[2023-06-18 19:52:17,740] [INFO] DFAST_QC pipeline started.
[2023-06-18 19:52:17,742] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 19:52:17,743] [INFO] DQC Reference Directory: /var/lib/cwl/stg7799fcfd-b1fd-4336-bd7e-a219d3295234/dqc_reference
[2023-06-18 19:52:19,111] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 19:52:19,112] [INFO] Task started: Prodigal
[2023-06-18 19:52:19,112] [INFO] Running command: gunzip -c /var/lib/cwl/stgb990a5c1-436c-48de-941d-b7d8e7f32c3d/GCA_013697345.1_ASM1369734v1_genomic.fna.gz | prodigal -d GCA_013697345.1_ASM1369734v1_genomic.fna/cds.fna -a GCA_013697345.1_ASM1369734v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 19:52:29,706] [INFO] Task succeeded: Prodigal
[2023-06-18 19:52:29,706] [INFO] Task started: HMMsearch
[2023-06-18 19:52:29,706] [INFO] Running command: hmmsearch --tblout GCA_013697345.1_ASM1369734v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7799fcfd-b1fd-4336-bd7e-a219d3295234/dqc_reference/reference_markers.hmm GCA_013697345.1_ASM1369734v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 19:52:29,895] [INFO] Task succeeded: HMMsearch
[2023-06-18 19:52:29,896] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgb990a5c1-436c-48de-941d-b7d8e7f32c3d/GCA_013697345.1_ASM1369734v1_genomic.fna.gz]
[2023-06-18 19:52:29,922] [INFO] Query marker FASTA was written to GCA_013697345.1_ASM1369734v1_genomic.fna/markers.fasta
[2023-06-18 19:52:29,922] [INFO] Task started: Blastn
[2023-06-18 19:52:29,922] [INFO] Running command: blastn -query GCA_013697345.1_ASM1369734v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7799fcfd-b1fd-4336-bd7e-a219d3295234/dqc_reference/reference_markers.fasta -out GCA_013697345.1_ASM1369734v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 19:52:30,506] [INFO] Task succeeded: Blastn
[2023-06-18 19:52:30,511] [INFO] Selected 14 target genomes.
[2023-06-18 19:52:30,511] [INFO] Target genome list was writen to GCA_013697345.1_ASM1369734v1_genomic.fna/target_genomes.txt
[2023-06-18 19:52:30,514] [INFO] Task started: fastANI
[2023-06-18 19:52:30,515] [INFO] Running command: fastANI --query /var/lib/cwl/stgb990a5c1-436c-48de-941d-b7d8e7f32c3d/GCA_013697345.1_ASM1369734v1_genomic.fna.gz --refList GCA_013697345.1_ASM1369734v1_genomic.fna/target_genomes.txt --output GCA_013697345.1_ASM1369734v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 19:52:39,366] [INFO] Task succeeded: fastANI
[2023-06-18 19:52:39,366] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7799fcfd-b1fd-4336-bd7e-a219d3295234/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 19:52:39,367] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7799fcfd-b1fd-4336-bd7e-a219d3295234/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 19:52:39,374] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 19:52:39,375] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 19:52:39,375] [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
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	77.2277	141	360	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.8729	122	360	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	76.8098	98	360	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	76.2444	116	360	95	below_threshold
Nocardioides perillae	strain=DSM 24552	GCA_013409425.1	1119534	1119534	type	True	75.6945	70	360	95	below_threshold
Saccharothrix australiensis	strain=DSM 43800	GCA_003634935.1	2072	2072	type	True	75.1133	92	360	95	below_threshold
Saccharothrix algeriensis	strain=DSM 44581	GCA_016907655.1	173560	173560	type	True	75.0408	84	360	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 19:52:39,377] [INFO] DFAST Taxonomy check result was written to GCA_013697345.1_ASM1369734v1_genomic.fna/tc_result.tsv
[2023-06-18 19:52:39,377] [INFO] ===== Taxonomy check completed =====
[2023-06-18 19:52:39,378] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 19:52:39,378] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7799fcfd-b1fd-4336-bd7e-a219d3295234/dqc_reference/checkm_data
[2023-06-18 19:52:39,379] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 19:52:39,406] [INFO] Task started: CheckM
[2023-06-18 19:52:39,407] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013697345.1_ASM1369734v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013697345.1_ASM1369734v1_genomic.fna/checkm_input GCA_013697345.1_ASM1369734v1_genomic.fna/checkm_result
[2023-06-18 19:53:05,255] [INFO] Task succeeded: CheckM
[2023-06-18 19:53:05,258] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.27%
Contamintation: 5.07%
Strain heterogeneity: 25.00%
--------------------------------------------------------------------------------
[2023-06-18 19:53:05,283] [INFO] ===== Completeness check finished =====
[2023-06-18 19:53:05,283] [INFO] ===== Start GTDB Search =====
[2023-06-18 19:53:05,284] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013697345.1_ASM1369734v1_genomic.fna/markers.fasta)
[2023-06-18 19:53:05,284] [INFO] Task started: Blastn
[2023-06-18 19:53:05,284] [INFO] Running command: blastn -query GCA_013697345.1_ASM1369734v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7799fcfd-b1fd-4336-bd7e-a219d3295234/dqc_reference/reference_markers_gtdb.fasta -out GCA_013697345.1_ASM1369734v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 19:53:06,104] [INFO] Task succeeded: Blastn
[2023-06-18 19:53:06,108] [INFO] Selected 18 target genomes.
