[2023-03-17 11:38:03,753] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:38:03,753] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:38:03,753] [INFO] DQC Reference Directory: /var/lib/cwl/stg7326a9eb-98e5-48b8-8678-113f08134f1a/dqc_reference
[2023-03-17 11:38:04,837] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:38:04,837] [INFO] Task started: Prodigal
[2023-03-17 11:38:04,837] [INFO] Running command: cat /var/lib/cwl/stgcdac7cae-db0a-40a4-bef1-1532e0ef2a57/OceanDNA-b3711.fa | prodigal -d OceanDNA-b3711/cds.fna -a OceanDNA-b3711/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:38:32,650] [INFO] Task succeeded: Prodigal
[2023-03-17 11:38:32,650] [INFO] Task started: HMMsearch
[2023-03-17 11:38:32,650] [INFO] Running command: hmmsearch --tblout OceanDNA-b3711/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7326a9eb-98e5-48b8-8678-113f08134f1a/dqc_reference/reference_markers.hmm OceanDNA-b3711/protein.faa > /dev/null
[2023-03-17 11:38:32,850] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:38:32,850] [INFO] Found 6/6 markers.
[2023-03-17 11:38:32,882] [INFO] Query marker FASTA was written to OceanDNA-b3711/markers.fasta
[2023-03-17 11:38:32,883] [INFO] Task started: Blastn
[2023-03-17 11:38:32,883] [INFO] Running command: blastn -query OceanDNA-b3711/markers.fasta -db /var/lib/cwl/stg7326a9eb-98e5-48b8-8678-113f08134f1a/dqc_reference/reference_markers.fasta -out OceanDNA-b3711/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:38:33,461] [INFO] Task succeeded: Blastn
[2023-03-17 11:38:33,463] [INFO] Selected 7 target genomes.
[2023-03-17 11:38:33,463] [INFO] Target genome list was writen to OceanDNA-b3711/target_genomes.txt
[2023-03-17 11:38:33,466] [INFO] Task started: fastANI
[2023-03-17 11:38:33,467] [INFO] Running command: fastANI --query /var/lib/cwl/stgcdac7cae-db0a-40a4-bef1-1532e0ef2a57/OceanDNA-b3711.fa --refList OceanDNA-b3711/target_genomes.txt --output OceanDNA-b3711/fastani_result.tsv --threads 1
[2023-03-17 11:38:39,240] [INFO] Task succeeded: fastANI
[2023-03-17 11:38:39,240] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7326a9eb-98e5-48b8-8678-113f08134f1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:38:39,240] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7326a9eb-98e5-48b8-8678-113f08134f1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:38:39,246] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:38:39,246] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 11:38:39,246] [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 marina	strain=DSM 104084	GCA_011927705.1	438751	438751	type	True	79.4299	502	1005	95	below_threshold
Neolewinella marina	strain=MKG-38	GCA_002631205.1	438751	438751	type	True	79.3997	504	1005	95	below_threshold
Neolewinella xylanilytica	strain=DSM 29526	GCA_002934605.1	1514080	1514080	type	True	79.2563	495	1005	95	below_threshold
Neolewinella litorea	strain=HSMS-39	GCA_004803465.1	2562452	2562452	type	True	78.7375	445	1005	95	below_threshold
Neolewinella maritima	strain=CECT 8419, type strain	GCA_923081025.1	1383882	1383882	type	True	78.2983	356	1005	95	below_threshold
Neolewinella aquimaris	strain=DSM 105137	GCA_014197245.1	1835722	1835722	type	True	78.009	387	1005	95	below_threshold
Neolewinella lacunae	strain=KCTC 42187	GCA_014349155.1	1517758	1517758	type	True	76.79	213	1005	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 11:38:39,247] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3711/tc_result.tsv
[2023-03-17 11:38:39,247] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:38:39,248] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:38:39,248] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7326a9eb-98e5-48b8-8678-113f08134f1a/dqc_reference/checkm_data
[2023-03-17 11:38:39,248] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:38:39,255] [INFO] Task started: CheckM
[2023-03-17 11:38:39,255] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3711/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3711/checkm_input OceanDNA-b3711/checkm_result
[2023-03-17 11:39:46,111] [INFO] Task succeeded: CheckM
[2023-03-17 11:39:46,111] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 11:39:46,146] [INFO] ===== Completeness check finished =====
[2023-03-17 11:39:46,147] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:39:46,147] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3711/markers.fasta)
[2023-03-17 11:39:46,148] [INFO] Task started: Blastn
[2023-03-17 11:39:46,148] [INFO] Running command: blastn -query OceanDNA-b3711/markers.fasta -db /var/lib/cwl/stg7326a9eb-98e5-48b8-8678-113f08134f1a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3711/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:39:47,058] [INFO] Task succeeded: Blastn
[2023-03-17 11:39:47,060] [INFO] Selected 8 target genomes.
[2023-03-17 11:39:47,060] [INFO] Target genome list was writen to OceanDNA-b3711/target_genomes_gtdb.txt
[2023-03-17 11:39:47,064] [INFO] Task started: fastANI
[2023-03-17 11:39:47,064] [INFO] Running command: fastANI --query /var/lib/cwl/stgcdac7cae-db0a-40a4-bef1-1532e0ef2a57/OceanDNA-b3711.fa --refList OceanDNA-b3711/target_genomes_gtdb.txt --output OceanDNA-b3711/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:39:53,513] [INFO] Task succeeded: fastANI
[2023-03-17 11:39:53,517] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 11:39:53,518] [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_002631205.1	s__Lewinella_A marina	79.3997	504	1005	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	79.2509	496	1005	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_003390915.1	s__Lewinella_A sp003390915	79.2484	505	1005	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_003390935.1	s__Lewinella_A sp003390935	79.0462	501	1005	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	78.7281	446	1005	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	78.009	387	1005	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_014349155.1	s__Lewinella_A lacunae	76.79	213	1005	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 11:39:53,520] [INFO] GTDB search result was written to OceanDNA-b3711/result_gtdb.tsv
[2023-03-17 11:39:53,520] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:39:53,522] [INFO] DFAST_QC result json was written to OceanDNA-b3711/dqc_result.json
[2023-03-17 11:39:53,522] [INFO] DFAST_QC completed!
[2023-03-17 11:39:53,522] [INFO] Total running time: 0h1m50s