[2023-06-19 12:58:47,340] [INFO] DFAST_QC pipeline started.
[2023-06-19 12:58:47,356] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 12:58:47,356] [INFO] DQC Reference Directory: /var/lib/cwl/stga48d88ee-9d96-4bd2-867c-064ecf986db7/dqc_reference
[2023-06-19 12:58:48,997] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 12:58:48,999] [INFO] Task started: Prodigal
[2023-06-19 12:58:48,999] [INFO] Running command: gunzip -c /var/lib/cwl/stg391c459b-9949-41a7-acc6-88857099629c/GCA_018970145.1_ASM1897014v1_genomic.fna.gz | prodigal -d GCA_018970145.1_ASM1897014v1_genomic.fna/cds.fna -a GCA_018970145.1_ASM1897014v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 12:58:56,732] [INFO] Task succeeded: Prodigal
[2023-06-19 12:58:56,733] [INFO] Task started: HMMsearch
[2023-06-19 12:58:56,733] [INFO] Running command: hmmsearch --tblout GCA_018970145.1_ASM1897014v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga48d88ee-9d96-4bd2-867c-064ecf986db7/dqc_reference/reference_markers.hmm GCA_018970145.1_ASM1897014v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 12:58:57,006] [INFO] Task succeeded: HMMsearch
[2023-06-19 12:58:57,007] [INFO] Found 6/6 markers.
[2023-06-19 12:58:57,036] [INFO] Query marker FASTA was written to GCA_018970145.1_ASM1897014v1_genomic.fna/markers.fasta
[2023-06-19 12:58:57,036] [INFO] Task started: Blastn
[2023-06-19 12:58:57,037] [INFO] Running command: blastn -query GCA_018970145.1_ASM1897014v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga48d88ee-9d96-4bd2-867c-064ecf986db7/dqc_reference/reference_markers.fasta -out GCA_018970145.1_ASM1897014v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 12:58:57,809] [INFO] Task succeeded: Blastn
[2023-06-19 12:58:57,813] [INFO] Selected 28 target genomes.
[2023-06-19 12:58:57,813] [INFO] Target genome list was writen to GCA_018970145.1_ASM1897014v1_genomic.fna/target_genomes.txt
[2023-06-19 12:58:57,819] [INFO] Task started: fastANI
[2023-06-19 12:58:57,819] [INFO] Running command: fastANI --query /var/lib/cwl/stg391c459b-9949-41a7-acc6-88857099629c/GCA_018970145.1_ASM1897014v1_genomic.fna.gz --refList GCA_018970145.1_ASM1897014v1_genomic.fna/target_genomes.txt --output GCA_018970145.1_ASM1897014v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 12:59:16,951] [INFO] Task succeeded: fastANI
[2023-06-19 12:59:16,952] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga48d88ee-9d96-4bd2-867c-064ecf986db7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 12:59:16,952] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga48d88ee-9d96-4bd2-867c-064ecf986db7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 12:59:16,969] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 12:59:16,969] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 12:59:16,969] [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
Povalibacter uvarum	strain=DSM 26723	GCA_014202975.1	732238	732238	type	True	76.995	64	797	95	below_threshold
Steroidobacter soli	strain=JW-3	GCA_004138485.1	2497877	2497877	type	True	76.8755	73	797	95	below_threshold
Steroidobacter agariperforans	strain=KA5-B	GCA_004138335.1	268404	268404	type	True	76.6418	67	797	95	below_threshold
Steroidobacter agaridevorans	strain=SA29-B	GCA_009932555.1	2695856	2695856	type	True	76.4707	76	797	95	below_threshold
Steroidobacter cummioxidans	strain=35Y	GCA_003104955.1	1803913	1803913	type	True	76.4443	64	797	95	below_threshold
Steroidobacter gossypii	strain=S1-65	GCA_016801985.1	2805490	2805490	type	True	76.2012	79	797	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	75.9147	52	797	95	below_threshold
Solimonas soli	strain=DSM 21787	GCA_000474945.1	413479	413479	type	True	75.7863	53	797	95	below_threshold
Luteimonas fraxinea	strain=D4P002	GCA_021233355.1	2901869	2901869	type	True	75.6442	51	797	95	below_threshold
Sulfurifustis variabilis	strain=skN76	GCA_002355415.1	1675686	1675686	type	True	75.5273	50	797	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 12:59:16,972] [INFO] DFAST Taxonomy check result was written to GCA_018970145.1_ASM1897014v1_genomic.fna/tc_result.tsv
