[2023-06-29 03:47:09,185] [INFO] DFAST_QC pipeline started.
[2023-06-29 03:47:09,187] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 03:47:09,187] [INFO] DQC Reference Directory: /var/lib/cwl/stg62c08c30-838e-46eb-9d3b-b8538990decf/dqc_reference
[2023-06-29 03:47:10,610] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 03:47:10,611] [INFO] Task started: Prodigal
[2023-06-29 03:47:10,611] [INFO] Running command: gunzip -c /var/lib/cwl/stga545442c-7f1e-410c-a311-ed6bf25b49db/GCA_020439175.1_ASM2043917v1_genomic.fna.gz | prodigal -d GCA_020439175.1_ASM2043917v1_genomic.fna/cds.fna -a GCA_020439175.1_ASM2043917v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 03:47:20,487] [INFO] Task succeeded: Prodigal
[2023-06-29 03:47:20,487] [INFO] Task started: HMMsearch
[2023-06-29 03:47:20,487] [INFO] Running command: hmmsearch --tblout GCA_020439175.1_ASM2043917v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg62c08c30-838e-46eb-9d3b-b8538990decf/dqc_reference/reference_markers.hmm GCA_020439175.1_ASM2043917v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 03:47:20,750] [INFO] Task succeeded: HMMsearch
[2023-06-29 03:47:20,751] [WARNING] Found 4/6 markers. [/var/lib/cwl/stga545442c-7f1e-410c-a311-ed6bf25b49db/GCA_020439175.1_ASM2043917v1_genomic.fna.gz]
[2023-06-29 03:47:20,787] [INFO] Query marker FASTA was written to GCA_020439175.1_ASM2043917v1_genomic.fna/markers.fasta
[2023-06-29 03:47:20,787] [INFO] Task started: Blastn
[2023-06-29 03:47:20,787] [INFO] Running command: blastn -query GCA_020439175.1_ASM2043917v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg62c08c30-838e-46eb-9d3b-b8538990decf/dqc_reference/reference_markers.fasta -out GCA_020439175.1_ASM2043917v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 03:47:21,444] [INFO] Task succeeded: Blastn
[2023-06-29 03:47:21,448] [INFO] Selected 13 target genomes.
[2023-06-29 03:47:21,448] [INFO] Target genome list was writen to GCA_020439175.1_ASM2043917v1_genomic.fna/target_genomes.txt
[2023-06-29 03:47:21,461] [INFO] Task started: fastANI
[2023-06-29 03:47:21,462] [INFO] Running command: fastANI --query /var/lib/cwl/stga545442c-7f1e-410c-a311-ed6bf25b49db/GCA_020439175.1_ASM2043917v1_genomic.fna.gz --refList GCA_020439175.1_ASM2043917v1_genomic.fna/target_genomes.txt --output GCA_020439175.1_ASM2043917v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 03:47:32,609] [INFO] Task succeeded: fastANI
[2023-06-29 03:47:32,610] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg62c08c30-838e-46eb-9d3b-b8538990decf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 03:47:32,610] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg62c08c30-838e-46eb-9d3b-b8538990decf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 03:47:32,624] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 03:47:32,624] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 03:47:32,624] [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
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	77.6377	353	991	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	77.619	325	991	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	77.1808	346	991	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	76.0812	246	991	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	75.8781	322	991	95	below_threshold
Aeromicrobium erythreum	strain=AR18	GCA_001509405.1	2041	2041	type	True	75.394	180	991	95	below_threshold
Thermopolyspora flexuosa	strain=DSM 43186	GCA_006716785.1	103836	103836	type	True	75.1661	218	991	95	below_threshold
Thermopolyspora flexuosa	strain=JCM 3056	GCA_014647775.1	103836	103836	type	True	75.1645	214	991	95	below_threshold
Streptomyces flavofungini	strain=JCM 4753	GCA_014650815.1	68200	68200	type	True	75.1304	232	991	95	below_threshold
Streptomyces flavofungini	strain=JCM 4753	GCA_016411765.1	68200	68200	type	True	75.1207	240	991	95	below_threshold
Asanoa hainanensis	strain=CGMCC 4.5593	GCA_900188485.1	560556	560556	type	True	75.0874	244	991	95	below_threshold
Pilimelia terevasa	strain=JCM 3091	GCA_014647915.1	53372	53372	type	True	75.0343	192	991	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	74.9145	124	991	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 03:47:32,633] [INFO] DFAST Taxonomy check result was written to GCA_020439175.1_ASM2043917v1_genomic.fna/tc_result.tsv
[2023-06-29 03:47:32,635] [INFO] ===== Taxonomy check completed =====
[2023-06-29 03:47:32,635] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 03:47:32,635] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg62c08c30-838e-46eb-9d3b-b8538990decf/dqc_reference/checkm_data
[2023-06-29 03:47:32,637] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 03:47:32,681] [INFO] Task started: CheckM
[2023-06-29 03:47:32,681] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020439175.1_ASM2043917v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020439175.1_ASM2043917v1_genomic.fna/checkm_input GCA_020439175.1_ASM2043917v1_genomic.fna/checkm_result
