[2023-03-18 00:53:42,656] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:53:42,656] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:53:42,656] [INFO] DQC Reference Directory: /var/lib/cwl/stg9923c943-b430-42a4-91dd-15c3d09c6b36/dqc_reference
[2023-03-18 00:53:43,737] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:53:43,738] [INFO] Task started: Prodigal
[2023-03-18 00:53:43,738] [INFO] Running command: cat /var/lib/cwl/stgb2a18158-20a2-4ab5-9ebd-8d043b557c9e/OceanDNA-b3567.fa | prodigal -d OceanDNA-b3567/cds.fna -a OceanDNA-b3567/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:54:19,854] [INFO] Task succeeded: Prodigal
[2023-03-18 00:54:19,854] [INFO] Task started: HMMsearch
[2023-03-18 00:54:19,854] [INFO] Running command: hmmsearch --tblout OceanDNA-b3567/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9923c943-b430-42a4-91dd-15c3d09c6b36/dqc_reference/reference_markers.hmm OceanDNA-b3567/protein.faa > /dev/null
[2023-03-18 00:54:20,101] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:54:20,101] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb2a18158-20a2-4ab5-9ebd-8d043b557c9e/OceanDNA-b3567.fa]
[2023-03-18 00:54:20,146] [INFO] Query marker FASTA was written to OceanDNA-b3567/markers.fasta
[2023-03-18 00:54:20,147] [INFO] Task started: Blastn
[2023-03-18 00:54:20,147] [INFO] Running command: blastn -query OceanDNA-b3567/markers.fasta -db /var/lib/cwl/stg9923c943-b430-42a4-91dd-15c3d09c6b36/dqc_reference/reference_markers.fasta -out OceanDNA-b3567/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:54:20,705] [INFO] Task succeeded: Blastn
[2023-03-18 00:54:20,713] [INFO] Selected 16 target genomes.
[2023-03-18 00:54:20,714] [INFO] Target genome list was writen to OceanDNA-b3567/target_genomes.txt
[2023-03-18 00:54:20,724] [INFO] Task started: fastANI
[2023-03-18 00:54:20,724] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2a18158-20a2-4ab5-9ebd-8d043b557c9e/OceanDNA-b3567.fa --refList OceanDNA-b3567/target_genomes.txt --output OceanDNA-b3567/fastani_result.tsv --threads 1
[2023-03-18 00:54:33,612] [INFO] Task succeeded: fastANI
[2023-03-18 00:54:33,612] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9923c943-b430-42a4-91dd-15c3d09c6b36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:54:33,613] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9923c943-b430-42a4-91dd-15c3d09c6b36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:54:33,620] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:54:33,620] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 00:54:33,620] [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
Maribellus maritimus	strain=5E3	GCA_022267315.1	2870838	2870838	type	True	76.6454	276	1739	95	below_threshold
Draconibacterium orientale	strain=DSM 25947	GCA_900111425.1	1168034	1168034	type	True	76.5729	198	1739	95	below_threshold
Maribellus comscasis	strain=WC007	GCA_009762775.1	2681766	2681766	type	True	76.5608	284	1739	95	below_threshold
Draconibacterium orientale	strain=FH5	GCA_000626635.1	1168034	1168034	type	True	76.5529	201	1739	95	below_threshold
Draconibacterium halophilum	strain=M1	GCA_010448835.1	2706887	2706887	type	True	76.5081	204	1739	95	below_threshold
Maribellus luteus	strain=XSD2	GCA_003576475.1	2305463	2305463	type	True	76.4908	122	1739	95	below_threshold
Draconibacterium mangrovi	strain=GM2-18	GCA_010586825.1	2697469	2697469	type	True	76.4431	185	1739	95	below_threshold
Mariniphaga sediminis	strain=SY21	GCA_003573545.1	1628158	1628158	type	True	76.2955	120	1739	95	below_threshold
Maribellus sediminis	strain=Y2-1-60	GCA_011799805.1	2696285	2696285	type	True	76.2815	156	1739	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:54:33,620] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3567/tc_result.tsv
[2023-03-18 00:54:33,620] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:54:33,620] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:54:33,620] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9923c943-b430-42a4-91dd-15c3d09c6b36/dqc_reference/checkm_data
[2023-03-18 00:54:33,621] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:54:33,637] [INFO] Task started: CheckM
[2023-03-18 00:54:33,637] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3567/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3567/checkm_input OceanDNA-b3567/checkm_result
[2023-03-18 00:56:02,459] [INFO] Task succeeded: CheckM
[2023-03-18 00:56:02,459] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:56:02,463] [INFO] ===== Completeness check finished =====
[2023-03-18 00:56:02,463] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:56:02,463] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3567/markers.fasta)
[2023-03-18 00:56:02,464] [INFO] Task started: Blastn
[2023-03-18 00:56:02,464] [INFO] Running command: blastn -query OceanDNA-b3567/markers.fasta -db /var/lib/cwl/stg9923c943-b430-42a4-91dd-15c3d09c6b36/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3567/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:56:03,341] [INFO] Task succeeded: Blastn
[2023-03-18 00:56:03,343] [INFO] Selected 16 target genomes.
[2023-03-18 00:56:03,343] [INFO] Target genome list was writen to OceanDNA-b3567/target_genomes_gtdb.txt
[2023-03-18 00:56:03,360] [INFO] Task started: fastANI
[2023-03-18 00:56:03,360] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2a18158-20a2-4ab5-9ebd-8d043b557c9e/OceanDNA-b3567.fa --refList OceanDNA-b3567/target_genomes_gtdb.txt --output OceanDNA-b3567/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:56:17,280] [INFO] Task succeeded: fastANI
[2023-03-18 00:56:17,290] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 00:56:17,290] [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
GCA_018648265.1	s__Draconibacterium sp018648265	99.957	1635	1739	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	99.94	99.92	0.96	0.95	4	conclusive
GCA_013203755.1	s__Draconibacterium sp013203755	78.2716	382	1739	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009762775.1	s__Draconibacterium comscasis	76.5737	282	1739	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000626635.1	s__Draconibacterium orientale	76.5439	201	1739	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_010448835.1	s__Draconibacterium halophilum	76.5283	202	1739	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015493625.1	s__Draconibacterium sp015493625	76.5067	181	1739	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003576475.1	s__Draconibacterium luteum	76.5063	121	1739	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016705335.1	s__Draconibacterium sp016705335	76.4566	269	1739	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010586825.1	s__Draconibacterium mangrovi	76.453	184	1739	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016931875.1	s__Draconibacterium sp016931875	76.4404	167	1739	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009773765.1	s__Draconibacterium sp009773765	76.4331	217	1739	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003573545.1	s__Mariniphaga sediminis	76.3234	118	1739	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Mariniphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011799805.1	s__Draconibacterium sp011799805	76.3	153	1739	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	96.71	96.71	0.85	0.85	2	-
GCA_011620585.1	s__Draconibacterium sp011620585	76.0983	151	1739	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003516705.1	s__Draconibacterium sp003516705	75.6541	130	1739	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:56:17,291] [INFO] GTDB search result was written to OceanDNA-b3567/result_gtdb.tsv
[2023-03-18 00:56:17,291] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:56:17,293] [INFO] DFAST_QC result json was written to OceanDNA-b3567/dqc_result.json
[2023-03-18 00:56:17,293] [INFO] DFAST_QC completed!
[2023-03-18 00:56:17,293] [INFO] Total running time: 0h2m35s