[2023-03-18 08:55:50,621] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:55:50,621] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:55:50,621] [INFO] DQC Reference Directory: /var/lib/cwl/stg03f1c473-74bc-471d-a5fc-60500977ca3e/dqc_reference
[2023-03-18 08:55:51,845] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:55:51,845] [INFO] Task started: Prodigal
[2023-03-18 08:55:51,846] [INFO] Running command: cat /var/lib/cwl/stg4f0bede7-82b6-40cc-9c21-659276690fa1/OceanDNA-b33419.fa | prodigal -d OceanDNA-b33419/cds.fna -a OceanDNA-b33419/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:56:12,108] [INFO] Task succeeded: Prodigal
[2023-03-18 08:56:12,109] [INFO] Task started: HMMsearch
[2023-03-18 08:56:12,109] [INFO] Running command: hmmsearch --tblout OceanDNA-b33419/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg03f1c473-74bc-471d-a5fc-60500977ca3e/dqc_reference/reference_markers.hmm OceanDNA-b33419/protein.faa > /dev/null
[2023-03-18 08:56:12,373] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:56:12,373] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4f0bede7-82b6-40cc-9c21-659276690fa1/OceanDNA-b33419.fa]
[2023-03-18 08:56:12,394] [INFO] Query marker FASTA was written to OceanDNA-b33419/markers.fasta
[2023-03-18 08:56:12,396] [INFO] Task started: Blastn
[2023-03-18 08:56:12,396] [INFO] Running command: blastn -query OceanDNA-b33419/markers.fasta -db /var/lib/cwl/stg03f1c473-74bc-471d-a5fc-60500977ca3e/dqc_reference/reference_markers.fasta -out OceanDNA-b33419/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:56:12,978] [INFO] Task succeeded: Blastn
[2023-03-18 08:56:12,979] [INFO] Selected 24 target genomes.
[2023-03-18 08:56:12,979] [INFO] Target genome list was writen to OceanDNA-b33419/target_genomes.txt
[2023-03-18 08:56:12,991] [INFO] Task started: fastANI
[2023-03-18 08:56:12,991] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f0bede7-82b6-40cc-9c21-659276690fa1/OceanDNA-b33419.fa --refList OceanDNA-b33419/target_genomes.txt --output OceanDNA-b33419/fastani_result.tsv --threads 1
[2023-03-18 08:56:28,434] [INFO] Task succeeded: fastANI
[2023-03-18 08:56:28,434] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg03f1c473-74bc-471d-a5fc-60500977ca3e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:56:28,434] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg03f1c473-74bc-471d-a5fc-60500977ca3e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:56:28,443] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:56:28,443] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 08:56:28,443] [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
Pusillimonas maritima	strain=17-4A	GCA_003576595.1	2026239	2026239	type	True	83.7189	745	1045	95	below_threshold
Pusillimonas minor	strain=YC-7-48	GCA_014237865.1	2697024	2697024	type	True	77.6125	250	1045	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_022688825.1	645616	645616	type	True	77.3943	172	1045	95	below_threshold
Pusillimonas noertemannii	strain=DSM 10065	GCA_003096595.1	305977	305977	type	True	77.3322	171	1045	95	below_threshold
Pusillimonas noertemannii	strain=DSM 10065	GCA_003545825.1	305977	305977	type	True	77.3201	172	1045	95	below_threshold
Candidimonas humi	strain=DSM 25336	GCA_019166065.1	683355	683355	type	True	77.2809	109	1045	95	below_threshold
Pusillimonas harenae	strain=JCM 16917	GCA_004153685.1	657015	657015	type	True	77.0852	125	1045	95	below_threshold
Pusillimonas harenae	strain=DSM 25667	GCA_013416515.1	657015	657015	type	True	77.0837	125	1045	95	below_threshold
Paralcaligenes ureilyticus	strain=DSM 24591	GCA_004346225.1	627131	627131	type	True	76.7733	109	1045	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	76.5971	104	1045	95	below_threshold
Paracandidimonas soli	strain=DSM 100048	GCA_004342005.1	1917182	1917182	type	True	76.5581	103	1045	95	below_threshold
Castellaniella defragrans	strain=CCUG 39790	GCA_008801975.1	75697	75697	type	True	76.4429	87	1045	95	below_threshold
Castellaniella defragrans	strain=DSM 12141	GCA_014203015.1	75697	75697	type	True	76.4277	89	1045	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 08:56:28,444] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33419/tc_result.tsv
