[2023-03-17 00:02:20,731] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:02:20,731] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:02:20,731] [INFO] DQC Reference Directory: /var/lib/cwl/stg070c568b-597a-4013-890e-4d197d5c9028/dqc_reference
[2023-03-17 00:02:21,844] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:02:21,845] [INFO] Task started: Prodigal
[2023-03-17 00:02:21,845] [INFO] Running command: cat /var/lib/cwl/stg9c616fcb-5519-4c5b-892d-86e536b784c8/OceanDNA-b3714.fa | prodigal -d OceanDNA-b3714/cds.fna -a OceanDNA-b3714/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:02:48,931] [INFO] Task succeeded: Prodigal
[2023-03-17 00:02:48,932] [INFO] Task started: HMMsearch
[2023-03-17 00:02:48,932] [INFO] Running command: hmmsearch --tblout OceanDNA-b3714/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg070c568b-597a-4013-890e-4d197d5c9028/dqc_reference/reference_markers.hmm OceanDNA-b3714/protein.faa > /dev/null
[2023-03-17 00:02:49,149] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:02:49,150] [INFO] Found 6/6 markers.
[2023-03-17 00:02:49,175] [INFO] Query marker FASTA was written to OceanDNA-b3714/markers.fasta
[2023-03-17 00:02:49,176] [INFO] Task started: Blastn
[2023-03-17 00:02:49,176] [INFO] Running command: blastn -query OceanDNA-b3714/markers.fasta -db /var/lib/cwl/stg070c568b-597a-4013-890e-4d197d5c9028/dqc_reference/reference_markers.fasta -out OceanDNA-b3714/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:02:49,737] [INFO] Task succeeded: Blastn
[2023-03-17 00:02:49,738] [INFO] Selected 11 target genomes.
[2023-03-17 00:02:49,739] [INFO] Target genome list was writen to OceanDNA-b3714/target_genomes.txt
[2023-03-17 00:02:49,763] [INFO] Task started: fastANI
[2023-03-17 00:02:49,763] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c616fcb-5519-4c5b-892d-86e536b784c8/OceanDNA-b3714.fa --refList OceanDNA-b3714/target_genomes.txt --output OceanDNA-b3714/fastani_result.tsv --threads 1
[2023-03-17 00:02:58,250] [INFO] Task succeeded: fastANI
[2023-03-17 00:02:58,250] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg070c568b-597a-4013-890e-4d197d5c9028/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:02:58,251] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg070c568b-597a-4013-890e-4d197d5c9028/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:02:58,258] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 00:02:58,258] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 00:02:58,258] [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 maritima	strain=CECT 8419, type strain	GCA_923081025.1	1383882	1383882	type	True	79.943	683	1144	95	below_threshold
Neolewinella marina	strain=MKG-38	GCA_002631205.1	438751	438751	type	True	79.7493	601	1144	95	below_threshold
Neolewinella marina	strain=DSM 104084	GCA_011927705.1	438751	438751	type	True	79.7237	607	1144	95	below_threshold
Neolewinella litorea	strain=HSMS-39	GCA_004803465.1	2562452	2562452	type	True	78.8084	515	1144	95	below_threshold
Neolewinella aquimaris	strain=DSM 105137	GCA_014197245.1	1835722	1835722	type	True	78.6222	526	1144	95	below_threshold
Neolewinella xylanilytica	strain=DSM 29526	GCA_002934605.1	1514080	1514080	type	True	77.8426	433	1144	95	below_threshold
Neolewinella lacunae	strain=KCTC 42187	GCA_014349155.1	1517758	1517758	type	True	77.0082	263	1144	95	below_threshold
Hymenobacter piscis	strain=NST-14	GCA_018760735.1	2839984	2839984	type	True	75.6085	59	1144	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 00:02:58,258] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3714/tc_result.tsv
[2023-03-17 00:02:58,259] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:02:58,259] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:02:58,259] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg070c568b-597a-4013-890e-4d197d5c9028/dqc_reference/checkm_data
[2023-03-17 00:02:58,259] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:02:58,321] [INFO] Task started: CheckM
[2023-03-17 00:02:58,321] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3714/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3714/checkm_input OceanDNA-b3714/checkm_result
[2023-03-17 00:04:03,712] [INFO] Task succeeded: CheckM
[2023-03-17 00:04:03,712] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 00:04:03,738] [INFO] ===== Completeness check finished =====
[2023-03-17 00:04:03,738] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:04:03,738] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3714/markers.fasta)
[2023-03-17 00:04:03,739] [INFO] Task started: Blastn
[2023-03-17 00:04:03,739] [INFO] Running command: blastn -query OceanDNA-b3714/markers.fasta -db /var/lib/cwl/stg070c568b-597a-4013-890e-4d197d5c9028/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3714/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:04:04,575] [INFO] Task succeeded: Blastn
[2023-03-17 00:04:04,584] [INFO] Selected 7 target genomes.
[2023-03-17 00:04:04,584] [INFO] Target genome list was writen to OceanDNA-b3714/target_genomes_gtdb.txt
[2023-03-17 00:04:04,803] [INFO] Task started: fastANI
[2023-03-17 00:04:04,803] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c616fcb-5519-4c5b-892d-86e536b784c8/OceanDNA-b3714.fa --refList OceanDNA-b3714/target_genomes_gtdb.txt --output OceanDNA-b3714/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:04:11,199] [INFO] Task succeeded: fastANI
[2023-03-17 00:04:11,205] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 00:04:11,205] [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	79.7323	603	1144	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_003390915.1	s__Lewinella_A sp003390915	79.3247	580	1144	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	78.8168	514	1144	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	78.6379	524	1144	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	77.9244	436	1144	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_002934605.1	s__Lewinella_A xylanilytica	77.8426	433	1144	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	76.9901	265	1144	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 00:04:11,207] [INFO] GTDB search result was written to OceanDNA-b3714/result_gtdb.tsv
[2023-03-17 00:04:11,207] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:04:11,208] [INFO] DFAST_QC result json was written to OceanDNA-b3714/dqc_result.json
[2023-03-17 00:04:11,208] [INFO] DFAST_QC completed!
[2023-03-17 00:04:11,208] [INFO] Total running time: 0h1m50s