[2023-06-29 03:48:24,499] [INFO] Task succeeded: CheckM
[2023-06-29 03:48:24,500] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 03:48:24,526] [INFO] ===== Completeness check finished =====
[2023-06-29 03:48:24,527] [INFO] ===== Start GTDB Search =====
[2023-06-29 03:48:24,527] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020439175.1_ASM2043917v1_genomic.fna/markers.fasta)
[2023-06-29 03:48:24,528] [INFO] Task started: Blastn
[2023-06-29 03:48:24,528] [INFO] Running command: blastn -query GCA_020439175.1_ASM2043917v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg62c08c30-838e-46eb-9d3b-b8538990decf/dqc_reference/reference_markers_gtdb.fasta -out GCA_020439175.1_ASM2043917v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 03:48:25,299] [INFO] Task succeeded: Blastn
[2023-06-29 03:48:25,304] [INFO] Selected 17 target genomes.
[2023-06-29 03:48:25,304] [INFO] Target genome list was writen to GCA_020439175.1_ASM2043917v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 03:48:25,307] [INFO] Task started: fastANI
[2023-06-29 03:48:25,307] [INFO] Running command: fastANI --query /var/lib/cwl/stga545442c-7f1e-410c-a311-ed6bf25b49db/GCA_020439175.1_ASM2043917v1_genomic.fna.gz --refList GCA_020439175.1_ASM2043917v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020439175.1_ASM2043917v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 03:48:36,862] [INFO] Task succeeded: fastANI
[2023-06-29 03:48:36,888] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 03:48:36,888] [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_014805525.1	s__Rhabdothermincola sediminis	77.6193	325	991	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__Rhabdothermincola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018969405.1	s__F1-20-MAGs160 sp018969405	77.3338	209	991	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__F1-20-MAGs160	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017577565.1	s__ZC4RG19 sp017577565	77.2409	349	991	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__ZC4RG19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794585.1	s__JAEUJM01 sp016794585	77.2054	431	991	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAEUJM01;g__JAEUJM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009650215.1	s__Actinomarinicola tropica	77.1515	350	991	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__Actinomarinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018882825.1	s__F1-20-MAGs160 sp018882825	76.9741	165	991	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__F1-20-MAGs160	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002403895.1	s__UBA4742 sp002403895	76.9191	238	991	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__UBA4742	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016936035.1	s__ZC4RG19 sp016936035	76.9122	252	991	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__ZC4RG19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903868545.1	s__CAIPVR01 sp903868545	76.8966	259	991	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__CAIPVR01	95.0	99.51	99.50	0.87	0.86	3	-
GCA_016716005.1	s__JADJXE01 sp016716005	76.8715	301	991	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JADJXE01;g__JADJXE01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019048865.1	s__Aquihabitans sp019048865	76.8575	404	991	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__Aquihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004366205.1	s__SIRW01 sp004366205	76.7841	321	991	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SIRW01;g__SIRW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903921205.1	s__CAIXPF01 sp903921205	76.3238	237	991	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__CAIXPF01;g__CAIXPF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003155135.1	s__Bog-515 sp003155135	76.0224	155	991	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-515	95.0	99.89	99.76	0.97	0.95	17	-
GCA_002255565.1	s__RAAP-2 sp002255565	75.9672	109	991	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003426815.1	s__Desertimonas flava	75.8742	321	991	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Desertimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004919085.1	s__Nocardioides sp004919085	75.156	178	991	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 03:48:36,904] [INFO] GTDB search result was written to GCA_020439175.1_ASM2043917v1_genomic.fna/result_gtdb.tsv
[2023-06-29 03:48:36,904] [INFO] ===== GTDB Search completed =====
[2023-06-29 03:48:36,911] [INFO] DFAST_QC result json was written to GCA_020439175.1_ASM2043917v1_genomic.fna/dqc_result.json
[2023-06-29 03:48:36,911] [INFO] DFAST_QC completed!
[2023-06-29 03:48:36,911] [INFO] Total running time: 0h1m28s