[2023-06-27 09:22:20,400] [INFO] DFAST_QC pipeline started.
[2023-06-27 09:22:20,403] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 09:22:20,403] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a5af5aa-cdd4-494f-83cb-f2e9d275d3ac/dqc_reference
[2023-06-27 09:22:22,187] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 09:22:22,188] [INFO] Task started: Prodigal
[2023-06-27 09:22:22,188] [INFO] Running command: gunzip -c /var/lib/cwl/stg2da0f2d3-95f5-4245-b84e-ae522b111cb7/GCA_026708285.1_ASM2670828v1_genomic.fna.gz | prodigal -d GCA_026708285.1_ASM2670828v1_genomic.fna/cds.fna -a GCA_026708285.1_ASM2670828v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 09:22:33,754] [INFO] Task succeeded: Prodigal
[2023-06-27 09:22:33,755] [INFO] Task started: HMMsearch
[2023-06-27 09:22:33,755] [INFO] Running command: hmmsearch --tblout GCA_026708285.1_ASM2670828v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a5af5aa-cdd4-494f-83cb-f2e9d275d3ac/dqc_reference/reference_markers.hmm GCA_026708285.1_ASM2670828v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 09:22:34,089] [INFO] Task succeeded: HMMsearch
[2023-06-27 09:22:34,091] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg2da0f2d3-95f5-4245-b84e-ae522b111cb7/GCA_026708285.1_ASM2670828v1_genomic.fna.gz]
[2023-06-27 09:22:34,156] [INFO] Query marker FASTA was written to GCA_026708285.1_ASM2670828v1_genomic.fna/markers.fasta
[2023-06-27 09:22:34,157] [INFO] Task started: Blastn
[2023-06-27 09:22:34,158] [INFO] Running command: blastn -query GCA_026708285.1_ASM2670828v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a5af5aa-cdd4-494f-83cb-f2e9d275d3ac/dqc_reference/reference_markers.fasta -out GCA_026708285.1_ASM2670828v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 09:22:34,862] [INFO] Task succeeded: Blastn
[2023-06-27 09:22:34,881] [INFO] Selected 20 target genomes.
[2023-06-27 09:22:34,881] [INFO] Target genome list was writen to GCA_026708285.1_ASM2670828v1_genomic.fna/target_genomes.txt
[2023-06-27 09:22:34,892] [INFO] Task started: fastANI
[2023-06-27 09:22:34,892] [INFO] Running command: fastANI --query /var/lib/cwl/stg2da0f2d3-95f5-4245-b84e-ae522b111cb7/GCA_026708285.1_ASM2670828v1_genomic.fna.gz --refList GCA_026708285.1_ASM2670828v1_genomic.fna/target_genomes.txt --output GCA_026708285.1_ASM2670828v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 09:22:55,875] [INFO] Task succeeded: fastANI
[2023-06-27 09:22:55,876] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a5af5aa-cdd4-494f-83cb-f2e9d275d3ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 09:22:55,876] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a5af5aa-cdd4-494f-83cb-f2e9d275d3ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 09:22:55,894] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 09:22:55,894] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 09:22:55,894] [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 virescens	strain=NBRC 100334	GCA_007989405.1	83456	83456	type	True	75.262	78	1446	95	below_threshold
Myxococcus virescens	strain=DSM 2260	GCA_900101905.1	83456	83456	type	True	75.2361	75	1446	95	below_threshold
Myxococcus vastator	strain=AM301	GCA_010894475.1	2709664	2709664	type	True	75.2095	62	1446	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	75.2061	152	1446	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	75.1965	110	1446	95	below_threshold
Methylobacterium crusticola	strain=MIMD6	GCA_003574465.1	1697972	1697972	type	True	75.1909	145	1446	95	below_threshold
Myxococcus xanthus	strain=DSM 16526	GCA_900106535.1	34	34	type	True	75.1552	72	1446	95	below_threshold
Corallococcus exercitus	strain=AB043A	GCA_003611585.1	2316736	2316736	type	True	75.1226	100	1446	95	below_threshold
Streptomyces roseifaciens	strain=MBT76	GCA_001445655.1	1488406	1488406	type	True	75.0998	117	1446	95	below_threshold
Streptomyces klenkii	strain=KCTC 29202	GCA_003626645.1	1420899	1420899	type	True	75.053	129	1446	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	75.0491	114	1446	95	below_threshold
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	75.0114	108	1446	95	below_threshold
Methylorubrum aminovorans	strain=NBRC 15686	GCA_022179725.1	269069	269069	type	True	74.999	85	1446	95	below_threshold
