[2023-06-13 14:05:32,551] [INFO] DFAST_QC pipeline started.
[2023-06-13 14:05:32,555] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 14:05:32,555] [INFO] DQC Reference Directory: /var/lib/cwl/stg4bb073fb-5507-4b03-9d51-b99ddbfad76c/dqc_reference
[2023-06-13 14:05:34,944] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 14:05:34,945] [INFO] Task started: Prodigal
[2023-06-13 14:05:34,945] [INFO] Running command: gunzip -c /var/lib/cwl/stg0a303189-907d-44aa-922e-673a57c7cd94/GCA_022708845.1_ASM2270884v1_genomic.fna.gz | prodigal -d GCA_022708845.1_ASM2270884v1_genomic.fna/cds.fna -a GCA_022708845.1_ASM2270884v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 14:05:43,520] [INFO] Task succeeded: Prodigal
[2023-06-13 14:05:43,520] [INFO] Task started: HMMsearch
[2023-06-13 14:05:43,521] [INFO] Running command: hmmsearch --tblout GCA_022708845.1_ASM2270884v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4bb073fb-5507-4b03-9d51-b99ddbfad76c/dqc_reference/reference_markers.hmm GCA_022708845.1_ASM2270884v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 14:05:43,778] [INFO] Task succeeded: HMMsearch
[2023-06-13 14:05:43,780] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0a303189-907d-44aa-922e-673a57c7cd94/GCA_022708845.1_ASM2270884v1_genomic.fna.gz]
[2023-06-13 14:05:43,812] [INFO] Query marker FASTA was written to GCA_022708845.1_ASM2270884v1_genomic.fna/markers.fasta
[2023-06-13 14:05:43,813] [INFO] Task started: Blastn
[2023-06-13 14:05:43,813] [INFO] Running command: blastn -query GCA_022708845.1_ASM2270884v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4bb073fb-5507-4b03-9d51-b99ddbfad76c/dqc_reference/reference_markers.fasta -out GCA_022708845.1_ASM2270884v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:05:44,602] [INFO] Task succeeded: Blastn
[2023-06-13 14:05:44,607] [INFO] Selected 30 target genomes.
[2023-06-13 14:05:44,608] [INFO] Target genome list was writen to GCA_022708845.1_ASM2270884v1_genomic.fna/target_genomes.txt
[2023-06-13 14:05:44,641] [INFO] Task started: fastANI
[2023-06-13 14:05:44,641] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a303189-907d-44aa-922e-673a57c7cd94/GCA_022708845.1_ASM2270884v1_genomic.fna.gz --refList GCA_022708845.1_ASM2270884v1_genomic.fna/target_genomes.txt --output GCA_022708845.1_ASM2270884v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 14:06:10,436] [INFO] Task succeeded: fastANI
[2023-06-13 14:06:10,437] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4bb073fb-5507-4b03-9d51-b99ddbfad76c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 14:06:10,438] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4bb073fb-5507-4b03-9d51-b99ddbfad76c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 14:06:10,463] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 14:06:10,463] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 14:06:10,463] [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
Pseudokineococcus marinus	strain=JCM 14547	GCA_013004605.1	351215	351215	type	True	76.6518	73	808	95	below_threshold
Motilibacter deserti	strain=E257	GCA_011250635.1	2714956	2714956	type	True	76.6343	99	808	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	76.6033	99	808	95	below_threshold
Motilibacter aurantiacus	strain=K478	GCA_011250645.1	2714955	2714955	type	True	76.5937	118	808	95	below_threshold
Nocardioides soli	strain=DSM 105498	GCA_014191495.1	1036020	1036020	type	True	76.5597	120	808	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	76.5423	117	808	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	76.5295	111	808	95	below_threshold
Kineococcus indalonis	strain=T90	GCA_009906395.1	2696566	2696566	type	True	76.4337	86	808	95	below_threshold
Streptomyces griseoruber	strain=NRRL B-1818	GCA_001418585.1	1943	1943	type	True	76.378	112	808	95	below_threshold
Peterkaempfera bronchialis	strain=DSM 106435	GCA_003258605.2	2126346	2126346	type	True	76.3698	115	808	95	below_threshold
