[2023-06-28 18:46:08,685] [INFO] DFAST_QC pipeline started.
[2023-06-28 18:46:08,687] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 18:46:08,688] [INFO] DQC Reference Directory: /var/lib/cwl/stg4bfbfe99-e74c-43f7-8ef1-1ab882d120fe/dqc_reference
[2023-06-28 18:46:10,071] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 18:46:10,072] [INFO] Task started: Prodigal
[2023-06-28 18:46:10,072] [INFO] Running command: gunzip -c /var/lib/cwl/stg68638e13-322c-4585-8e4b-bc0050f8fc8c/GCA_005787035.1_ASM578703v1_genomic.fna.gz | prodigal -d GCA_005787035.1_ASM578703v1_genomic.fna/cds.fna -a GCA_005787035.1_ASM578703v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 18:46:16,524] [INFO] Task succeeded: Prodigal
[2023-06-28 18:46:16,524] [INFO] Task started: HMMsearch
[2023-06-28 18:46:16,524] [INFO] Running command: hmmsearch --tblout GCA_005787035.1_ASM578703v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4bfbfe99-e74c-43f7-8ef1-1ab882d120fe/dqc_reference/reference_markers.hmm GCA_005787035.1_ASM578703v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 18:46:16,778] [INFO] Task succeeded: HMMsearch
[2023-06-28 18:46:16,779] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg68638e13-322c-4585-8e4b-bc0050f8fc8c/GCA_005787035.1_ASM578703v1_genomic.fna.gz]
[2023-06-28 18:46:16,811] [INFO] Query marker FASTA was written to GCA_005787035.1_ASM578703v1_genomic.fna/markers.fasta
[2023-06-28 18:46:16,812] [INFO] Task started: Blastn
[2023-06-28 18:46:16,812] [INFO] Running command: blastn -query GCA_005787035.1_ASM578703v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4bfbfe99-e74c-43f7-8ef1-1ab882d120fe/dqc_reference/reference_markers.fasta -out GCA_005787035.1_ASM578703v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:46:17,469] [INFO] Task succeeded: Blastn
[2023-06-28 18:46:17,473] [INFO] Selected 17 target genomes.
[2023-06-28 18:46:17,473] [INFO] Target genome list was writen to GCA_005787035.1_ASM578703v1_genomic.fna/target_genomes.txt
[2023-06-28 18:46:17,538] [INFO] Task started: fastANI
[2023-06-28 18:46:17,538] [INFO] Running command: fastANI --query /var/lib/cwl/stg68638e13-322c-4585-8e4b-bc0050f8fc8c/GCA_005787035.1_ASM578703v1_genomic.fna.gz --refList GCA_005787035.1_ASM578703v1_genomic.fna/target_genomes.txt --output GCA_005787035.1_ASM578703v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 18:46:30,450] [INFO] Task succeeded: fastANI
[2023-06-28 18:46:30,450] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4bfbfe99-e74c-43f7-8ef1-1ab882d120fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 18:46:30,451] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4bfbfe99-e74c-43f7-8ef1-1ab882d120fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 18:46:30,462] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 18:46:30,463] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 18:46:30,463] [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
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	76.1813	146	647	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	76.1332	126	647	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	76.1225	127	647	95	below_threshold
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	75.9129	95	647	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	75.6993	78	647	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	75.6215	77	647	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 18:46:30,466] [INFO] DFAST Taxonomy check result was written to GCA_005787035.1_ASM578703v1_genomic.fna/tc_result.tsv
[2023-06-28 18:46:30,466] [INFO] ===== Taxonomy check completed =====
[2023-06-28 18:46:30,467] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 18:46:30,467] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4bfbfe99-e74c-43f7-8ef1-1ab882d120fe/dqc_reference/checkm_data
[2023-06-28 18:46:30,468] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 18:46:30,495] [INFO] Task started: CheckM
[2023-06-28 18:46:30,495] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_005787035.1_ASM578703v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_005787035.1_ASM578703v1_genomic.fna/checkm_input GCA_005787035.1_ASM578703v1_genomic.fna/checkm_result
[2023-06-28 18:46:58,932] [INFO] Task succeeded: CheckM
[2023-06-28 18:46:58,934] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.68%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 18:46:58,975] [INFO] ===== Completeness check finished =====
[2023-06-28 18:46:58,976] [INFO] ===== Start GTDB Search =====
[2023-06-28 18:46:58,976] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_005787035.1_ASM578703v1_genomic.fna/markers.fasta)
[2023-06-28 18:46:58,977] [INFO] Task started: Blastn
[2023-06-28 18:46:58,977] [INFO] Running command: blastn -query GCA_005787035.1_ASM578703v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4bfbfe99-e74c-43f7-8ef1-1ab882d120fe/dqc_reference/reference_markers_gtdb.fasta -out GCA_005787035.1_ASM578703v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:46:59,755] [INFO] Task succeeded: Blastn
[2023-06-28 18:46:59,760] [INFO] Selected 10 target genomes.
[2023-06-28 18:46:59,760] [INFO] Target genome list was writen to GCA_005787035.1_ASM578703v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 18:46:59,792] [INFO] Task started: fastANI
[2023-06-28 18:46:59,793] [INFO] Running command: fastANI --query /var/lib/cwl/stg68638e13-322c-4585-8e4b-bc0050f8fc8c/GCA_005787035.1_ASM578703v1_genomic.fna.gz --refList GCA_005787035.1_ASM578703v1_genomic.fna/target_genomes_gtdb.txt --output GCA_005787035.1_ASM578703v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 18:47:04,250] [INFO] Task succeeded: fastANI
[2023-06-28 18:47:04,260] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 18:47:04,261] [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_005787035.1	s__Casp-actino8 sp005787035	100.0	639	647	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino8	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016871355.1	s__Casp-actino8 sp016871355	79.6191	329	647	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004379135.1	s__Casp-actino8 sp004379135	79.5428	350	647	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino8	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018882725.1	s__Casp-actino8 sp018882725	78.9927	263	647	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009923785.1	s__Casp-actino8 sp009923785	78.2361	227	647	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino8	95.0	98.73	98.56	0.91	0.86	10	-
GCA_010030605.1	s__Casp-actino8 sp010030605	78.1565	160	647	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino8	95.0	98.08	98.01	0.74	0.72	5	-
GCA_001510455.1	s__Casp-actino8 sp001510455	78.043	134	647	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013213745.1	s__JABSQH01 sp013213745	76.2906	83	647	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__JABSQH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018969405.1	s__F1-20-MAGs160 sp018969405	75.922	56	647	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	-
--------------------------------------------------------------------------------
[2023-06-28 18:47:04,263] [INFO] GTDB search result was written to GCA_005787035.1_ASM578703v1_genomic.fna/result_gtdb.tsv
[2023-06-28 18:47:04,264] [INFO] ===== GTDB Search completed =====
[2023-06-28 18:47:04,268] [INFO] DFAST_QC result json was written to GCA_005787035.1_ASM578703v1_genomic.fna/dqc_result.json
[2023-06-28 18:47:04,269] [INFO] DFAST_QC completed!
[2023-06-28 18:47:04,269] [INFO] Total running time: 0h0m56s