[2023-03-15 23:07:02,633] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:07:02,633] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:07:02,633] [INFO] DQC Reference Directory: /var/lib/cwl/stg76daed87-5d95-47db-8a74-b8fa21c29c06/dqc_reference
[2023-03-15 23:07:03,966] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:07:03,967] [INFO] Task started: Prodigal
[2023-03-15 23:07:03,967] [INFO] Running command: cat /var/lib/cwl/stg5d3c3e98-8a7b-4963-b604-47a61ddbe5bf/OceanDNA-b11030.fa | prodigal -d OceanDNA-b11030/cds.fna -a OceanDNA-b11030/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:07:19,296] [INFO] Task succeeded: Prodigal
[2023-03-15 23:07:19,296] [INFO] Task started: HMMsearch
[2023-03-15 23:07:19,296] [INFO] Running command: hmmsearch --tblout OceanDNA-b11030/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg76daed87-5d95-47db-8a74-b8fa21c29c06/dqc_reference/reference_markers.hmm OceanDNA-b11030/protein.faa > /dev/null
[2023-03-15 23:07:19,489] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:07:19,490] [INFO] Found 6/6 markers.
[2023-03-15 23:07:19,504] [INFO] Query marker FASTA was written to OceanDNA-b11030/markers.fasta
[2023-03-15 23:07:19,504] [INFO] Task started: Blastn
[2023-03-15 23:07:19,504] [INFO] Running command: blastn -query OceanDNA-b11030/markers.fasta -db /var/lib/cwl/stg76daed87-5d95-47db-8a74-b8fa21c29c06/dqc_reference/reference_markers.fasta -out OceanDNA-b11030/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:07:20,055] [INFO] Task succeeded: Blastn
[2023-03-15 23:07:20,056] [INFO] Selected 32 target genomes.
[2023-03-15 23:07:20,056] [INFO] Target genome list was writen to OceanDNA-b11030/target_genomes.txt
[2023-03-15 23:07:20,085] [INFO] Task started: fastANI
[2023-03-15 23:07:20,085] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d3c3e98-8a7b-4963-b604-47a61ddbe5bf/OceanDNA-b11030.fa --refList OceanDNA-b11030/target_genomes.txt --output OceanDNA-b11030/fastani_result.tsv --threads 1
[2023-03-15 23:07:36,887] [INFO] Task succeeded: fastANI
[2023-03-15 23:07:36,887] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg76daed87-5d95-47db-8a74-b8fa21c29c06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:07:36,887] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg76daed87-5d95-47db-8a74-b8fa21c29c06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:07:36,895] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:07:36,895] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 23:07:36,895] [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 marina	strain=2A-7	GCA_009193215.1	1475951	1475951	type	True	77.4113	116	578	95	below_threshold
Flavicella sediminum	strain=ALS 84	GCA_006381105.1	2585141	2585141	type	True	77.1576	161	578	95	below_threshold
Wenyingzhuangia fucanilytica	strain=CZ1127	GCA_001697185.1	1790137	1790137	type	True	76.8408	56	578	95	below_threshold
Wenyingzhuangia heitensis	strain=DSM 101599	GCA_011762155.1	1487859	1487859	type	True	76.8058	57	578	95	below_threshold
Lutibacter flavus	strain=DSM 27993	GCA_900188355.1	691689	691689	type	True	76.5304	60	578	95	below_threshold
Wenyingzhuangia aestuarii	strain=DSM 105044	GCA_011927765.1	1647582	1647582	type	True	76.4974	62	578	95	below_threshold
Wenyingzhuangia marina	strain=DSM 100572	GCA_900130035.1	1195760	1195760	type	True	76.4973	63	578	95	below_threshold
Wenyingzhuangia marina	strain=CGMCC 1.12162	GCA_014636515.1	1195760	1195760	type	True	76.4973	63	578	95	below_threshold
Lutibacter maritimus	strain=DSM 24450	GCA_900116115.1	593133	593133	type	True	76.1927	52	578	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	76.0105	55	578	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 23:07:36,895] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11030/tc_result.tsv
[2023-03-15 23:07:36,895] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:07:36,895] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:07:36,895] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg76daed87-5d95-47db-8a74-b8fa21c29c06/dqc_reference/checkm_data
[2023-03-15 23:07:36,896] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:07:36,899] [INFO] Task started: CheckM
[2023-03-15 23:07:36,899] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11030/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11030/checkm_input OceanDNA-b11030/checkm_result
[2023-03-15 23:08:19,233] [INFO] Task succeeded: CheckM
[2023-03-15 23:08:19,233] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.93%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 23:08:19,241] [INFO] ===== Completeness check finished =====
[2023-03-15 23:08:19,241] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:08:19,241] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11030/markers.fasta)
[2023-03-15 23:08:19,242] [INFO] Task started: Blastn
[2023-03-15 23:08:19,243] [INFO] Running command: blastn -query OceanDNA-b11030/markers.fasta -db /var/lib/cwl/stg76daed87-5d95-47db-8a74-b8fa21c29c06/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11030/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:08:19,978] [INFO] Task succeeded: Blastn
[2023-03-15 23:08:19,984] [INFO] Selected 23 target genomes.
[2023-03-15 23:08:19,984] [INFO] Target genome list was writen to OceanDNA-b11030/target_genomes_gtdb.txt
[2023-03-15 23:08:20,001] [INFO] Task started: fastANI
[2023-03-15 23:08:20,002] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d3c3e98-8a7b-4963-b604-47a61ddbe5bf/OceanDNA-b11030.fa --refList OceanDNA-b11030/target_genomes_gtdb.txt --output OceanDNA-b11030/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:08:31,978] [INFO] Task succeeded: fastANI
[2023-03-15 23:08:31,984] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 23:08:31,985] [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	94.0868	482	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavicella	95.0	98.32	98.32	0.91	0.91	2	-
GCA_905479475.1	s__Flavicella sp905479475	77.894	152	578	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	77.4113	116	578	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	77.1622	159	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762155.1	s__Wenyingzhuangia heitensis	76.8119	58	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wenyingzhuangia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900130035.1	s__Wenyingzhuangia marina	76.4973	63	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wenyingzhuangia	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016342705.1	s__Lutibacter sp016342705	76.3132	55	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116115.1	s__Lutibacter maritimus	76.1759	51	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014352875.1	s__Polaribacter sp014352875	76.0105	55	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 23:08:31,987] [INFO] GTDB search result was written to OceanDNA-b11030/result_gtdb.tsv
[2023-03-15 23:08:31,987] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:08:31,990] [INFO] DFAST_QC result json was written to OceanDNA-b11030/dqc_result.json
[2023-03-15 23:08:31,990] [INFO] DFAST_QC completed!
[2023-03-15 23:08:31,990] [INFO] Total running time: 0h1m29s