[2023-03-15 23:07:02,639] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:07:02,640] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:07:02,640] [INFO] DQC Reference Directory: /var/lib/cwl/stg37874fd3-baf2-43b6-97a1-d2160803b254/dqc_reference
[2023-03-15 23:07:03,966] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:07:03,966] [INFO] Task started: Prodigal
[2023-03-15 23:07:03,967] [INFO] Running command: cat /var/lib/cwl/stgb9da0ea0-9dc1-4e26-9823-f5c67c373106/OceanDNA-b3708.fa | prodigal -d OceanDNA-b3708/cds.fna -a OceanDNA-b3708/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:07:24,293] [INFO] Task succeeded: Prodigal
[2023-03-15 23:07:24,293] [INFO] Task started: HMMsearch
[2023-03-15 23:07:24,293] [INFO] Running command: hmmsearch --tblout OceanDNA-b3708/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg37874fd3-baf2-43b6-97a1-d2160803b254/dqc_reference/reference_markers.hmm OceanDNA-b3708/protein.faa > /dev/null
[2023-03-15 23:07:24,513] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:07:24,513] [INFO] Found 6/6 markers.
[2023-03-15 23:07:24,538] [INFO] Query marker FASTA was written to OceanDNA-b3708/markers.fasta
[2023-03-15 23:07:24,540] [INFO] Task started: Blastn
[2023-03-15 23:07:24,540] [INFO] Running command: blastn -query OceanDNA-b3708/markers.fasta -db /var/lib/cwl/stg37874fd3-baf2-43b6-97a1-d2160803b254/dqc_reference/reference_markers.fasta -out OceanDNA-b3708/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:07:25,072] [INFO] Task succeeded: Blastn
[2023-03-15 23:07:25,073] [INFO] Selected 17 target genomes.
[2023-03-15 23:07:25,073] [INFO] Target genome list was writen to OceanDNA-b3708/target_genomes.txt
[2023-03-15 23:07:25,085] [INFO] Task started: fastANI
[2023-03-15 23:07:25,086] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9da0ea0-9dc1-4e26-9823-f5c67c373106/OceanDNA-b3708.fa --refList OceanDNA-b3708/target_genomes.txt --output OceanDNA-b3708/fastani_result.tsv --threads 1
[2023-03-15 23:07:39,750] [INFO] Task succeeded: fastANI
[2023-03-15 23:07:39,751] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg37874fd3-baf2-43b6-97a1-d2160803b254/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:07:39,751] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg37874fd3-baf2-43b6-97a1-d2160803b254/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:07:39,758] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:07:39,758] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 23:07:39,758] [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 aurantiaca	strain=SSH13	GCA_008014675.1	2602767	2602767	type	True	78.6237	313	635	95	below_threshold
Neolewinella agarilytica	strain=DSM 24740	GCA_900110645.1	478744	478744	type	True	77.1801	130	635	95	below_threshold
Neolewinella persica	strain=DSM 23188	GCA_000373105.1	70998	70998	type	True	76.9649	160	635	95	below_threshold
Neolewinella marina	strain=MKG-38	GCA_002631205.1	438751	438751	type	True	76.5194	80	635	95	below_threshold
Neolewinella marina	strain=DSM 104084	GCA_011927705.1	438751	438751	type	True	76.4914	82	635	95	below_threshold
Neolewinella lacunae	strain=KCTC 42187	GCA_014349155.1	1517758	1517758	type	True	76.4422	128	635	95	below_threshold
Neolewinella antarctica	strain=DSM 105096	GCA_011927835.1	442734	442734	type	True	76.3404	85	635	95	below_threshold
Neolewinella aquimaris	strain=DSM 105137	GCA_014197245.1	1835722	1835722	type	True	76.1443	62	635	95	below_threshold
Neolewinella litorea	strain=HSMS-39	GCA_004803465.1	2562452	2562452	type	True	75.8594	63	635	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 23:07:39,763] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3708/tc_result.tsv
[2023-03-15 23:07:39,764] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:07:39,764] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:07:39,764] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg37874fd3-baf2-43b6-97a1-d2160803b254/dqc_reference/checkm_data
[2023-03-15 23:07:39,765] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:07:39,773] [INFO] Task started: CheckM
[2023-03-15 23:07:39,773] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3708/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3708/checkm_input OceanDNA-b3708/checkm_result
[2023-03-15 23:08:31,389] [INFO] Task succeeded: CheckM
[2023-03-15 23:08:31,390] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.45%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 23:08:31,423] [INFO] ===== Completeness check finished =====
[2023-03-15 23:08:31,423] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:08:31,423] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3708/markers.fasta)
[2023-03-15 23:08:31,424] [INFO] Task started: Blastn
[2023-03-15 23:08:31,424] [INFO] Running command: blastn -query OceanDNA-b3708/markers.fasta -db /var/lib/cwl/stg37874fd3-baf2-43b6-97a1-d2160803b254/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3708/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:08:32,189] [INFO] Task succeeded: Blastn
[2023-03-15 23:08:32,192] [INFO] Selected 21 target genomes.
[2023-03-15 23:08:32,192] [INFO] Target genome list was writen to OceanDNA-b3708/target_genomes_gtdb.txt
[2023-03-15 23:08:32,208] [INFO] Task started: fastANI
[2023-03-15 23:08:32,208] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9da0ea0-9dc1-4e26-9823-f5c67c373106/OceanDNA-b3708.fa --refList OceanDNA-b3708/target_genomes_gtdb.txt --output OceanDNA-b3708/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:08:49,313] [INFO] Task succeeded: fastANI
[2023-03-15 23:08:49,321] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 23:08:49,321] [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_008014675.1	s__Lewinella_A aurantiaca	78.618	314	635	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_900110645.1	s__Lewinella_A agarilytica	77.1801	130	635	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	76.9646	160	635	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	76.7782	80	635	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	76.5194	80	635	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_014349155.1	s__Lewinella_A lacunae	76.4573	127	635	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	76.3928	80	635	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	76.3177	86	635	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	76.2012	88	635	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	76.1443	62	635	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	76.0802	59	635	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	75.8594	63	635	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 23:08:49,323] [INFO] GTDB search result was written to OceanDNA-b3708/result_gtdb.tsv
[2023-03-15 23:08:49,325] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:08:49,331] [INFO] DFAST_QC result json was written to OceanDNA-b3708/dqc_result.json
[2023-03-15 23:08:49,331] [INFO] DFAST_QC completed!
[2023-03-15 23:08:49,332] [INFO] Total running time: 0h1m47s