[2023-03-15 12:44:24,469] [INFO] DFAST_QC pipeline started.
[2023-03-15 12:44:24,469] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 12:44:24,470] [INFO] DQC Reference Directory: /var/lib/cwl/stg84cc28fb-f463-4e2d-88a7-082716c3c8b8/dqc_reference
[2023-03-15 12:44:26,206] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 12:44:26,206] [INFO] Task started: Prodigal
[2023-03-15 12:44:26,206] [INFO] Running command: cat /var/lib/cwl/stg45921465-e53f-4472-a4ec-eb83daad9146/OceanDNA-b518.fa | prodigal -d OceanDNA-b518/cds.fna -a OceanDNA-b518/protein.faa -g 11 -q > /dev/null
[2023-03-15 12:44:41,837] [INFO] Task succeeded: Prodigal
[2023-03-15 12:44:41,837] [INFO] Task started: HMMsearch
[2023-03-15 12:44:41,837] [INFO] Running command: hmmsearch --tblout OceanDNA-b518/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84cc28fb-f463-4e2d-88a7-082716c3c8b8/dqc_reference/reference_markers.hmm OceanDNA-b518/protein.faa > /dev/null
[2023-03-15 12:44:42,086] [INFO] Task succeeded: HMMsearch
[2023-03-15 12:44:42,086] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg45921465-e53f-4472-a4ec-eb83daad9146/OceanDNA-b518.fa]
[2023-03-15 12:44:42,113] [INFO] Query marker FASTA was written to OceanDNA-b518/markers.fasta
[2023-03-15 12:44:42,113] [INFO] Task started: Blastn
[2023-03-15 12:44:42,113] [INFO] Running command: blastn -query OceanDNA-b518/markers.fasta -db /var/lib/cwl/stg84cc28fb-f463-4e2d-88a7-082716c3c8b8/dqc_reference/reference_markers.fasta -out OceanDNA-b518/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:44:42,760] [INFO] Task succeeded: Blastn
[2023-03-15 12:44:42,761] [INFO] Selected 12 target genomes.
[2023-03-15 12:44:42,761] [INFO] Target genome list was writen to OceanDNA-b518/target_genomes.txt
[2023-03-15 12:44:42,767] [INFO] Task started: fastANI
[2023-03-15 12:44:42,767] [INFO] Running command: fastANI --query /var/lib/cwl/stg45921465-e53f-4472-a4ec-eb83daad9146/OceanDNA-b518.fa --refList OceanDNA-b518/target_genomes.txt --output OceanDNA-b518/fastani_result.tsv --threads 1
[2023-03-15 12:44:52,706] [INFO] Task succeeded: fastANI
[2023-03-15 12:44:52,707] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84cc28fb-f463-4e2d-88a7-082716c3c8b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 12:44:52,707] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84cc28fb-f463-4e2d-88a7-082716c3c8b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 12:44:52,715] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 12:44:52,715] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 12:44:52,716] [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	79.6247	386	724	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	77.3563	261	724	95	below_threshold
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	77.2896	195	724	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	77.196	263	724	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.3594	163	724	95	below_threshold
Nocardioides seonyuensis	strain=MMS17-SY207-3	GCA_004683965.1	2518371	2518371	type	True	75.5389	67	724	95	below_threshold
Ornithinimicrobium humiphilum	strain=DSM 12362	GCA_006716885.1	125288	125288	type	True	75.1227	77	724	95	below_threshold
Nocardioides humi	strain=DCY24	GCA_006494775.1	449461	449461	type	True	75.062	123	724	95	below_threshold
Egibacter rhizosphaerae	strain=EGI 80759	GCA_004322855.1	1670831	1670831	type	True	75.0485	65	724	95	below_threshold
Actinokineospora terrae	strain=DSM 44260	GCA_900111175.1	155974	155974	type	True	74.9794	108	724	95	below_threshold
Amycolatopsis eburnea	strain=GLM-1	GCA_003937945.1	2267691	2267691	type	True	74.9353	149	724	95	below_threshold
Actinokineospora cianjurensis	strain=DSM 45657	GCA_003663795.1	585224	585224	type	True	74.9218	105	724	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 12:44:52,716] [INFO] DFAST Taxonomy check result was written to OceanDNA-b518/tc_result.tsv
