5236	2635	3360	95	below_threshold
Corallococcus exercitus	strain=AB043A	GCA_003611585.1	2316736	2316736	type	True	92.4449	2419	3360	95	below_threshold
Corallococcus silvisoli	strain=c25j21	GCA_009909145.1	2697031	2697031	type	True	89.87	2467	3360	95	below_threshold
Corallococcus soli	strain=ZKHCc1 1396	GCA_014930455.1	2710757	2710757	type	True	88.5211	2507	3360	95	below_threshold
Longimicrobium terrae	strain=CB-286315	GCA_013000925.1	1639882	1639882	type	True	75.4507	377	3360	95	below_threshold
Longimicrobium terrae	strain=CECT 8660	GCA_014198875.1	1639882	1639882	type	True	75.3378	376	3360	95	below_threshold
Longimicrobium terrae	strain=DSM 29007	GCA_014202995.1	1639882	1639882	type	True	75.3337	381	3360	95	below_threshold
Ancylobacter rudongensis	strain=CGMCC 1.1761	GCA_900100155.1	177413	177413	type	True	75.0799	166	3360	95	below_threshold
Ancylobacter aquaticus	strain=DSM 101	GCA_004339465.1	100	100	type	True	75.0421	139	3360	95	below_threshold
Saccharothrix tamanrassetensis	strain=CECT 8640	GCA_014203665.1	1051531	1051531	type	True	74.9613	354	3360	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:51,119] [INFO] DFAST Taxonomy check result was written to GCF_000255295.1_ASM25529v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:51,120] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:51,120] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:51,120] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga4ec750d-b288-4839-94bc-8ab8ad0735c8/dqc_reference/checkm_data
[2024-01-24 13:50:51,122] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:51,210] [INFO] Task started: CheckM
[2024-01-24 13:50:51,211] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000255295.1_ASM25529v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000255295.1_ASM25529v1_genomic.fna/checkm_input GCF_000255295.1_ASM25529v1_genomic.fna/checkm_result
[2024-01-24 13:57:17,949] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:17,951] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:17,980] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:17,981] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:17,982] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000255295.1_ASM25529v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:17,983] [INFO] Task started: Blastn
[2024-01-24 13:57:17,983] [INFO] Running command: blastn -query GCF_000255295.1_ASM25529v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga4ec750d-b288-4839-94bc-8ab8ad0735c8/dqc_reference/reference_markers_gtdb.fasta -out GCF_000255295.1_ASM25529v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:19,395] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:19,398] [INFO] Selected 8 target genomes.
[2024-01-24 13:57:19,398] [INFO] Target genome list was writen to GCF_000255295.1_ASM25529v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:19,405] [INFO] Task started: fastANI
[2024-01-24 13:57:19,405] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a6201a7-2f8c-4a54-891f-e43f23f6506b/GCF_000255295.1_ASM25529v1_genomic.fna.gz --refList GCF_000255295.1_ASM25529v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000255295.1_ASM25529v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:45,764] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:45,777] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:45,777] [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_000255295.1	s__Corallococcus coralloides	100.0	3359	3360	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	95.87	95.41	0.89	0.88	6	conclusive
GCF_017309135.1	s__Corallococcus sp017309135	94.5921	2814	3360	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009909105.1	s__Corallococcus exiguus	94.4996	2953	3360	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	97.29	96.40	0.91	0.89	16	-
GCF_003668875.1	s__Corallococcus interemptor	93.0767	2645	3360	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	99.20	99.20	0.95	0.95	2	-
GCF_003612165.1	s__Corallococcus aberystwythensis	92.562	2602	3360	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003611695.1	s__Corallococcus carmarthensis	92.5207	2636	3360	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003611585.1	s__Corallococcus exercitus	92.4634	2416	3360	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	96.95	95.08	0.87	0.82	3	-
GCF_017302985.1	s__Corallococcus macrosporus_A	92.3755	2765	3360	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:45,779] [INFO] GTDB search result was written to GCF_000255295.1_ASM25529v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:45,780] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:45,786] [INFO] DFAST_QC result json was written to GCF_000255295.1_ASM25529v1_genomic.fna/dqc_result.json
[2024-01-24 13:57:45,786] [INFO] DFAST_QC completed!
[2024-01-24 13:57:45,786] [INFO] Total running time: 0h8m46s