[2024-01-24 10:57:39,033] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:39,035] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:39,035] [INFO] DQC Reference Directory: /var/lib/cwl/stg0888a66d-e6be-459f-9e2e-4a35f88e7477/dqc_reference
[2024-01-24 10:57:40,376] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:40,377] [INFO] Task started: Prodigal
[2024-01-24 10:57:40,377] [INFO] Running command: gunzip -c /var/lib/cwl/stgd83437d0-cd65-43fb-8833-3c46536840b0/GCF_024198255.1_ASM2419825v1_genomic.fna.gz | prodigal -d GCF_024198255.1_ASM2419825v1_genomic.fna/cds.fna -a GCF_024198255.1_ASM2419825v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:36,602] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:36,603] [INFO] Task started: HMMsearch
[2024-01-24 10:58:36,603] [INFO] Running command: hmmsearch --tblout GCF_024198255.1_ASM2419825v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0888a66d-e6be-459f-9e2e-4a35f88e7477/dqc_reference/reference_markers.hmm GCF_024198255.1_ASM2419825v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:37,037] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:37,038] [INFO] Found 6/6 markers.
[2024-01-24 10:58:37,127] [INFO] Query marker FASTA was written to GCF_024198255.1_ASM2419825v1_genomic.fna/markers.fasta
[2024-01-24 10:58:37,128] [INFO] Task started: Blastn
[2024-01-24 10:58:37,128] [INFO] Running command: blastn -query GCF_024198255.1_ASM2419825v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0888a66d-e6be-459f-9e2e-4a35f88e7477/dqc_reference/reference_markers.fasta -out GCF_024198255.1_ASM2419825v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:37,899] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:37,903] [INFO] Selected 15 target genomes.
[2024-01-24 10:58:37,903] [INFO] Target genome list was writen to GCF_024198255.1_ASM2419825v1_genomic.fna/target_genomes.txt
[2024-01-24 10:58:37,934] [INFO] Task started: fastANI
[2024-01-24 10:58:37,935] [INFO] Running command: fastANI --query /var/lib/cwl/stgd83437d0-cd65-43fb-8833-3c46536840b0/GCF_024198255.1_ASM2419825v1_genomic.fna.gz --refList GCF_024198255.1_ASM2419825v1_genomic.fna/target_genomes.txt --output GCF_024198255.1_ASM2419825v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:59:12,580] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:12,581] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0888a66d-e6be-459f-9e2e-4a35f88e7477/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:59:12,582] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0888a66d-e6be-459f-9e2e-4a35f88e7477/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:59:12,600] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:59:12,600] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:59:12,601] [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
Myxococcus fulvus	strain=NBRC 100333	GCA_007991095.1	33	33	type	True	94.5937	3225	3702	95	below_threshold
Myxococcus fulvus	strain=DSM 16525	GCA_900111765.1	33	33	type	True	94.5916	3262	3702	95	below_threshold
Myxococcus eversor	strain=AB053B	GCA_010894455.1	2709661	2709661	type	True	86.8436	2880	3702	95	below_threshold
Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis	strain=AM401	GCA_006636215.1	2590453	2590453	type	True	86.7767	2714	3702	95	below_threshold
Myxococcus stipitatus	strain=DSM 14675	GCA_000331735.1	83455	83455	neotype	True	85.9358	2573	3702	95	below_threshold
Pyxidicoccus caerfyrddinensis	strain=CA032A	GCA_010894405.1	2709663	2709663	type	True	83.7061	2394	3702	95	below_threshold
Myxococcus virescens	strain=DSM 2260	GCA_900101905.1	83456	83456	type	True	83.241	1997	3702	95	below_threshold
Corallococcus silvisoli	strain=c25j21	GCA_009909145.1	2697031	2697031	type	True	82.2156	1879	3702	95	below_threshold
Corallococcus soli	strain=ZKHCc1 1396	GCA_014930455.1	2710757	2710757	type	True	82.1916	1880	3702	95	below_threshold
Azohydromonas lata	strain=NBRC 102462	GCA_001571085.1	45677	45677	type	True	75.0889	394	3702	95	below_threshold
Pseudoduganella namucuonensis	strain=CGMCC 1.11014	GCA_900116645.1	1035707	1035707	type	True	75.0129	367	3702	95	below_threshold
