[2023-03-18 10:32:24,493] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:32:24,493] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:32:24,493] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa3299d3-70df-4913-ba09-7eb142794961/dqc_reference
[2023-03-18 10:32:25,616] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:32:25,617] [INFO] Task started: Prodigal
[2023-03-18 10:32:25,617] [INFO] Running command: cat /var/lib/cwl/stg755d5b94-4db2-4416-b548-585b2506207d/OceanDNA-b3704.fa | prodigal -d OceanDNA-b3704/cds.fna -a OceanDNA-b3704/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:32:47,461] [INFO] Task succeeded: Prodigal
[2023-03-18 10:32:47,461] [INFO] Task started: HMMsearch
[2023-03-18 10:32:47,461] [INFO] Running command: hmmsearch --tblout OceanDNA-b3704/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa3299d3-70df-4913-ba09-7eb142794961/dqc_reference/reference_markers.hmm OceanDNA-b3704/protein.faa > /dev/null
[2023-03-18 10:32:47,662] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:32:47,662] [INFO] Found 6/6 markers.
[2023-03-18 10:32:47,690] [INFO] Query marker FASTA was written to OceanDNA-b3704/markers.fasta
[2023-03-18 10:32:47,691] [INFO] Task started: Blastn
[2023-03-18 10:32:47,691] [INFO] Running command: blastn -query OceanDNA-b3704/markers.fasta -db /var/lib/cwl/stgaa3299d3-70df-4913-ba09-7eb142794961/dqc_reference/reference_markers.fasta -out OceanDNA-b3704/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:32:48,244] [INFO] Task succeeded: Blastn
[2023-03-18 10:32:48,246] [INFO] Selected 19 target genomes.
[2023-03-18 10:32:48,246] [INFO] Target genome list was writen to OceanDNA-b3704/target_genomes.txt
[2023-03-18 10:32:48,259] [INFO] Task started: fastANI
[2023-03-18 10:32:48,259] [INFO] Running command: fastANI --query /var/lib/cwl/stg755d5b94-4db2-4416-b548-585b2506207d/OceanDNA-b3704.fa --refList OceanDNA-b3704/target_genomes.txt --output OceanDNA-b3704/fastani_result.tsv --threads 1
[2023-03-18 10:33:03,317] [INFO] Task succeeded: fastANI
[2023-03-18 10:33:03,317] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa3299d3-70df-4913-ba09-7eb142794961/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:33:03,317] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa3299d3-70df-4913-ba09-7eb142794961/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:33:03,325] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:33:03,325] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 10:33:03,325] [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	78.0165	197	641	95	below_threshold
Neolewinella marina	strain=MKG-38	GCA_002631205.1	438751	438751	type	True	77.963	198	641	95	below_threshold
Neolewinella maritima	strain=CECT 8419, type strain	GCA_923081025.1	1383882	1383882	type	True	77.4283	181	641	95	below_threshold
Neolewinella litorea	strain=HSMS-39	GCA_004803465.1	2562452	2562452	type	True	77.2838	164	641	95	below_threshold
Neolewinella aquimaris	strain=DSM 105137	GCA_014197245.1	1835722	1835722	type	True	77.2797	125	641	95	below_threshold
Neolewinella lacunae	strain=KCTC 42187	GCA_014349155.1	1517758	1517758	type	True	77.2607	218	641	95	below_threshold
Neolewinella antarctica	strain=DSM 105096	GCA_011927835.1	442734	442734	type	True	77.0488	119	641	95	below_threshold
Neolewinella persica	strain=DSM 23188	GCA_000373105.1	70998	70998	type	True	77.0307	115	641	95	below_threshold
Neolewinella aurantiaca	strain=SSH13	GCA_008014675.1	2602767	2602767	type	True	77.006	147	641	95	below_threshold
Neolewinella xylanilytica	strain=DSM 29526	GCA_002934605.1	1514080	1514080	type	True	76.9585	116	641	95	below_threshold
Neolewinella agarilytica	strain=DSM 24740	GCA_900110645.1	478744	478744	type	True	76.6903	109	641	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 10:33:03,325] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3704/tc_result.tsv
[2023-03-18 10:33:03,325] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:33:03,325] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:33:03,326] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa3299d3-70df-4913-ba09-7eb142794961/dqc_reference/checkm_data
[2023-03-18 10:33:03,326] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:33:03,346] [INFO] Task started: CheckM
[2023-03-18 10:33:03,346] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3704/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3704/checkm_input OceanDNA-b3704/checkm_result
[2023-03-18 10:33:57,792] [INFO] Task succeeded: CheckM
[2023-03-18 10:33:57,793] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 2.60%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-18 10:33:57,797] [INFO] ===== Completeness check finished =====
[2023-03-18 10:33:57,797] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:33:57,797] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3704/markers.fasta)
[2023-03-18 10:33:57,798] [INFO] Task started: Blastn
[2023-03-18 10:33:57,798] [INFO] Running command: blastn -query OceanDNA-b3704/markers.fasta -db /var/lib/cwl/stgaa3299d3-70df-4913-ba09-7eb142794961/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3704/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:33:58,632] [INFO] Task succeeded: Blastn
[2023-03-18 10:33:58,636] [INFO] Selected 18 target genomes.
[2023-03-18 10:33:58,636] [INFO] Target genome list was writen to OceanDNA-b3704/target_genomes_gtdb.txt
[2023-03-18 10:33:58,646] [INFO] Task started: fastANI
[2023-03-18 10:33:58,646] [INFO] Running command: fastANI --query /var/lib/cwl/stg755d5b94-4db2-4416-b548-585b2506207d/OceanDNA-b3704.fa --refList OceanDNA-b3704/target_genomes_gtdb.txt --output OceanDNA-b3704/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:34:11,936] [INFO] Task succeeded: fastANI
[2023-03-18 10:34:11,944] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 10:34:11,944] [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	77.963	198	641	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	77.3934	178	641	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	77.2838	164	641	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	77.2797	125	641	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	77.2607	218	641	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_001625015.1	s__Lewinella_A sp001625015	77.0972	137	641	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_011927835.1	s__Lewinella_A antarctica	77.0488	119	641	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_000373105.1	s__Lewinella_A persica	77.0307	115	641	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_008014675.1	s__Lewinella_A aurantiaca	77.006	147	641	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	76.9676	127	641	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_004375085.3	s__Lewinella_A sp004375085	76.8974	156	641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 10:34:11,944] [INFO] GTDB search result was written to OceanDNA-b3704/result_gtdb.tsv
[2023-03-18 10:34:11,944] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:34:11,945] [INFO] DFAST_QC result json was written to OceanDNA-b3704/dqc_result.json
[2023-03-18 10:34:11,946] [INFO] DFAST_QC completed!
[2023-03-18 10:34:11,946] [INFO] Total running time: 0h1m47s