[2023-03-17 22:53:52,846] [INFO] DFAST_QC pipeline started.
[2023-03-17 22:53:52,846] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 22:53:52,846] [INFO] DQC Reference Directory: /var/lib/cwl/stg85cc2139-404d-4714-b78d-7cc1ae93dfb9/dqc_reference
[2023-03-17 22:53:53,952] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 22:53:53,953] [INFO] Task started: Prodigal
[2023-03-17 22:53:53,953] [INFO] Running command: cat /var/lib/cwl/stgec8d9192-fec4-40c1-88c0-dc136cf1e444/OceanDNA-b11041.fa | prodigal -d OceanDNA-b11041/cds.fna -a OceanDNA-b11041/protein.faa -g 11 -q > /dev/null
[2023-03-17 22:54:08,581] [INFO] Task succeeded: Prodigal
[2023-03-17 22:54:08,582] [INFO] Task started: HMMsearch
[2023-03-17 22:54:08,582] [INFO] Running command: hmmsearch --tblout OceanDNA-b11041/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg85cc2139-404d-4714-b78d-7cc1ae93dfb9/dqc_reference/reference_markers.hmm OceanDNA-b11041/protein.faa > /dev/null
[2023-03-17 22:54:08,753] [INFO] Task succeeded: HMMsearch
[2023-03-17 22:54:08,754] [INFO] Found 6/6 markers.
[2023-03-17 22:54:08,766] [INFO] Query marker FASTA was written to OceanDNA-b11041/markers.fasta
[2023-03-17 22:54:08,767] [INFO] Task started: Blastn
[2023-03-17 22:54:08,767] [INFO] Running command: blastn -query OceanDNA-b11041/markers.fasta -db /var/lib/cwl/stg85cc2139-404d-4714-b78d-7cc1ae93dfb9/dqc_reference/reference_markers.fasta -out OceanDNA-b11041/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:54:09,322] [INFO] Task succeeded: Blastn
[2023-03-17 22:54:09,323] [INFO] Selected 30 target genomes.
[2023-03-17 22:54:09,323] [INFO] Target genome list was writen to OceanDNA-b11041/target_genomes.txt
[2023-03-17 22:54:09,332] [INFO] Task started: fastANI
[2023-03-17 22:54:09,333] [INFO] Running command: fastANI --query /var/lib/cwl/stgec8d9192-fec4-40c1-88c0-dc136cf1e444/OceanDNA-b11041.fa --refList OceanDNA-b11041/target_genomes.txt --output OceanDNA-b11041/fastani_result.tsv --threads 1
[2023-03-17 22:54:25,036] [INFO] Task succeeded: fastANI
[2023-03-17 22:54:25,036] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg85cc2139-404d-4714-b78d-7cc1ae93dfb9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 22:54:25,037] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg85cc2139-404d-4714-b78d-7cc1ae93dfb9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 22:54:25,042] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 22:54:25,042] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 22:54:25,042] [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
Flavicella sediminum	strain=ALS 84	GCA_006381105.1	2585141	2585141	type	True	77.7389	139	544	95	below_threshold
Flavicella marina	strain=2A-7	GCA_009193215.1	1475951	1475951	type	True	77.4402	105	544	95	below_threshold
Wenyingzhuangia heitensis	strain=DSM 101599	GCA_011762155.1	1487859	1487859	type	True	76.449	56	544	95	below_threshold
Lutibacter maritimus	strain=DSM 24450	GCA_900116115.1	593133	593133	type	True	76.414	50	544	95	below_threshold
Wenyingzhuangia fucanilytica	strain=CZ1127	GCA_001697185.1	1790137	1790137	type	True	76.3978	57	544	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 22:54:25,042] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11041/tc_result.tsv
[2023-03-17 22:54:25,042] [INFO] ===== Taxonomy check completed =====
[2023-03-17 22:54:25,043] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 22:54:25,043] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg85cc2139-404d-4714-b78d-7cc1ae93dfb9/dqc_reference/checkm_data
[2023-03-17 22:54:25,043] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 22:54:25,047] [INFO] Task started: CheckM
[2023-03-17 22:54:25,047] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11041/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11041/checkm_input OceanDNA-b11041/checkm_result
[2023-03-17 22:55:04,935] [INFO] Task succeeded: CheckM
[2023-03-17 22:55:04,936] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 22:55:04,937] [INFO] ===== Completeness check finished =====
[2023-03-17 22:55:04,938] [INFO] ===== Start GTDB Search =====
[2023-03-17 22:55:04,938] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11041/markers.fasta)
[2023-03-17 22:55:04,939] [INFO] Task started: Blastn
[2023-03-17 22:55:04,939] [INFO] Running command: blastn -query OceanDNA-b11041/markers.fasta -db /var/lib/cwl/stg85cc2139-404d-4714-b78d-7cc1ae93dfb9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11041/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:55:05,667] [INFO] Task succeeded: Blastn
[2023-03-17 22:55:05,667] [INFO] Selected 25 target genomes.
[2023-03-17 22:55:05,667] [INFO] Target genome list was writen to OceanDNA-b11041/target_genomes_gtdb.txt
[2023-03-17 22:55:05,689] [INFO] Task started: fastANI
[2023-03-17 22:55:05,689] [INFO] Running command: fastANI --query /var/lib/cwl/stgec8d9192-fec4-40c1-88c0-dc136cf1e444/OceanDNA-b11041.fa --refList OceanDNA-b11041/target_genomes_gtdb.txt --output OceanDNA-b11041/fastani_result_gtdb.tsv --threads 1
[2023-03-17 22:55:18,527] [INFO] Task succeeded: fastANI
[2023-03-17 22:55:18,532] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 22:55:18,532] [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_002477565.1	s__Flavicella sp002477565	99.7683	484	544	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavicella	95.0	98.32	98.32	0.91	0.91	2	conclusive
GCA_905479475.1	s__Flavicella sp905479475	78.2147	144	544	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006381105.1	s__Flavicella sediminum	77.7389	139	544	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009193215.1	s__Flavicella marina	77.4412	105	544	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016342705.1	s__Lutibacter sp016342705	76.5103	52	544	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762155.1	s__Wenyingzhuangia heitensis	76.449	56	544	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wenyingzhuangia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001697185.1	s__Wenyingzhuangia fucanilytica	76.3978	57	544	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wenyingzhuangia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 22:55:18,532] [INFO] GTDB search result was written to OceanDNA-b11041/result_gtdb.tsv
[2023-03-17 22:55:18,533] [INFO] ===== GTDB Search completed =====
[2023-03-17 22:55:18,534] [INFO] DFAST_QC result json was written to OceanDNA-b11041/dqc_result.json
[2023-03-17 22:55:18,534] [INFO] DFAST_QC completed!
[2023-03-17 22:55:18,534] [INFO] Total running time: 0h1m26s