[2023-03-15 23:56:02,646] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:56:02,648] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:56:02,648] [INFO] DQC Reference Directory: /var/lib/cwl/stg7423149a-d35b-4bfd-b773-12f78cff12a8/dqc_reference
[2023-03-15 23:56:03,734] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:56:03,734] [INFO] Task started: Prodigal
[2023-03-15 23:56:03,734] [INFO] Running command: cat /var/lib/cwl/stg811202bd-9cc6-472f-9369-318ffb5b4efa/OceanDNA-b3912.fa | prodigal -d OceanDNA-b3912/cds.fna -a OceanDNA-b3912/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:56:33,164] [INFO] Task succeeded: Prodigal
[2023-03-15 23:56:33,164] [INFO] Task started: HMMsearch
[2023-03-15 23:56:33,164] [INFO] Running command: hmmsearch --tblout OceanDNA-b3912/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7423149a-d35b-4bfd-b773-12f78cff12a8/dqc_reference/reference_markers.hmm OceanDNA-b3912/protein.faa > /dev/null
[2023-03-15 23:56:33,395] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:56:33,395] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg811202bd-9cc6-472f-9369-318ffb5b4efa/OceanDNA-b3912.fa]
[2023-03-15 23:56:33,436] [INFO] Query marker FASTA was written to OceanDNA-b3912/markers.fasta
[2023-03-15 23:56:33,438] [INFO] Task started: Blastn
[2023-03-15 23:56:33,439] [INFO] Running command: blastn -query OceanDNA-b3912/markers.fasta -db /var/lib/cwl/stg7423149a-d35b-4bfd-b773-12f78cff12a8/dqc_reference/reference_markers.fasta -out OceanDNA-b3912/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:56:33,980] [INFO] Task succeeded: Blastn
[2023-03-15 23:56:33,985] [INFO] Selected 23 target genomes.
[2023-03-15 23:56:33,985] [INFO] Target genome list was writen to OceanDNA-b3912/target_genomes.txt
[2023-03-15 23:56:34,015] [INFO] Task started: fastANI
[2023-03-15 23:56:34,015] [INFO] Running command: fastANI --query /var/lib/cwl/stg811202bd-9cc6-472f-9369-318ffb5b4efa/OceanDNA-b3912.fa --refList OceanDNA-b3912/target_genomes.txt --output OceanDNA-b3912/fastani_result.tsv --threads 1
[2023-03-15 23:56:50,347] [INFO] Task succeeded: fastANI
[2023-03-15 23:56:50,347] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7423149a-d35b-4bfd-b773-12f78cff12a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:56:50,348] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7423149a-d35b-4bfd-b773-12f78cff12a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:56:50,353] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:56:50,353] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 23:56:50,353] [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
Hymenobacter piscis	strain=NST-14	GCA_018760735.1	2839984	2839984	type	True	75.9173	65	1058	95	below_threshold
Hymenobacter caeli	strain=9A	GCA_013294115.1	2735894	2735894	type	True	75.829	56	1058	95	below_threshold
Hymenobacter busanensis	strain=MA3	GCA_008727865.1	2607656	2607656	type	True	75.7186	50	1058	95	below_threshold
Hymenobacter polaris	strain=RP-2-7	GCA_012927305.1	2682546	2682546	type	True	75.6211	59	1058	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	75.5801	59	1058	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 23:56:50,354] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3912/tc_result.tsv
[2023-03-15 23:56:50,355] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:56:50,355] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:56:50,355] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7423149a-d35b-4bfd-b773-12f78cff12a8/dqc_reference/checkm_data
[2023-03-15 23:56:50,356] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:56:50,363] [INFO] Task started: CheckM
[2023-03-15 23:56:50,363] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3912/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3912/checkm_input OceanDNA-b3912/checkm_result
[2023-03-15 23:58:02,518] [INFO] Task succeeded: CheckM
[2023-03-15 23:58:02,519] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.59%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 23:58:02,568] [INFO] ===== Completeness check finished =====
[2023-03-15 23:58:02,569] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:58:02,569] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3912/markers.fasta)
[2023-03-15 23:58:02,570] [INFO] Task started: Blastn
[2023-03-15 23:58:02,571] [INFO] Running command: blastn -query OceanDNA-b3912/markers.fasta -db /var/lib/cwl/stg7423149a-d35b-4bfd-b773-12f78cff12a8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3912/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:58:03,386] [INFO] Task succeeded: Blastn
[2023-03-15 23:58:03,410] [INFO] Selected 30 target genomes.
[2023-03-15 23:58:03,410] [INFO] Target genome list was writen to OceanDNA-b3912/target_genomes_gtdb.txt
[2023-03-15 23:58:03,430] [INFO] Task started: fastANI
[2023-03-15 23:58:03,430] [INFO] Running command: fastANI --query /var/lib/cwl/stg811202bd-9cc6-472f-9369-318ffb5b4efa/OceanDNA-b3912.fa --refList OceanDNA-b3912/target_genomes_gtdb.txt --output OceanDNA-b3912/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:58:25,063] [INFO] Task succeeded: fastANI
[2023-03-15 23:58:25,069] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 23:58:25,069] [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_004167665.1	s__Hymenobacter persicinus	75.9514	51	1058	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018760735.1	s__Hymenobacter sp018760735	75.9173	65	1058	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006439025.1	s__Hymenobacter nivis_A	75.9071	56	1058	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013294115.1	s__Hymenobacter caeli	75.829	56	1058	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005771675.1	s__Solirubrum jeollabukense	75.7753	71	1058	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Solirubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008727865.1	s__Solirubrum busanensis	75.7186	50	1058	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Solirubrum	95.0	100.00	100.00	0.99	0.99	2	-
GCF_016427455.1	s__Hymenobacter sp016427455	75.6453	63	1058	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	95.46	95.46	0.89	0.89	2	-
GCF_004765605.1	s__Hymenobacter aquaticus	75.5257	70	1058	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004684095.1	s__Hymenobacter sp004684095	75.3461	52	1058	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-15 23:58:25,073] [INFO] GTDB search result was written to OceanDNA-b3912/result_gtdb.tsv
[2023-03-15 23:58:25,077] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:58:25,083] [INFO] DFAST_QC result json was written to OceanDNA-b3912/dqc_result.json
[2023-03-15 23:58:25,083] [INFO] DFAST_QC completed!
[2023-03-15 23:58:25,083] [INFO] Total running time: 0h2m22s