[2023-06-18 11:47:10,338] [INFO] DFAST_QC pipeline started.
[2023-06-18 11:47:10,340] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 11:47:10,340] [INFO] DQC Reference Directory: /var/lib/cwl/stgb74e960a-844c-48b8-b8ec-4d8a12068354/dqc_reference
[2023-06-18 11:47:11,728] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 11:47:11,729] [INFO] Task started: Prodigal
[2023-06-18 11:47:11,729] [INFO] Running command: gunzip -c /var/lib/cwl/stg28a94399-413f-438a-89f2-0b7ab4e20fc4/GCA_018057085.1_ASM1805708v1_genomic.fna.gz | prodigal -d GCA_018057085.1_ASM1805708v1_genomic.fna/cds.fna -a GCA_018057085.1_ASM1805708v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 11:47:21,798] [INFO] Task succeeded: Prodigal
[2023-06-18 11:47:21,799] [INFO] Task started: HMMsearch
[2023-06-18 11:47:21,799] [INFO] Running command: hmmsearch --tblout GCA_018057085.1_ASM1805708v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb74e960a-844c-48b8-b8ec-4d8a12068354/dqc_reference/reference_markers.hmm GCA_018057085.1_ASM1805708v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 11:47:21,996] [INFO] Task succeeded: HMMsearch
[2023-06-18 11:47:21,997] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg28a94399-413f-438a-89f2-0b7ab4e20fc4/GCA_018057085.1_ASM1805708v1_genomic.fna.gz]
[2023-06-18 11:47:22,029] [INFO] Query marker FASTA was written to GCA_018057085.1_ASM1805708v1_genomic.fna/markers.fasta
[2023-06-18 11:47:22,029] [INFO] Task started: Blastn
[2023-06-18 11:47:22,029] [INFO] Running command: blastn -query GCA_018057085.1_ASM1805708v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb74e960a-844c-48b8-b8ec-4d8a12068354/dqc_reference/reference_markers.fasta -out GCA_018057085.1_ASM1805708v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 11:47:22,772] [INFO] Task succeeded: Blastn
[2023-06-18 11:47:22,775] [INFO] Selected 15 target genomes.
[2023-06-18 11:47:22,776] [INFO] Target genome list was writen to GCA_018057085.1_ASM1805708v1_genomic.fna/target_genomes.txt
[2023-06-18 11:47:22,779] [INFO] Task started: fastANI
[2023-06-18 11:47:22,779] [INFO] Running command: fastANI --query /var/lib/cwl/stg28a94399-413f-438a-89f2-0b7ab4e20fc4/GCA_018057085.1_ASM1805708v1_genomic.fna.gz --refList GCA_018057085.1_ASM1805708v1_genomic.fna/target_genomes.txt --output GCA_018057085.1_ASM1805708v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 11:47:34,457] [INFO] Task succeeded: fastANI
[2023-06-18 11:47:34,457] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb74e960a-844c-48b8-b8ec-4d8a12068354/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 11:47:34,458] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb74e960a-844c-48b8-b8ec-4d8a12068354/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 11:47:34,471] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 11:47:34,471] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 11:47:34,471] [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
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	77.3859	205	889	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	77.2281	257	889	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	76.8366	213	889	95	below_threshold
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	76.7439	142	889	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.5915	160	889	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.5801	153	889	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	76.1736	102	889	95	below_threshold
Nakamurella deserti	strain=12Sc4-1	GCA_003260015.1	2164074	2164074	type	True	75.3631	74	889	95	below_threshold
Actinomadura macrotermitis	strain=RB68	GCA_009604375.1	2585200	2585200	type	True	75.3558	140	889	95	below_threshold
Saccharomonospora cyanea	strain=NA-134	GCA_000244975.1	40989	40989	type	True	75.3502	66	889	95	below_threshold
Dietzia massiliensis	strain=Marseille-Q0999	GCA_018390595.1	2697499	2697499	type	True	75.2978	53	889	95	below_threshold
Actinomadura nitritigenes	strain=L46	GCA_017573545.1	134602	134602	type	True	75.0997	145	889	95	below_threshold
Actinomadura physcomitrii	strain=LD22	GCA_008923205.2	2650748	2650748	type	True	75.0789	123	889	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	74.895	53	889	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 11:47:34,473] [INFO] DFAST Taxonomy check result was written to GCA_018057085.1_ASM1805708v1_genomic.fna/tc_result.tsv