[2023-03-15 12:44:52,716] [INFO] ===== Taxonomy check completed =====
[2023-03-15 12:44:52,716] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 12:44:52,716] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84cc28fb-f463-4e2d-88a7-082716c3c8b8/dqc_reference/checkm_data
[2023-03-15 12:44:52,717] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 12:44:52,723] [INFO] Task started: CheckM
[2023-03-15 12:44:52,723] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b518/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b518/checkm_input OceanDNA-b518/checkm_result
[2023-03-15 12:45:33,700] [INFO] Task succeeded: CheckM
[2023-03-15 12:45:33,701] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 12:45:33,704] [INFO] ===== Completeness check finished =====
[2023-03-15 12:45:33,704] [INFO] ===== Start GTDB Search =====
[2023-03-15 12:45:33,704] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b518/markers.fasta)
[2023-03-15 12:45:33,705] [INFO] Task started: Blastn
[2023-03-15 12:45:33,705] [INFO] Running command: blastn -query OceanDNA-b518/markers.fasta -db /var/lib/cwl/stg84cc28fb-f463-4e2d-88a7-082716c3c8b8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b518/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:45:34,625] [INFO] Task succeeded: Blastn
[2023-03-15 12:45:34,626] [INFO] Selected 12 target genomes.
[2023-03-15 12:45:34,626] [INFO] Target genome list was writen to OceanDNA-b518/target_genomes_gtdb.txt
[2023-03-15 12:45:34,676] [INFO] Task started: fastANI
[2023-03-15 12:45:34,676] [INFO] Running command: fastANI --query /var/lib/cwl/stg45921465-e53f-4472-a4ec-eb83daad9146/OceanDNA-b518.fa --refList OceanDNA-b518/target_genomes_gtdb.txt --output OceanDNA-b518/fastani_result_gtdb.tsv --threads 1
[2023-03-15 12:45:43,288] [INFO] Task succeeded: fastANI
[2023-03-15 12:45:43,295] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 12:45:43,295] [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_002698945.1	s__Ilumatobacter sp002698945	80.0901	343	724	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364865.1	s__Ilumatobacter fluminis	79.6517	384	724	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007122945.1	s__SKSP01 sp007122945	78.1991	241	724	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__SKSP01	95.0	99.05	99.05	0.83	0.83	2	-
GCA_007693335.1	s__SKSP01 sp007693335	78.0902	237	724	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__SKSP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002175.1	s__Ilumatobacter_A sp013002175	77.7171	208	724	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009704985.1	s__VFMC01 sp009704985	77.6166	241	724	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__VFMC01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000348785.1	s__Ilumatobacter_A coccineus	77.3895	258	724	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000350145.1	s__Ilumatobacter_A nonamiensis	77.2749	196	724	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003426815.1	s__Desertimonas flava	77.2067	262	724	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Desertimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013815505.1	s__JACDHN01 sp013815505	76.9228	132	724	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__JACDHN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012730075.1	s__JAAYBP01 sp012730075	76.2234	125	724	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JAAYBP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003937945.1	s__Amycolatopsis eburnea	74.9303	151	724	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 12:45:43,296] [INFO] GTDB search result was written to OceanDNA-b518/result_gtdb.tsv
[2023-03-15 12:45:43,296] [INFO] ===== GTDB Search completed =====
[2023-03-15 12:45:43,297] [INFO] DFAST_QC result json was written to OceanDNA-b518/dqc_result.json
[2023-03-15 12:45:43,297] [INFO] DFAST_QC completed!
[2023-03-15 12:45:43,297] [INFO] Total running time: 0h1m19s