[2023-03-15 14:37:46,950] [INFO] DFAST_QC pipeline started.
[2023-03-15 14:37:46,959] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 14:37:46,959] [INFO] DQC Reference Directory: /var/lib/cwl/stg6014ae2b-27e5-4e8e-aae5-5f97311c6729/dqc_reference
[2023-03-15 14:37:48,672] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 14:37:48,673] [INFO] Task started: Prodigal
[2023-03-15 14:37:48,673] [INFO] Running command: cat /var/lib/cwl/stgd9ded223-c774-4df0-84a3-1dc6fa05703b/OceanDNA-b11355.fa | prodigal -d OceanDNA-b11355/cds.fna -a OceanDNA-b11355/protein.faa -g 11 -q > /dev/null
[2023-03-15 14:37:56,404] [INFO] Task succeeded: Prodigal
[2023-03-15 14:37:56,405] [INFO] Task started: HMMsearch
[2023-03-15 14:37:56,405] [INFO] Running command: hmmsearch --tblout OceanDNA-b11355/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6014ae2b-27e5-4e8e-aae5-5f97311c6729/dqc_reference/reference_markers.hmm OceanDNA-b11355/protein.faa > /dev/null
[2023-03-15 14:37:56,570] [INFO] Task succeeded: HMMsearch
[2023-03-15 14:37:56,571] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd9ded223-c774-4df0-84a3-1dc6fa05703b/OceanDNA-b11355.fa]
[2023-03-15 14:37:56,583] [INFO] Query marker FASTA was written to OceanDNA-b11355/markers.fasta
[2023-03-15 14:37:56,584] [INFO] Task started: Blastn
[2023-03-15 14:37:56,584] [INFO] Running command: blastn -query OceanDNA-b11355/markers.fasta -db /var/lib/cwl/stg6014ae2b-27e5-4e8e-aae5-5f97311c6729/dqc_reference/reference_markers.fasta -out OceanDNA-b11355/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:37:57,751] [INFO] Task succeeded: Blastn
[2023-03-15 14:37:57,753] [INFO] Selected 10 target genomes.
[2023-03-15 14:37:57,753] [INFO] Target genome list was writen to OceanDNA-b11355/target_genomes.txt
[2023-03-15 14:37:57,783] [INFO] Task started: fastANI
[2023-03-15 14:37:57,783] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9ded223-c774-4df0-84a3-1dc6fa05703b/OceanDNA-b11355.fa --refList OceanDNA-b11355/target_genomes.txt --output OceanDNA-b11355/fastani_result.tsv --threads 1
[2023-03-15 14:38:02,947] [INFO] Task succeeded: fastANI
[2023-03-15 14:38:02,947] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6014ae2b-27e5-4e8e-aae5-5f97311c6729/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 14:38:02,947] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6014ae2b-27e5-4e8e-aae5-5f97311c6729/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 14:38:02,962] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 14:38:02,962] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 14:38:02,962] [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
Wenyingzhuangia marina	strain=DSM 100572	GCA_900130035.1	1195760	1195760	type	True	92.82	330	354	95	below_threshold
Wenyingzhuangia marina	strain=CGMCC 1.12162	GCA_014636515.1	1195760	1195760	type	True	92.7826	333	354	95	below_threshold
Wenyingzhuangia fucanilytica	strain=CZ1127	GCA_001697185.1	1790137	1790137	type	True	85.3233	315	354	95	below_threshold
Wenyingzhuangia aestuarii	strain=DSM 105044	GCA_011927765.1	1647582	1647582	type	True	81.8272	268	354	95	below_threshold
Wenyingzhuangia heitensis	strain=DSM 101599	GCA_011762155.1	1487859	1487859	type	True	81.6031	265	354	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	76.8287	64	354	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	76.628	68	354	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	76.5758	76	354	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	76.5426	78	354	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	76.5273	74	354	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 14:38:02,963] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11355/tc_result.tsv
[2023-03-15 14:38:02,963] [INFO] ===== Taxonomy check completed =====
[2023-03-15 14:38:02,963] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 14:38:02,963] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6014ae2b-27e5-4e8e-aae5-5f97311c6729/dqc_reference/checkm_data
[2023-03-15 14:38:02,964] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 14:38:02,967] [INFO] Task started: CheckM
[2023-03-15 14:38:02,967] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11355/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11355/checkm_input OceanDNA-b11355/checkm_result
[2023-03-15 14:38:27,250] [INFO] Task succeeded: CheckM
[2023-03-15 14:38:27,251] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 14:38:27,253] [INFO] ===== Completeness check finished =====
[2023-03-15 14:38:27,253] [INFO] ===== Start GTDB Search =====
[2023-03-15 14:38:27,253] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11355/markers.fasta)
[2023-03-15 14:38:27,254] [INFO] Task started: Blastn
[2023-03-15 14:38:27,254] [INFO] Running command: blastn -query OceanDNA-b11355/markers.fasta -db /var/lib/cwl/stg6014ae2b-27e5-4e8e-aae5-5f97311c6729/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11355/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:38:28,154] [INFO] Task succeeded: Blastn
[2023-03-15 14:38:28,155] [INFO] Selected 9 target genomes.
[2023-03-15 14:38:28,155] [INFO] Target genome list was writen to OceanDNA-b11355/target_genomes_gtdb.txt
[2023-03-15 14:38:28,169] [INFO] Task started: fastANI
[2023-03-15 14:38:28,170] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9ded223-c774-4df0-84a3-1dc6fa05703b/OceanDNA-b11355.fa --refList OceanDNA-b11355/target_genomes_gtdb.txt --output OceanDNA-b11355/fastani_result_gtdb.tsv --threads 1
[2023-03-15 14:38:33,678] [INFO] Task succeeded: fastANI
[2023-03-15 14:38:33,684] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 14:38:33,684] [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
GCF_900130035.1	s__Wenyingzhuangia marina	92.82	330	354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wenyingzhuangia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001697185.1	s__Wenyingzhuangia fucanilytica	85.3233	315	354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wenyingzhuangia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011927765.1	s__Wenyingzhuangia aestuarii	81.8272	268	354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wenyingzhuangia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762155.1	s__Wenyingzhuangia heitensis	81.6031	265	354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wenyingzhuangia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000220525.1	s__Ochrovirga pacifica	78.6048	181	354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ochrovirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954605.1	s__Polaribacter butkevichii	76.8797	95	354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116115.1	s__Lutibacter maritimus	76.508	70	354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345825.1	s__Tenacibaculum skagerrakense	76.3241	67	354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 14:38:33,684] [INFO] GTDB search result was written to OceanDNA-b11355/result_gtdb.tsv
[2023-03-15 14:38:33,685] [INFO] ===== GTDB Search completed =====
[2023-03-15 14:38:33,686] [INFO] DFAST_QC result json was written to OceanDNA-b11355/dqc_result.json
[2023-03-15 14:38:33,686] [INFO] DFAST_QC completed!
[2023-03-15 14:38:33,686] [INFO] Total running time: 0h0m47s