[2023-06-18 11:47:34,474] [INFO] ===== Taxonomy check completed =====
[2023-06-18 11:47:34,474] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 11:47:34,474] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb74e960a-844c-48b8-b8ec-4d8a12068354/dqc_reference/checkm_data
[2023-06-18 11:47:34,476] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 11:47:34,513] [INFO] Task started: CheckM
[2023-06-18 11:47:34,514] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018057085.1_ASM1805708v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018057085.1_ASM1805708v1_genomic.fna/checkm_input GCA_018057085.1_ASM1805708v1_genomic.fna/checkm_result
[2023-06-18 11:48:11,140] [INFO] Task succeeded: CheckM
[2023-06-18 11:48:11,141] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.34%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 11:48:11,157] [INFO] ===== Completeness check finished =====
[2023-06-18 11:48:11,158] [INFO] ===== Start GTDB Search =====
[2023-06-18 11:48:11,158] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018057085.1_ASM1805708v1_genomic.fna/markers.fasta)
[2023-06-18 11:48:11,158] [INFO] Task started: Blastn
[2023-06-18 11:48:11,158] [INFO] Running command: blastn -query GCA_018057085.1_ASM1805708v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb74e960a-844c-48b8-b8ec-4d8a12068354/dqc_reference/reference_markers_gtdb.fasta -out GCA_018057085.1_ASM1805708v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 11:48:12,286] [INFO] Task succeeded: Blastn
[2023-06-18 11:48:12,289] [INFO] Selected 10 target genomes.
[2023-06-18 11:48:12,290] [INFO] Target genome list was writen to GCA_018057085.1_ASM1805708v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 11:48:12,294] [INFO] Task started: fastANI
[2023-06-18 11:48:12,294] [INFO] Running command: fastANI --query /var/lib/cwl/stg28a94399-413f-438a-89f2-0b7ab4e20fc4/GCA_018057085.1_ASM1805708v1_genomic.fna.gz --refList GCA_018057085.1_ASM1805708v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018057085.1_ASM1805708v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 11:48:19,891] [INFO] Task succeeded: fastANI
[2023-06-18 11:48:19,900] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 11:48:19,900] [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_016722025.1	s__UBA668 sp002299395	98.9811	800	889	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA668	95.0	99.06	98.90	0.95	0.90	7	conclusive
GCA_016213625.1	s__UBA668 sp016213625	80.5721	492	889	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA668	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003154135.1	s__UBA668 sp003154135	79.7606	419	889	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA668	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009702045.1	s__UBA668 sp009702045	79.5333	359	889	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA668	95.0	99.96	99.94	0.98	0.97	6	-
GCA_903919215.1	s__UBA668 sp903919215	79.4138	327	889	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA668	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903919455.1	s__UBA668 sp903919455	79.3368	390	889	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA668	95.0	99.17	98.79	0.93	0.92	4	-
GCA_016213665.1	s__UBA668 sp016213665	78.9091	265	889	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA668	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007122945.1	s__SKSP01 sp007122945	77.2854	192	889	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__SKSP01	95.0	99.05	99.05	0.83	0.83	2	-
GCA_002698945.1	s__Ilumatobacter sp002698945	77.0317	158	889	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805655.1	s__CADCTF01 sp902805655	76.2003	89	889	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__CADCTF01;g__CADCTF01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 11:48:19,902] [INFO] GTDB search result was written to GCA_018057085.1_ASM1805708v1_genomic.fna/result_gtdb.tsv
[2023-06-18 11:48:19,902] [INFO] ===== GTDB Search completed =====
[2023-06-18 11:48:19,906] [INFO] DFAST_QC result json was written to GCA_018057085.1_ASM1805708v1_genomic.fna/dqc_result.json
[2023-06-18 11:48:19,906] [INFO] DFAST_QC completed!
[2023-06-18 11:48:19,906] [INFO] Total running time: 0h1m10s