Kribbella flavida	strain=DSM 17836	GCA_000024345.1	182640	182640	type	True	76.3575	122	808	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	76.35	131	808	95	below_threshold
Cellulomonas hominis	strain=DSM 9581	GCA_014201095.1	156981	156981	suspected-type	True	76.3372	102	808	95	below_threshold
Streptomyces griseoruber	strain=DSM 40281	GCA_001514205.1	1943	1943	type	True	76.3091	122	808	95	below_threshold
Curtobacterium flaccumfaciens	strain=LMG3645	GCA_024997845.1	2035	2035	suspected-type	True	76.3021	53	808	95	below_threshold
Streptomyces zhihengii	strain=YIM T102	GCA_016919245.1	1818004	1818004	type	True	76.3004	129	808	95	below_threshold
Actinomadura barringtoniae	strain=GKU 128	GCA_017573505.1	1427535	1427535	type	True	76.2761	126	808	95	below_threshold
Microtetraspora niveoalba	strain=NBRC 15239	GCA_001570405.1	46175	46175	type	True	76.2304	119	808	95	below_threshold
Planobispora siamensis	strain=NBRC 107568	GCA_016863175.1	936338	936338	type	True	76.2084	130	808	95	below_threshold
Kineococcus siccus	strain=R8	GCA_009906795.1	2696567	2696567	type	True	76.1789	93	808	95	below_threshold
Phycicoccus flavus	strain=CMS6Z-2	GCA_004025965.2	2502783	2502783	type	True	76.1573	115	808	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	76.1493	117	808	95	below_threshold
Planobispora takensis	strain=NBRC 109077	GCA_016863195.1	1367882	1367882	type	True	76.1396	136	808	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	76.0824	137	808	95	below_threshold
Kineococcus rhizosphaerae	strain=DSM 19711	GCA_003002055.1	559628	559628	type	True	76.0101	109	808	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	75.9384	72	808	95	below_threshold
Amycolatopsis thailandensis	strain=JCM 16380	GCA_002234405.1	589330	589330	type	True	75.9365	102	808	95	below_threshold
Dactylosporangium sucinum	strain=JCM 19831	GCA_014647515.1	1424081	1424081	type	True	75.8016	154	808	95	below_threshold
Leucobacter massiliensis	strain=122RC15	GCA_002982315.1	1686285	1686285	type	True	75.7806	64	808	95	below_threshold
Phytoactinopolyspora halophila	strain=YIM 96934	GCA_003287285.1	1981511	1981511	type	True	75.5513	55	808	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 14:06:10,465] [INFO] DFAST Taxonomy check result was written to GCA_022708845.1_ASM2270884v1_genomic.fna/tc_result.tsv
[2023-06-13 14:06:10,466] [INFO] ===== Taxonomy check completed =====
[2023-06-13 14:06:10,466] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 14:06:10,466] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4bb073fb-5507-4b03-9d51-b99ddbfad76c/dqc_reference/checkm_data
[2023-06-13 14:06:10,467] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 14:06:10,506] [INFO] Task started: CheckM
[2023-06-13 14:06:10,507] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022708845.1_ASM2270884v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022708845.1_ASM2270884v1_genomic.fna/checkm_input GCA_022708845.1_ASM2270884v1_genomic.fna/checkm_result
[2023-06-13 14:06:41,980] [INFO] Task succeeded: CheckM
[2023-06-13 14:06:41,981] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 6.25%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 14:06:42,013] [INFO] ===== Completeness check finished =====
[2023-06-13 14:06:42,014] [INFO] ===== Start GTDB Search =====
[2023-06-13 14:06:42,014] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022708845.1_ASM2270884v1_genomic.fna/markers.fasta)
[2023-06-13 14:06:42,015] [INFO] Task started: Blastn
[2023-06-13 14:06:42,015] [INFO] Running command: blastn -query GCA_022708845.1_ASM2270884v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4bb073fb-5507-4b03-9d51-b99ddbfad76c/dqc_reference/reference_markers_gtdb.fasta -out GCA_022708845.1_ASM2270884v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:06:43,213] [INFO] Task succeeded: Blastn
[2023-06-13 14:06:43,218] [INFO] Selected 25 target genomes.
