[2024-01-24 12:54:39,538] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:54:39,540] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:54:39,540] [INFO] DQC Reference Directory: /var/lib/cwl/stg80e02c95-790e-4895-af09-46493e6058c7/dqc_reference
[2024-01-24 12:54:41,025] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:54:41,026] [INFO] Task started: Prodigal
[2024-01-24 12:54:41,027] [INFO] Running command: gunzip -c /var/lib/cwl/stg1be970c8-f319-4f3c-b648-f6d5e21eae4c/GCF_021277265.1_ASM2127726v1_genomic.fna.gz | prodigal -d GCF_021277265.1_ASM2127726v1_genomic.fna/cds.fna -a GCF_021277265.1_ASM2127726v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:55:10,658] [INFO] Task succeeded: Prodigal
[2024-01-24 12:55:10,658] [INFO] Task started: HMMsearch
[2024-01-24 12:55:10,658] [INFO] Running command: hmmsearch --tblout GCF_021277265.1_ASM2127726v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg80e02c95-790e-4895-af09-46493e6058c7/dqc_reference/reference_markers.hmm GCF_021277265.1_ASM2127726v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:55:11,053] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:55:11,055] [INFO] Found 6/6 markers.
[2024-01-24 12:55:11,124] [INFO] Query marker FASTA was written to GCF_021277265.1_ASM2127726v1_genomic.fna/markers.fasta
[2024-01-24 12:55:11,125] [INFO] Task started: Blastn
[2024-01-24 12:55:11,125] [INFO] Running command: blastn -query GCF_021277265.1_ASM2127726v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg80e02c95-790e-4895-af09-46493e6058c7/dqc_reference/reference_markers.fasta -out GCF_021277265.1_ASM2127726v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:12,469] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:12,473] [INFO] Selected 17 target genomes.
[2024-01-24 12:55:12,473] [INFO] Target genome list was writen to GCF_021277265.1_ASM2127726v1_genomic.fna/target_genomes.txt
[2024-01-24 12:55:12,483] [INFO] Task started: fastANI
[2024-01-24 12:55:12,483] [INFO] Running command: fastANI --query /var/lib/cwl/stg1be970c8-f319-4f3c-b648-f6d5e21eae4c/GCF_021277265.1_ASM2127726v1_genomic.fna.gz --refList GCF_021277265.1_ASM2127726v1_genomic.fna/target_genomes.txt --output GCF_021277265.1_ASM2127726v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:55:32,591] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:32,591] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg80e02c95-790e-4895-af09-46493e6058c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:55:32,592] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg80e02c95-790e-4895-af09-46493e6058c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:55:32,605] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:55:32,605] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:55:32,605] [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
Kineosporia rhizophila	strain=JCM 9960	GCA_021277265.1	84633	84633	type	True	100.0	2729	2733	95	conclusive
Kineosporia corallincola	strain=J2-2	GCA_018499875.1	2835133	2835133	type	True	83.8824	1648	2733	95	below_threshold
Kineosporia mesophila	strain=JCM 16902	GCA_021129235.1	566012	566012	type	True	83.2033	1547	2733	95	below_threshold
Kineococcus indalonis	strain=T90	GCA_009906395.1	2696566	2696566	type	True	77.3478	443	2733	95	below_threshold
Cellulomonas denverensis	strain=ATCC BAA-788	GCA_012396125.1	264297	264297	type	True	77.2214	502	2733	95	below_threshold
Ornithinicoccus hortensis	strain=HKI0125	GCA_009602515.1	82346	82346	type	True	77.2154	388	2733	95	below_threshold
Ornithinicoccus hortensis	strain=DSM 12335	GCA_006716185.1	82346	82346	type	True	77.2092	398	2733	95	below_threshold
Kineococcus rubinsiae	strain=B12	GCA_011839805.1	2609562	2609562	type	True	76.9877	486	2733	95	below_threshold
Kineococcus xinjiangensis	strain=DSM 22857	GCA_002934625.1	512762	512762	type	True	76.9575	496	2733	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	76.8456	363	2733	95	below_threshold
Ornithinimicrobium murale	strain=DSM 22056	GCA_003352835.1	1050153	1050153	type	True	76.7554	233	2733	95	below_threshold
Georgenia thermotolerans	strain=NBRC 104148	GCA_009193185.1	527326	527326	type	True	76.7367	466	2733	95	below_threshold
Pseudokineococcus lusitanus	strain=CECT 7306	GCA_003751265.1	763993	763993	type	True	76.5236	406	2733	95	below_threshold
Streptoalloteichus hindustanus	strain=DSM 44523	GCA_900129375.1	2017	2017	type	True	76.4676	534	2733	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	76.3152	498	2733	95	below_threshold
Kocuria flava	strain=HO-9041	GCA_001482365.1	446860	446860	type	True	76.2957	369	2733	95	below_threshold
Streptomyces xanthii	strain=CRXT-Y-14	GCA_014621695.1	2768069	2768069	type	True	76.1023	556	2733	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:55:32,607] [INFO] DFAST Taxonomy check result was written to GCF_021277265.1_ASM2127726v1_genomic.fna/tc_result.tsv
[2024-01-24 12:55:32,607] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:55:32,607] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:55:32,608] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg80e02c95-790e-4895-af09-46493e6058c7/dqc_reference/checkm_data
[2024-01-24 12:55:32,609] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:55:32,687] [INFO] Task started: CheckM