Streptomyces decoyicus	strain=NRRL 2666	GCA_001270575.1	249567	249567	type	True	74.9302	116	1446	95	below_threshold
Streptomyces decoyicus	strain=NRRL 2666	GCA_019880305.1	249567	249567	type	True	74.93	116	1446	95	below_threshold
Streptomyces hiroshimensis	strain=JCM 4586	GCA_014650335.1	66424	66424	type	True	74.8779	126	1446	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 09:22:55,896] [INFO] DFAST Taxonomy check result was written to GCA_026708285.1_ASM2670828v1_genomic.fna/tc_result.tsv
[2023-06-27 09:22:55,897] [INFO] ===== Taxonomy check completed =====
[2023-06-27 09:22:55,897] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 09:22:55,898] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a5af5aa-cdd4-494f-83cb-f2e9d275d3ac/dqc_reference/checkm_data
[2023-06-27 09:22:55,900] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 09:22:55,965] [INFO] Task started: CheckM
[2023-06-27 09:22:55,965] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026708285.1_ASM2670828v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026708285.1_ASM2670828v1_genomic.fna/checkm_input GCA_026708285.1_ASM2670828v1_genomic.fna/checkm_result
[2023-06-27 09:23:32,262] [INFO] Task succeeded: CheckM
[2023-06-27 09:23:32,264] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 09:23:32,290] [INFO] ===== Completeness check finished =====
[2023-06-27 09:23:32,291] [INFO] ===== Start GTDB Search =====
[2023-06-27 09:23:32,291] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026708285.1_ASM2670828v1_genomic.fna/markers.fasta)
[2023-06-27 09:23:32,292] [INFO] Task started: Blastn
[2023-06-27 09:23:32,292] [INFO] Running command: blastn -query GCA_026708285.1_ASM2670828v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a5af5aa-cdd4-494f-83cb-f2e9d275d3ac/dqc_reference/reference_markers_gtdb.fasta -out GCA_026708285.1_ASM2670828v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 09:23:33,249] [INFO] Task succeeded: Blastn
[2023-06-27 09:23:33,263] [INFO] Selected 8 target genomes.
[2023-06-27 09:23:33,263] [INFO] Target genome list was writen to GCA_026708285.1_ASM2670828v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 09:23:33,271] [INFO] Task started: fastANI
[2023-06-27 09:23:33,271] [INFO] Running command: fastANI --query /var/lib/cwl/stg2da0f2d3-95f5-4245-b84e-ae522b111cb7/GCA_026708285.1_ASM2670828v1_genomic.fna.gz --refList GCA_026708285.1_ASM2670828v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026708285.1_ASM2670828v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 09:23:42,104] [INFO] Task succeeded: fastANI
[2023-06-27 09:23:42,113] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 09:23:42,113] [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_011523565.1	s__WTGL01 sp011523565	90.9903	875	1446	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012270995.1	s__WTGL01 sp012270995	90.3123	1095	1446	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009843505.1	s__WTGL01 sp009843505	87.5217	1080	1446	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	99.97	99.97	0.99	0.99	2	-
GCA_009837085.1	s__WTGL01 sp009837085	87.4769	1067	1446	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	99.78	99.78	0.96	0.95	3	-
GCA_009845425.1	s__WTGL01 sp009845425	87.4221	1085	1446	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	99.99	99.99	0.99	0.99	3	-
GCA_009836625.1	s__WTGL01 sp009836625	87.2687	1083	1446	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	99.03	98.03	0.95	0.91	5	-
GCA_011525365.1	s__WTGL01 sp011525365	87.2044	1101	1446	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009837885.1	s__WTGL01 sp009837885	87.0326	1066	1446	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	99.92	99.92	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-06-27 09:23:42,116] [INFO] GTDB search result was written to GCA_026708285.1_ASM2670828v1_genomic.fna/result_gtdb.tsv
[2023-06-27 09:23:42,116] [INFO] ===== GTDB Search completed =====
[2023-06-27 09:23:42,121] [INFO] DFAST_QC result json was written to GCA_026708285.1_ASM2670828v1_genomic.fna/dqc_result.json
[2023-06-27 09:23:42,121] [INFO] DFAST_QC completed!
[2023-06-27 09:23:42,121] [INFO] Total running time: 0h1m22s