[2023-03-16 23:05:03,887] [INFO] DFAST_QC pipeline started.
[2023-03-16 23:05:03,887] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 23:05:03,887] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b5309d3-18f7-4012-9543-2f7f166a19be/dqc_reference
[2023-03-16 23:05:05,096] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 23:05:05,096] [INFO] Task started: Prodigal
[2023-03-16 23:05:05,096] [INFO] Running command: cat /var/lib/cwl/stg015ce8c8-6733-4988-990d-93909fac4970/OceanDNA-b1835.fa | prodigal -d OceanDNA-b1835/cds.fna -a OceanDNA-b1835/protein.faa -g 11 -q > /dev/null
[2023-03-16 23:05:14,551] [INFO] Task succeeded: Prodigal
[2023-03-16 23:05:14,551] [INFO] Task started: HMMsearch
[2023-03-16 23:05:14,552] [INFO] Running command: hmmsearch --tblout OceanDNA-b1835/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b5309d3-18f7-4012-9543-2f7f166a19be/dqc_reference/reference_markers.hmm OceanDNA-b1835/protein.faa > /dev/null
[2023-03-16 23:05:14,764] [INFO] Task succeeded: HMMsearch
[2023-03-16 23:05:14,764] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg015ce8c8-6733-4988-990d-93909fac4970/OceanDNA-b1835.fa]
[2023-03-16 23:05:14,785] [INFO] Query marker FASTA was written to OceanDNA-b1835/markers.fasta
[2023-03-16 23:05:14,785] [INFO] Task started: Blastn
[2023-03-16 23:05:14,785] [INFO] Running command: blastn -query OceanDNA-b1835/markers.fasta -db /var/lib/cwl/stg7b5309d3-18f7-4012-9543-2f7f166a19be/dqc_reference/reference_markers.fasta -out OceanDNA-b1835/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:05:15,443] [INFO] Task succeeded: Blastn
[2023-03-16 23:05:15,443] [INFO] Selected 12 target genomes.
[2023-03-16 23:05:15,444] [INFO] Target genome list was writen to OceanDNA-b1835/target_genomes.txt
[2023-03-16 23:05:15,450] [INFO] Task started: fastANI
[2023-03-16 23:05:15,450] [INFO] Running command: fastANI --query /var/lib/cwl/stg015ce8c8-6733-4988-990d-93909fac4970/OceanDNA-b1835.fa --refList OceanDNA-b1835/target_genomes.txt --output OceanDNA-b1835/fastani_result.tsv --threads 1
[2023-03-16 23:05:25,581] [INFO] Task succeeded: fastANI
[2023-03-16 23:05:25,582] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b5309d3-18f7-4012-9543-2f7f166a19be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 23:05:25,582] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b5309d3-18f7-4012-9543-2f7f166a19be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 23:05:25,589] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 23:05:25,589] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 23:05:25,589] [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	77.2239	130	368	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.7676	101	368	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	76.0925	61	368	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	75.9274	100	368	95	below_threshold
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	75.9167	58	368	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	75.8986	117	368	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	75.7009	83	368	95	below_threshold
Glycomyces arizonensis	strain=DSM 44726	GCA_000482705.1	256035	256035	type	True	75.1067	58	368	95	below_threshold
Frankia asymbiotica	strain=NRRL B-16386	GCA_001983105.1	1834516	1834516	type	True	75.0196	77	368	95	below_threshold
Jiangella alkaliphila	strain=DSM 45079	GCA_900105925.1	419479	419479	type	True	74.9308	87	368	95	below_threshold
Jiangella alkaliphila	strain=KCTC 19222	GCA_001005145.1	419479	419479	type	True	74.9308	87	368	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 23:05:25,590] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1835/tc_result.tsv
[2023-03-16 23:05:25,590] [INFO] ===== Taxonomy check completed =====
[2023-03-16 23:05:25,590] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 23:05:25,590] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b5309d3-18f7-4012-9543-2f7f166a19be/dqc_reference/checkm_data
[2023-03-16 23:05:25,591] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 23:05:25,595] [INFO] Task started: CheckM
[2023-03-16 23:05:25,595] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1835/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1835/checkm_input OceanDNA-b1835/checkm_result
[2023-03-16 23:05:53,516] [INFO] Task succeeded: CheckM
[2023-03-16 23:05:53,516] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.82%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 23:05:53,519] [INFO] ===== Completeness check finished =====
[2023-03-16 23:05:53,519] [INFO] ===== Start GTDB Search =====
[2023-03-16 23:05:53,519] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1835/markers.fasta)
[2023-03-16 23:05:53,519] [INFO] Task started: Blastn
[2023-03-16 23:05:53,519] [INFO] Running command: blastn -query OceanDNA-b1835/markers.fasta -db /var/lib/cwl/stg7b5309d3-18f7-4012-9543-2f7f166a19be/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1835/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:05:54,402] [INFO] Task succeeded: Blastn
[2023-03-16 23:05:54,403] [INFO] Selected 15 target genomes.
[2023-03-16 23:05:54,403] [INFO] Target genome list was writen to OceanDNA-b1835/target_genomes_gtdb.txt
[2023-03-16 23:05:54,925] [INFO] Task started: fastANI
[2023-03-16 23:05:54,926] [INFO] Running command: fastANI --query /var/lib/cwl/stg015ce8c8-6733-4988-990d-93909fac4970/OceanDNA-b1835.fa --refList OceanDNA-b1835/target_genomes_gtdb.txt --output OceanDNA-b1835/fastani_result_gtdb.tsv --threads 1
[2023-03-16 23:06:02,979] [INFO] Task succeeded: fastANI
[2023-03-16 23:06:02,987] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 23:06:02,987] [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_009650215.1	s__Actinomarinicola tropica	77.2474	129	368	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__Actinomarinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016649895.1	s__Actinomarinicola sp016649895	76.8776	84	368	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__Actinomarinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017577565.1	s__ZC4RG19 sp017577565	76.8712	125	368	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__ZC4RG19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013694495.1	s__JACDCH01 sp013694495	76.7139	108	368	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__JACDCH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019048865.1	s__Aquihabitans sp019048865	76.5883	113	368	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__Aquihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012730075.1	s__JAAYBP01 sp012730075	76.5501	84	368	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JAAYBP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016936035.1	s__ZC4RG19 sp016936035	76.5377	80	368	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	76.4683	69	368	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__CAIPVR01	95.0	99.51	99.50	0.87	0.86	3	-
GCA_016185275.1	s__JACPNX01 sp016185275	76.3338	83	368	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JACPNX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805555.1	s__CADCSY01 sp902805555	76.2209	71	368	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__CADCSY01;g__CADCSY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794585.1	s__JAEUJM01 sp016794585	76.0599	108	368	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAEUJM01;g__JAEUJM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002329075.1	s__S20-B6 sp002329075	75.7725	50	368	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	98.53	97.43	0.90	0.85	7	-
GCA_016700055.1	s__Kalu-18 sp016700055	75.5951	73	368	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Kalu-18	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 23:06:02,987] [INFO] GTDB search result was written to OceanDNA-b1835/result_gtdb.tsv
[2023-03-16 23:06:02,987] [INFO] ===== GTDB Search completed =====
[2023-03-16 23:06:02,988] [INFO] DFAST_QC result json was written to OceanDNA-b1835/dqc_result.json
[2023-03-16 23:06:02,989] [INFO] DFAST_QC completed!
[2023-03-16 23:06:02,989] [INFO] Total running time: 0h0m59s