[2023-06-19 12:59:16,972] [INFO] ===== Taxonomy check completed =====
[2023-06-19 12:59:16,973] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 12:59:16,973] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga48d88ee-9d96-4bd2-867c-064ecf986db7/dqc_reference/checkm_data
[2023-06-19 12:59:16,975] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 12:59:17,002] [INFO] Task started: CheckM
[2023-06-19 12:59:17,002] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018970145.1_ASM1897014v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018970145.1_ASM1897014v1_genomic.fna/checkm_input GCA_018970145.1_ASM1897014v1_genomic.fna/checkm_result
[2023-06-19 12:59:45,164] [INFO] Task succeeded: CheckM
[2023-06-19 12:59:45,166] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 12:59:45,185] [INFO] ===== Completeness check finished =====
[2023-06-19 12:59:45,186] [INFO] ===== Start GTDB Search =====
[2023-06-19 12:59:45,186] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018970145.1_ASM1897014v1_genomic.fna/markers.fasta)
[2023-06-19 12:59:45,187] [INFO] Task started: Blastn
[2023-06-19 12:59:45,187] [INFO] Running command: blastn -query GCA_018970145.1_ASM1897014v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga48d88ee-9d96-4bd2-867c-064ecf986db7/dqc_reference/reference_markers_gtdb.fasta -out GCA_018970145.1_ASM1897014v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 12:59:46,508] [INFO] Task succeeded: Blastn
[2023-06-19 12:59:46,514] [INFO] Selected 16 target genomes.
[2023-06-19 12:59:46,514] [INFO] Target genome list was writen to GCA_018970145.1_ASM1897014v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 12:59:46,547] [INFO] Task started: fastANI
[2023-06-19 12:59:46,548] [INFO] Running command: fastANI --query /var/lib/cwl/stg391c459b-9949-41a7-acc6-88857099629c/GCA_018970145.1_ASM1897014v1_genomic.fna.gz --refList GCA_018970145.1_ASM1897014v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018970145.1_ASM1897014v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 12:59:53,825] [INFO] Task succeeded: fastANI
[2023-06-19 12:59:53,841] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 12:59:53,842] [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_018970145.1	s__UBA964 sp018970145	100.0	797	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903910215.1	s__UBA964 sp903910215	85.3336	480	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	98.86	98.86	0.82	0.82	2	-
GCA_018883185.1	s__UBA964 sp018883185	78.3759	208	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903885195.1	s__UBA964 sp903885195	78.3486	230	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	99.55	99.16	0.90	0.86	6	-
GCA_010031985.1	s__UBA964 sp010031985	78.1922	160	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	98.93	98.76	0.80	0.76	12	-
GCA_017853175.1	s__UBA964 sp017853175	77.9309	149	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016874235.1	s__UBA964 sp016874235	77.9075	182	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	95.25	95.25	0.78	0.78	2	-
GCA_009923475.1	s__UBA964 sp009923475	77.8337	132	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016874175.1	s__UBA964 sp016874175	77.7846	219	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010029775.1	s__UBA964 sp010029775	77.616	138	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903938365.1	s__UBA964 sp903938365	77.385	151	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	99.27	99.13	0.88	0.87	4	-
GCA_016874555.1	s__UBA964 sp016874555	77.3351	169	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010027845.1	s__UBA964 sp010027845	77.2262	182	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 12:59:53,844] [INFO] GTDB search result was written to GCA_018970145.1_ASM1897014v1_genomic.fna/result_gtdb.tsv
[2023-06-19 12:59:53,844] [INFO] ===== GTDB Search completed =====
[2023-06-19 12:59:53,848] [INFO] DFAST_QC result json was written to GCA_018970145.1_ASM1897014v1_genomic.fna/dqc_result.json
[2023-06-19 12:59:53,849] [INFO] DFAST_QC completed!
[2023-06-19 12:59:53,849] [INFO] Total running time: 0h1m7s