[2023-03-15 13:03:53,445] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:03:53,446] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:03:53,446] [INFO] DQC Reference Directory: /var/lib/cwl/stge3844956-8b34-4532-99b0-9be5833be9ec/dqc_reference
[2023-03-15 13:03:54,589] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:03:54,589] [INFO] Task started: Prodigal
[2023-03-15 13:03:54,589] [INFO] Running command: cat /var/lib/cwl/stg9c047344-b8ed-40ca-84a0-7be860842476/OceanDNA-b22637.fa | prodigal -d OceanDNA-b22637/cds.fna -a OceanDNA-b22637/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:04:13,591] [INFO] Task succeeded: Prodigal
[2023-03-15 13:04:13,592] [INFO] Task started: HMMsearch
[2023-03-15 13:04:13,592] [INFO] Running command: hmmsearch --tblout OceanDNA-b22637/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge3844956-8b34-4532-99b0-9be5833be9ec/dqc_reference/reference_markers.hmm OceanDNA-b22637/protein.faa > /dev/null
[2023-03-15 13:04:13,826] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:04:13,826] [INFO] Found 6/6 markers.
[2023-03-15 13:04:13,848] [INFO] Query marker FASTA was written to OceanDNA-b22637/markers.fasta
[2023-03-15 13:04:13,848] [INFO] Task started: Blastn
[2023-03-15 13:04:13,848] [INFO] Running command: blastn -query OceanDNA-b22637/markers.fasta -db /var/lib/cwl/stge3844956-8b34-4532-99b0-9be5833be9ec/dqc_reference/reference_markers.fasta -out OceanDNA-b22637/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:04:14,401] [INFO] Task succeeded: Blastn
[2023-03-15 13:04:14,401] [INFO] Selected 19 target genomes.
[2023-03-15 13:04:14,402] [INFO] Target genome list was writen to OceanDNA-b22637/target_genomes.txt
[2023-03-15 13:04:14,465] [INFO] Task started: fastANI
[2023-03-15 13:04:14,466] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c047344-b8ed-40ca-84a0-7be860842476/OceanDNA-b22637.fa --refList OceanDNA-b22637/target_genomes.txt --output OceanDNA-b22637/fastani_result.tsv --threads 1
[2023-03-15 13:04:32,323] [INFO] Task succeeded: fastANI
[2023-03-15 13:04:32,323] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge3844956-8b34-4532-99b0-9be5833be9ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:04:32,324] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge3844956-8b34-4532-99b0-9be5833be9ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:04:32,331] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:04:32,331] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 13:04:32,331] [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
Botrimarina colliarenosi	strain=Pla108	GCA_007859955.1	2528001	2528001	type	True	76.4246	115	1027	95	below_threshold
Pirellulimonas nuda	strain=Pla175	GCA_007750855.1	2528009	2528009	type	True	76.3069	117	1027	95	below_threshold
Pseudobythopirellula maris	strain=Mal64	GCA_007859945.1	2527991	2527991	type	True	76.2774	127	1027	95	below_threshold
Botrimarina mediterranea	strain=Spa11	GCA_007753265.1	2528022	2528022	type	True	76.235	100	1027	95	below_threshold
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	76.1911	144	1027	95	below_threshold
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	76.1498	160	1027	95	below_threshold
Lacipirellula limnantheis	strain=I41	GCA_007746075.1	2528024	2528024	type	True	75.6872	87	1027	95	below_threshold
Lacipirellula parvula	strain=PX69	GCA_009177095.1	2650471	2650471	type	True	75.6438	104	1027	95	below_threshold
Botrimarina hoheduenensis	strain=Pla111	GCA_007859815.1	2528000	2528000	type	True	75.6154	74	1027	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	75.5119	167	1027	95	below_threshold
Luteimonas arsenica	strain=26-35	GCA_004352825.1	1586242	1586242	type	True	75.0049	53	1027	95	below_threshold
Baekduia soli	strain=BR7-21	GCA_007970665.1	496014	496014	type	True	74.7626	99	1027	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 13:04:32,332] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22637/tc_result.tsv
[2023-03-15 13:04:32,332] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:04:32,332] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:04:32,332] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge3844956-8b34-4532-99b0-9be5833be9ec/dqc_reference/checkm_data
[2023-03-15 13:04:32,333] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:04:32,337] [INFO] Task started: CheckM
[2023-03-15 13:04:32,337] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22637/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22637/checkm_input OceanDNA-b22637/checkm_result
[2023-03-15 13:05:20,393] [INFO] Task succeeded: CheckM
[2023-03-15 13:05:20,394] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:05:20,397] [INFO] ===== Completeness check finished =====
[2023-03-15 13:05:20,397] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:05:20,397] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22637/markers.fasta)
[2023-03-15 13:05:20,398] [INFO] Task started: Blastn
[2023-03-15 13:05:20,399] [INFO] Running command: blastn -query OceanDNA-b22637/markers.fasta -db /var/lib/cwl/stge3844956-8b34-4532-99b0-9be5833be9ec/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22637/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:05:21,217] [INFO] Task succeeded: Blastn
[2023-03-15 13:05:21,218] [INFO] Selected 12 target genomes.
[2023-03-15 13:05:21,218] [INFO] Target genome list was writen to OceanDNA-b22637/target_genomes_gtdb.txt
[2023-03-15 13:05:21,396] [INFO] Task started: fastANI
[2023-03-15 13:05:21,396] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c047344-b8ed-40ca-84a0-7be860842476/OceanDNA-b22637.fa --refList OceanDNA-b22637/target_genomes_gtdb.txt --output OceanDNA-b22637/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:05:28,760] [INFO] Task succeeded: fastANI
[2023-03-15 13:05:28,768] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 13:05:28,768] [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_016872955.1	s__QWPN01 sp016872955	79.2746	414	1027	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903831155.1	s__QWPN01 sp903831155	79.1501	418	1027	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872925.1	s__QWPN01 sp016872925	79.0959	420	1027	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014192425.1	s__QWPN01 sp014192425	78.9245	417	1027	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018970605.1	s__QWPN01 sp018970605	78.916	366	1027	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003669255.1	s__QWPN01 sp003669255	78.7323	226	1027	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003670825.1	s__QWPN01 sp003670825	78.6768	229	1027	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903919035.1	s__QWPN01 sp903919035	78.482	343	1027	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	99.57	99.56	0.90	0.89	5	-
GCA_003671185.1	s__QWPN01 sp003671185	78.1736	336	1027	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010027105.1	s__RGVT01 sp010027105	78.1289	308	1027	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__RGVT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009924545.1	s__F1-20-MAGs016 sp009924545	78.0387	337	1027	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__F1-20-MAGs016	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009923125.1	s__RGVT01 sp009923125	77.6077	252	1027	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__RGVT01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 13:05:28,768] [INFO] GTDB search result was written to OceanDNA-b22637/result_gtdb.tsv
[2023-03-15 13:05:28,768] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:05:28,770] [INFO] DFAST_QC result json was written to OceanDNA-b22637/dqc_result.json
[2023-03-15 13:05:28,770] [INFO] DFAST_QC completed!
[2023-03-15 13:05:28,770] [INFO] Total running time: 0h1m35s