[2024-01-24 13:46:01,284] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:01,288] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:01,288] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f20c9a3-5aed-477a-8c77-da0ac620b3d7/dqc_reference
[2024-01-24 13:46:02,621] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:02,622] [INFO] Task started: Prodigal
[2024-01-24 13:46:02,622] [INFO] Running command: gunzip -c /var/lib/cwl/stg224f39f5-200a-4665-b359-995fc088e3b3/GCF_014930455.1_ASM1493045v1_genomic.fna.gz | prodigal -d GCF_014930455.1_ASM1493045v1_genomic.fna/cds.fna -a GCF_014930455.1_ASM1493045v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:47:01,225] [INFO] Task succeeded: Prodigal
[2024-01-24 13:47:01,226] [INFO] Task started: HMMsearch
[2024-01-24 13:47:01,226] [INFO] Running command: hmmsearch --tblout GCF_014930455.1_ASM1493045v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f20c9a3-5aed-477a-8c77-da0ac620b3d7/dqc_reference/reference_markers.hmm GCF_014930455.1_ASM1493045v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:47:01,634] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:47:01,636] [INFO] Found 6/6 markers.
[2024-01-24 13:47:01,711] [INFO] Query marker FASTA was written to GCF_014930455.1_ASM1493045v1_genomic.fna/markers.fasta
[2024-01-24 13:47:01,711] [INFO] Task started: Blastn
[2024-01-24 13:47:01,711] [INFO] Running command: blastn -query GCF_014930455.1_ASM1493045v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f20c9a3-5aed-477a-8c77-da0ac620b3d7/dqc_reference/reference_markers.fasta -out GCF_014930455.1_ASM1493045v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:02,495] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:02,499] [INFO] Selected 12 target genomes.
[2024-01-24 13:47:02,499] [INFO] Target genome list was writen to GCF_014930455.1_ASM1493045v1_genomic.fna/target_genomes.txt
[2024-01-24 13:47:02,518] [INFO] Task started: fastANI
[2024-01-24 13:47:02,518] [INFO] Running command: fastANI --query /var/lib/cwl/stg224f39f5-200a-4665-b359-995fc088e3b3/GCF_014930455.1_ASM1493045v1_genomic.fna.gz --refList GCF_014930455.1_ASM1493045v1_genomic.fna/target_genomes.txt --output GCF_014930455.1_ASM1493045v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:32,588] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:32,589] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f20c9a3-5aed-477a-8c77-da0ac620b3d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:32,589] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f20c9a3-5aed-477a-8c77-da0ac620b3d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:32,600] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:47:32,600] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:32,600] [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 soli	strain=ZKHCc1 1396	GCA_014930455.1	2710757	2710757	type	True	100.0	3113	3113	95	conclusive
Corallococcus praedator	strain=CA031B	GCA_003612125.1	2316724	2316724	type	True	92.3361	2362	3113	95	below_threshold
Corallococcus terminator	strain=CA054A	GCA_003611635.1	2316733	2316733	type	True	92.1891	2446	3113	95	below_threshold
Corallococcus sicarius	strain=CA040B	GCA_003611735.1	2316726	2316726	type	True	90.3475	2329	3113	95	below_threshold
Corallococcus llansteffanensis	strain=CA051B	GCA_003612055.1	2316731	2316731	type	True	90.3197	2115	3113	95	below_threshold
Corallococcus silvisoli	strain=c25j21	GCA_009909145.1	2697031	2697031	type	True	89.1732	2278	3113	95	below_threshold
Longimicrobium terrae	strain=CB-286315	GCA_013000925.1	1639882	1639882	type	True	75.3315	376	3113	95	below_threshold
Longimicrobium terrae	strain=DSM 29007	GCA_014202995.1	1639882	1639882	type	True	75.3295	378	3113	95	below_threshold
Longimicrobium terrae	strain=CECT 8660	GCA_014198875.1	1639882	1639882	type	True	75.3185	382	3113	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	75.0968	177	3113	95	below_threshold
Ancylobacter aquaticus	strain=DSM 101	GCA_004339465.1	100	100	type	True	75.0406	127	3113	95	below_threshold
Saccharothrix variisporea	strain=DSM 43911	GCA_003634995.1	543527	543527	type	True	75.0208	428	3113	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:32,602] [INFO] DFAST Taxonomy check result was written to GCF_014930455.1_ASM1493045v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:32,603] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:32,603] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:32,603] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f20c9a3-5aed-477a-8c77-da0ac620b3d7/dqc_reference/checkm_data
[2024-01-24 13:47:32,604] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:32,685] [INFO] Task started: CheckM
[2024-01-24 13:47:32,686] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014930455.1_ASM1493045v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014930455.1_ASM1493045v1_genomic.fna/checkm_input GCF_014930455.1_ASM1493045v1_genomic.fna/checkm_result
[2024-01-24 13:51:16,181] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:16,182] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:16,210] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:16,211] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:16,211] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014930455.1_ASM1493045v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:16,212] [INFO] Task started: Blastn
[2024-01-24 13:51:16,212] [INFO] Running command: blastn -query GCF_014930455.1_ASM1493045v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f20c9a3-5aed-477a-8c77-da0ac620b3d7/dqc_reference/reference_markers_gtdb.fasta -out GCF_014930455.1_ASM1493045v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:17,527] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:17,531] [INFO] Selected 8 target genomes.
[2024-01-24 13:51:17,531] [INFO] Target genome list was writen to GCF_014930455.1_ASM1493045v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:17,550] [INFO] Task started: fastANI
[2024-01-24 13:51:17,550] [INFO] Running command: fastANI --query /var/lib/cwl/stg224f39f5-200a-4665-b359-995fc088e3b3/GCF_014930455.1_ASM1493045v1_genomic.fna.gz --refList GCF_014930455.1_ASM1493045v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014930455.1_ASM1493045v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:44,078] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:44,093] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:44,093] [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_014930455.1	s__Corallococcus sp014930455	100.0	3113	3113	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003612115.1	s__Corallococcus sp003612115	92.4192	2448	3113	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	99.04	99.04	0.92	0.92	2	-
GCF_003611635.1	s__Corallococcus terminator	92.1743	2448	3113	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004173515.1	s__Corallococcus sp004173515	91.5283	2270	3113	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003611735.1	s__Corallococcus sicarius	90.3437	2329	3113	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003611675.1	s__Corallococcus sp003611675	90.1657	2228	3113	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009909145.1	s__Corallococcus sp009909145	89.1728	2279	3113	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	99.47	99.47	0.98	0.98	2	-
GCF_017302985.1	s__Corallococcus macrosporus_A	88.8674	2479	3113	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 13:51:44,095] [INFO] GTDB search result was written to GCF_014930455.1_ASM1493045v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:44,095] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:44,100] [INFO] DFAST_QC result json was written to GCF_014930455.1_ASM1493045v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:44,100] [INFO] DFAST_QC completed!
[2024-01-24 13:51:44,100] [INFO] Total running time: 0h5m43s