[2023-06-18 19:53:06,109] [INFO] Target genome list was writen to GCA_013697345.1_ASM1369734v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 19:53:06,116] [INFO] Task started: fastANI
[2023-06-18 19:53:06,116] [INFO] Running command: fastANI --query /var/lib/cwl/stgb990a5c1-436c-48de-941d-b7d8e7f32c3d/GCA_013697345.1_ASM1369734v1_genomic.fna.gz --refList GCA_013697345.1_ASM1369734v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013697345.1_ASM1369734v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 19:53:14,214] [INFO] Task succeeded: fastANI
[2023-06-18 19:53:14,232] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-18 19:53:14,232] [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_016781135.1	s__LC5-5 sp016781135	78.8196	116	360	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__CADCSY01;g__LC5-5	95.0	99.16	98.25	0.93	0.85	8	-
GCA_016781105.1	s__JADDRA01 sp016781105	78.4842	129	360	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__CADCSY01;g__JADDRA01	95.0	99.25	99.25	0.80	0.80	2	-
GCA_902805555.1	s__CADCSY01 sp902805555	78.4541	155	360	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__CADCSY01;g__CADCSY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004366205.1	s__SIRW01 sp004366205	78.4086	159	360	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SIRW01;g__SIRW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005884125.1	s__AC-35 sp005884125	77.405	120	360	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__AC-35;g__AC-35	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017577565.1	s__ZC4RG19 sp017577565	77.2457	155	360	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__ZC4RG19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005888395.1	s__AC-25 sp005888395	77.1875	94	360	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__AC-25;g__AC-25	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018969405.1	s__F1-20-MAGs160 sp018969405	77.0254	71	360	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_003138855.1	s__Bog-756 sp003138855	76.8303	64	360	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-756	95.0	99.82	99.61	0.95	0.93	14	-
GCA_902805655.1	s__CADCTF01 sp902805655	76.7799	95	360	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__CADCTF01;g__CADCTF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903941145.1	s__CAJANQ01 sp903941145	76.7497	62	360	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__CAJANQ01	95.0	98.35	98.35	0.80	0.80	2	-
GCA_016870245.1	s__CAIUKV01 sp016870245	76.6456	83	360	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__IMCC26256;f__PALSA-555;g__CAIUKV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018882825.1	s__F1-20-MAGs160 sp018882825	76.6219	57	360	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_012730075.1	s__JAAYBP01 sp012730075	76.5637	119	360	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JAAYBP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903868545.1	s__CAIPVR01 sp903868545	76.2712	88	360	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__CAIPVR01	95.0	99.51	99.50	0.87	0.86	3	-
--------------------------------------------------------------------------------
[2023-06-18 19:53:14,234] [INFO] GTDB search result was written to GCA_013697345.1_ASM1369734v1_genomic.fna/result_gtdb.tsv
[2023-06-18 19:53:14,235] [INFO] ===== GTDB Search completed =====
[2023-06-18 19:53:14,240] [INFO] DFAST_QC result json was written to GCA_013697345.1_ASM1369734v1_genomic.fna/dqc_result.json
[2023-06-18 19:53:14,240] [INFO] DFAST_QC completed!
[2023-06-18 19:53:14,241] [INFO] Total running time: 0h0m57s