[2023-03-16 00:42:12,742] [INFO] DFAST_QC pipeline started.
[2023-03-16 00:42:12,742] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 00:42:12,743] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a304345-0a83-41a9-a2ab-b3095ca9ab89/dqc_reference
[2023-03-16 00:42:14,522] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 00:42:14,523] [INFO] Task started: Prodigal
[2023-03-16 00:42:14,523] [INFO] Running command: cat /var/lib/cwl/stgb1f28ad6-b3c2-487d-964a-b16b249ce1b3/OceanDNA-b3607.fa | prodigal -d OceanDNA-b3607/cds.fna -a OceanDNA-b3607/protein.faa -g 11 -q > /dev/null
[2023-03-16 00:42:39,682] [INFO] Task succeeded: Prodigal
[2023-03-16 00:42:39,683] [INFO] Task started: HMMsearch
[2023-03-16 00:42:39,683] [INFO] Running command: hmmsearch --tblout OceanDNA-b3607/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a304345-0a83-41a9-a2ab-b3095ca9ab89/dqc_reference/reference_markers.hmm OceanDNA-b3607/protein.faa > /dev/null
[2023-03-16 00:42:39,892] [INFO] Task succeeded: HMMsearch
[2023-03-16 00:42:39,893] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgb1f28ad6-b3c2-487d-964a-b16b249ce1b3/OceanDNA-b3607.fa]
[2023-03-16 00:42:39,915] [INFO] Query marker FASTA was written to OceanDNA-b3607/markers.fasta
[2023-03-16 00:42:39,916] [INFO] Task started: Blastn
[2023-03-16 00:42:39,916] [INFO] Running command: blastn -query OceanDNA-b3607/markers.fasta -db /var/lib/cwl/stg4a304345-0a83-41a9-a2ab-b3095ca9ab89/dqc_reference/reference_markers.fasta -out OceanDNA-b3607/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:42:40,507] [INFO] Task succeeded: Blastn
[2023-03-16 00:42:40,508] [INFO] Selected 28 target genomes.
[2023-03-16 00:42:40,509] [INFO] Target genome list was writen to OceanDNA-b3607/target_genomes.txt
[2023-03-16 00:42:40,520] [INFO] Task started: fastANI
[2023-03-16 00:42:40,520] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1f28ad6-b3c2-487d-964a-b16b249ce1b3/OceanDNA-b3607.fa --refList OceanDNA-b3607/target_genomes.txt --output OceanDNA-b3607/fastani_result.tsv --threads 1
[2023-03-16 00:43:02,840] [INFO] Task succeeded: fastANI
[2023-03-16 00:43:02,840] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a304345-0a83-41a9-a2ab-b3095ca9ab89/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 00:43:02,840] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a304345-0a83-41a9-a2ab-b3095ca9ab89/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 00:43:02,846] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 00:43:02,847] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 00:43:02,847] [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
Neolewinella litorea	strain=HSMS-39	GCA_004803465.1	2562452	2562452	type	True	75.7156	50	913	95	below_threshold
Neolewinella marina	strain=MKG-38	GCA_002631205.1	438751	438751	type	True	75.6928	82	913	95	below_threshold
Neolewinella marina	strain=DSM 104084	GCA_011927705.1	438751	438751	type	True	75.6799	83	913	95	below_threshold
Neolewinella xylanilytica	strain=DSM 29526	GCA_002934605.1	1514080	1514080	type	True	75.5647	54	913	95	below_threshold
Neolewinella lacunae	strain=KCTC 42187	GCA_014349155.1	1517758	1517758	type	True	75.5164	55	913	95	below_threshold
Neolewinella aquimaris	strain=DSM 105137	GCA_014197245.1	1835722	1835722	type	True	75.3348	53	913	95	below_threshold
Neolewinella maritima	strain=CECT 8419, type strain	GCA_923081025.1	1383882	1383882	type	True	75.1739	52	913	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	74.9154	57	913	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 00:43:02,885] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3607/tc_result.tsv
[2023-03-16 00:43:02,885] [INFO] ===== Taxonomy check completed =====
[2023-03-16 00:43:02,886] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 00:43:02,886] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a304345-0a83-41a9-a2ab-b3095ca9ab89/dqc_reference/checkm_data
[2023-03-16 00:43:02,886] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 00:43:02,911] [INFO] Task started: CheckM
[2023-03-16 00:43:02,911] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3607/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3607/checkm_input OceanDNA-b3607/checkm_result
[2023-03-16 00:44:03,960] [INFO] Task succeeded: CheckM
[2023-03-16 00:44:03,961] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.42%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 00:44:03,969] [INFO] ===== Completeness check finished =====
[2023-03-16 00:44:03,969] [INFO] ===== Start GTDB Search =====
[2023-03-16 00:44:03,969] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3607/markers.fasta)
[2023-03-16 00:44:03,970] [INFO] Task started: Blastn
[2023-03-16 00:44:03,970] [INFO] Running command: blastn -query OceanDNA-b3607/markers.fasta -db /var/lib/cwl/stg4a304345-0a83-41a9-a2ab-b3095ca9ab89/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3607/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:44:04,940] [INFO] Task succeeded: Blastn
[2023-03-16 00:44:04,943] [INFO] Selected 33 target genomes.
[2023-03-16 00:44:04,943] [INFO] Target genome list was writen to OceanDNA-b3607/target_genomes_gtdb.txt
[2023-03-16 00:44:05,006] [INFO] Task started: fastANI
[2023-03-16 00:44:05,006] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1f28ad6-b3c2-487d-964a-b16b249ce1b3/OceanDNA-b3607.fa --refList OceanDNA-b3607/target_genomes_gtdb.txt --output OceanDNA-b3607/fastani_result_gtdb.tsv --threads 1
[2023-03-16 00:44:33,188] [INFO] Task succeeded: fastANI
[2023-03-16 00:44:33,194] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 00:44:33,194] [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_003390915.1	s__Lewinella_A sp003390915	76.0248	69	913	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004803465.1	s__Lewinella_A litorea	75.7156	50	913	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002631205.1	s__Lewinella_A marina	75.6928	82	913	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002934605.1	s__Lewinella_A xylanilytica	75.5647	54	913	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197245.1	s__Lewinella_A aquimaris	75.3348	53	913	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004765605.1	s__Hymenobacter aquaticus	75.1954	54	913	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008727865.1	s__Solirubrum busanensis	75.0817	54	913	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	75.0362	60	913	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	95.46	95.46	0.89	0.89	2	-
GCF_003970915.1	s__Solirubrum gummosum	75.0222	64	913	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Solirubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737515.1	s__Hymenobacter sp000737515	75.0177	54	913	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 00:44:33,196] [INFO] GTDB search result was written to OceanDNA-b3607/result_gtdb.tsv
[2023-03-16 00:44:33,197] [INFO] ===== GTDB Search completed =====
[2023-03-16 00:44:33,200] [INFO] DFAST_QC result json was written to OceanDNA-b3607/dqc_result.json
[2023-03-16 00:44:33,200] [INFO] DFAST_QC completed!
[2023-03-16 00:44:33,200] [INFO] Total running time: 0h2m20s