[2023-06-13 14:06:43,219] [INFO] Target genome list was writen to GCA_022708845.1_ASM2270884v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 14:06:43,380] [INFO] Task started: fastANI
[2023-06-13 14:06:43,380] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a303189-907d-44aa-922e-673a57c7cd94/GCA_022708845.1_ASM2270884v1_genomic.fna.gz --refList GCA_022708845.1_ASM2270884v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022708845.1_ASM2270884v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 14:07:05,801] [INFO] Task succeeded: fastANI
[2023-06-13 14:07:05,838] [INFO] Found 25 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 14:07:05,839] [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
GCA_016703125.1	s__JADKAV01 sp016703125	80.2165	439	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__UBA10799;g__JADKAV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719135.1	s__JADKAV01 sp016719135	79.2802	330	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__UBA10799;g__JADKAV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125335.1	s__WLRQ01 sp016125335	76.8756	169	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__CAIYMF01;g__WLRQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016717115.1	s__UBA10649 sp016717115	76.7941	106	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011250565.1	s__Nocardioides sp011250565	76.7311	113	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002117935.1	s__Nocardioides sp002117935	76.64	119	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	0.99	0.99	2	-
GCF_013004605.1	s__Pseudokineococcus marinus	76.627	74	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Quadrisphaeraceae;g__Pseudokineococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018970025.1	s__REEB460 sp018970025	76.5818	83	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__REEB460	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428125.1	s__Nocardioides sp001428125	76.5726	105	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001646665.1	s__Streptomyces albulus_A	76.5253	114	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001429625.1	s__Nocardioides sp001429625	76.3916	117	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002729525.1	s__Nocardioides sp002729525	76.3672	108	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019039255.1	s__JABFXA01 sp019039255	76.3478	130	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__JABFXA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001514205.1	s__Streptomyces griseoruber	76.3091	122	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016919245.1	s__Streptomyces zhihengii	76.3004	129	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017573505.1	s__Spirillospora barringtoniae	76.2761	126	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015390235.1	s__Quadrisphaera sp015390235	76.2685	83	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Quadrisphaeraceae;g__Quadrisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570405.1	s__Microtetraspora niveoalba	76.2304	119	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microtetraspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009733795.1	s__Pseudactinotalea caeni	76.0704	106	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Pseudactinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003594875.1	s__Bailinhaonella thermotolerans	76.0157	130	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Bailinhaonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002055.1	s__Kineococcus rhizosphaerae	75.9968	110	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineococcaceae;g__Kineococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014654365.1	s__Amycolatopsis oliviviridis	75.8548	108	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647515.1	s__Dactylosporangium sucinum	75.8004	156	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Dactylosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002982315.1	s__Leucobacter massiliensis	75.7958	65	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003287285.1	s__Phytoactinopolyspora halophila	75.5513	55	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Phytoactinopolyspora	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-13 14:07:05,846] [INFO] GTDB search result was written to GCA_022708845.1_ASM2270884v1_genomic.fna/result_gtdb.tsv
[2023-06-13 14:07:05,848] [INFO] ===== GTDB Search completed =====
[2023-06-13 14:07:05,857] [INFO] DFAST_QC result json was written to GCA_022708845.1_ASM2270884v1_genomic.fna/dqc_result.json
[2023-06-13 14:07:05,858] [INFO] DFAST_QC completed!
[2023-06-13 14:07:05,858] [INFO] Total running time: 0h1m33s