Burkholderia thailandensis	strain=E264	GCA_003568605.1	57975	57975	type	True	74.9335	242	3702	95	below_threshold
Burkholderia thailandensis	strain=E264; ATCC 700388	GCA_000012365.1	57975	57975	type	True	74.9211	248	3702	95	below_threshold
Burkholderia thailandensis	strain=ATCC 700388	GCA_000152285.1	57975	57975	type	True	74.8691	234	3702	95	below_threshold
Dactylosporangium sucinum	strain=JCM 19831	GCA_014647515.1	1424081	1424081	type	True	74.8353	441	3702	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:59:12,602] [INFO] DFAST Taxonomy check result was written to GCF_024198255.1_ASM2419825v1_genomic.fna/tc_result.tsv
[2024-01-24 10:59:12,603] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:59:12,603] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:59:12,603] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0888a66d-e6be-459f-9e2e-4a35f88e7477/dqc_reference/checkm_data
[2024-01-24 10:59:12,604] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:59:12,707] [INFO] Task started: CheckM
[2024-01-24 10:59:12,707] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024198255.1_ASM2419825v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024198255.1_ASM2419825v1_genomic.fna/checkm_input GCF_024198255.1_ASM2419825v1_genomic.fna/checkm_result
[2024-01-24 11:04:42,382] [INFO] Task succeeded: CheckM
[2024-01-24 11:04:42,384] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:04:42,416] [INFO] ===== Completeness check finished =====
[2024-01-24 11:04:42,416] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:04:42,418] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024198255.1_ASM2419825v1_genomic.fna/markers.fasta)
[2024-01-24 11:04:42,419] [INFO] Task started: Blastn
[2024-01-24 11:04:42,419] [INFO] Running command: blastn -query GCF_024198255.1_ASM2419825v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0888a66d-e6be-459f-9e2e-4a35f88e7477/dqc_reference/reference_markers_gtdb.fasta -out GCF_024198255.1_ASM2419825v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:04:43,757] [INFO] Task succeeded: Blastn
[2024-01-24 11:04:43,762] [INFO] Selected 8 target genomes.
[2024-01-24 11:04:43,763] [INFO] Target genome list was writen to GCF_024198255.1_ASM2419825v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:04:43,773] [INFO] Task started: fastANI
[2024-01-24 11:04:43,774] [INFO] Running command: fastANI --query /var/lib/cwl/stgd83437d0-cd65-43fb-8833-3c46536840b0/GCF_024198255.1_ASM2419825v1_genomic.fna.gz --refList GCF_024198255.1_ASM2419825v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024198255.1_ASM2419825v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:05:10,463] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:10,479] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:05:10,480] [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_900111765.1	s__Myxococcus fulvus	94.5977	3261	3702	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	98.03	95.70	0.96	0.91	4	-
GCF_013336725.1	s__Myxococcus sp013336725	86.8655	2891	3702	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	98.23	98.12	0.95	0.94	5	-
GCF_010894455.1	s__Myxococcus eversor	86.8606	2877	3702	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	99.18	99.18	0.94	0.94	2	-
GCF_000331735.1	s__Myxococcus stipitatus	85.9182	2578	3702	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017301635.1	s__Myxococcus sp017301635	85.9098	2566	3702	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010894405.1	s__Myxococcus caerfyrddinensis	83.7004	2395	3702	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017301735.1	s__Myxococcus sp017301735	83.6193	2370	3702	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656495.1	s__Myxococcus sp014656495	83.3934	2071	3702	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:05:10,482] [INFO] GTDB search result was written to GCF_024198255.1_ASM2419825v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:05:10,483] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:05:10,488] [INFO] DFAST_QC result json was written to GCF_024198255.1_ASM2419825v1_genomic.fna/dqc_result.json
[2024-01-24 11:05:10,489] [INFO] DFAST_QC completed!
[2024-01-24 11:05:10,489] [INFO] Total running time: 0h7m31s