[2024-01-24 12:55:32,687] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021277265.1_ASM2127726v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021277265.1_ASM2127726v1_genomic.fna/checkm_input GCF_021277265.1_ASM2127726v1_genomic.fna/checkm_result
[2024-01-24 12:57:02,891] [INFO] Task succeeded: CheckM
[2024-01-24 12:57:02,893] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:57:02,920] [INFO] ===== Completeness check finished =====
[2024-01-24 12:57:02,920] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:57:02,921] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021277265.1_ASM2127726v1_genomic.fna/markers.fasta)
[2024-01-24 12:57:02,921] [INFO] Task started: Blastn
[2024-01-24 12:57:02,921] [INFO] Running command: blastn -query GCF_021277265.1_ASM2127726v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg80e02c95-790e-4895-af09-46493e6058c7/dqc_reference/reference_markers_gtdb.fasta -out GCF_021277265.1_ASM2127726v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:57:04,915] [INFO] Task succeeded: Blastn
[2024-01-24 12:57:04,921] [INFO] Selected 18 target genomes.
[2024-01-24 12:57:04,921] [INFO] Target genome list was writen to GCF_021277265.1_ASM2127726v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:57:04,934] [INFO] Task started: fastANI
[2024-01-24 12:57:04,934] [INFO] Running command: fastANI --query /var/lib/cwl/stg1be970c8-f319-4f3c-b648-f6d5e21eae4c/GCF_021277265.1_ASM2127726v1_genomic.fna.gz --refList GCF_021277265.1_ASM2127726v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021277265.1_ASM2127726v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:57:23,264] [INFO] Task succeeded: fastANI
[2024-01-24 12:57:23,282] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:57:23,282] [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_018499875.1	s__Kineosporia sp018499875	83.9428	1638	2733	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineosporiaceae;g__Kineosporia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000719025.1	s__Kineosporia aurantiaca	83.8503	1662	2733	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineosporiaceae;g__Kineosporia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794595.1	s__JADJPO01 sp016794595	77.6158	540	2733	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineosporiaceae;g__JADJPO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716205.1	s__Oryzihumus leptocrescens	77.5978	484	2733	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Oryzihumus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111375.1	s__Pedococcus cremeus	77.3895	456	2733	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	95.41	95.41	0.91	0.91	2	-
GCA_016213575.1	s__R-H-3 sp016213575	77.2803	526	2733	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineosporiaceae;g__R-H-3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806005.1	s__Quadrisphaera sp902806005	77.2502	312	2733	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Quadrisphaeraceae;g__Quadrisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002198675.1	s__R-H-3 sp002198675	77.2477	650	2733	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineosporiaceae;g__R-H-3	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002198655.1	s__R-H-3 sp002198655	77.2448	632	2733	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineosporiaceae;g__R-H-3	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716185.1	s__Ornithinicoccus hortensis	77.2108	398	2733	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinicoccus	95.0	99.99	99.99	1.00	1.00	2	-
GCA_012719445.1	s__JAAYAH01 sp012719445	77.1797	477	2733	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineosporiaceae;g__JAAYAH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011839805.1	s__Kineococcus rubinsiae	77.0019	482	2733	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineococcaceae;g__Kineococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002934625.1	s__Kineococcus xinjiangensis	76.9291	498	2733	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineococcaceae;g__Kineococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003721155.3	s__Marihabitans melonis	76.8191	374	2733	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Marihabitans	95.0	99.04	97.16	0.97	0.90	16	-
GCA_902805925.1	s__Nocardioides sp902805925	76.7843	356	2733	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900016675.1	s__Arthrobacter_B saudimassiliensis	76.7271	345	2733	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008580665.1	s__Zafaria cholistanensis	76.6882	283	2733	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Zafaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129375.1	s__Streptoalloteichus hindustanus	76.4748	532	2733	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Streptoalloteichus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:57:23,285] [INFO] GTDB search result was written to GCF_021277265.1_ASM2127726v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:57:23,285] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:57:23,289] [INFO] DFAST_QC result json was written to GCF_021277265.1_ASM2127726v1_genomic.fna/dqc_result.json
[2024-01-24 12:57:23,289] [INFO] DFAST_QC completed!
[2024-01-24 12:57:23,289] [INFO] Total running time: 0h2m44s