[2023-03-18 08:56:28,444] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:56:28,444] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:56:28,444] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg03f1c473-74bc-471d-a5fc-60500977ca3e/dqc_reference/checkm_data
[2023-03-18 08:56:28,445] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:56:28,449] [INFO] Task started: CheckM
[2023-03-18 08:56:28,450] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33419/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33419/checkm_input OceanDNA-b33419/checkm_result
[2023-03-18 08:57:19,940] [INFO] Task succeeded: CheckM
[2023-03-18 08:57:19,941] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:57:19,944] [INFO] ===== Completeness check finished =====
[2023-03-18 08:57:19,944] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:57:19,944] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33419/markers.fasta)
[2023-03-18 08:57:19,946] [INFO] Task started: Blastn
[2023-03-18 08:57:19,946] [INFO] Running command: blastn -query OceanDNA-b33419/markers.fasta -db /var/lib/cwl/stg03f1c473-74bc-471d-a5fc-60500977ca3e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33419/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:57:20,790] [INFO] Task succeeded: Blastn
[2023-03-18 08:57:20,791] [INFO] Selected 18 target genomes.
[2023-03-18 08:57:20,791] [INFO] Target genome list was writen to OceanDNA-b33419/target_genomes_gtdb.txt
[2023-03-18 08:57:20,825] [INFO] Task started: fastANI
[2023-03-18 08:57:20,826] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f0bede7-82b6-40cc-9c21-659276690fa1/OceanDNA-b33419.fa --refList OceanDNA-b33419/target_genomes_gtdb.txt --output OceanDNA-b33419/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:57:33,464] [INFO] Task succeeded: fastANI
[2023-03-18 08:57:33,472] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 08:57:33,472] [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_002384935.1	s__Pusillimonas_A sp002384935	98.2642	933	1045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_A	95.0	98.90	98.23	0.90	0.79	9	conclusive
GCF_003576595.1	s__Pusillimonas_A maritima	83.7189	745	1045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_A	95.0	96.55	95.88	0.88	0.85	8	-
GCF_011388195.1	s__Pusillimonas_A sp011388195	83.0853	754	1045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002694155.1	s__Pusillimonas_A sp002694155	82.0613	298	1045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000209655.1	s__Pusillimonas_C sp000209655	78.2098	135	1045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014237865.1	s__Pusillimonas_A sp014237865	77.6125	250	1045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002236805.1	s__Pusillimonas_A sp002236805	77.5252	226	1045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_A	95.0	98.07	98.07	0.83	0.83	2	-
GCF_002849655.1	s__Candidimonas_A sp002849655	77.4327	120	1045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019166065.1	s__Candidimonas humi	77.2809	109	1045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012727555.1	s__JAAYGT01 sp012727555	76.7737	120	1045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAAYGT01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004346225.1	s__Paralcaligenes ureilyticus	76.7733	109	1045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paralcaligenes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016127315.1	s__Achromobacter insuavis_A	76.3354	108	1045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.6014	97.14	97.13	0.90	0.90	4	-
--------------------------------------------------------------------------------
[2023-03-18 08:57:33,472] [INFO] GTDB search result was written to OceanDNA-b33419/result_gtdb.tsv
[2023-03-18 08:57:33,472] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:57:33,474] [INFO] DFAST_QC result json was written to OceanDNA-b33419/dqc_result.json
[2023-03-18 08:57:33,474] [INFO] DFAST_QC completed!
[2023-03-18 08:57:33,474] [INFO] Total running time: 0h1m43s