[2023-03-16 04:52:20,123] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:52:20,123] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:52:20,123] [INFO] DQC Reference Directory: /var/lib/cwl/stg111c41ea-32e5-4da3-9212-57af7f879ab0/dqc_reference
[2023-03-16 04:52:21,249] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:52:21,250] [INFO] Task started: Prodigal
[2023-03-16 04:52:21,250] [INFO] Running command: cat /var/lib/cwl/stg74b52109-4a72-459e-aa69-827a7daac514/OceanDNA-b6781.fa | prodigal -d OceanDNA-b6781/cds.fna -a OceanDNA-b6781/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:52:40,101] [INFO] Task succeeded: Prodigal
[2023-03-16 04:52:40,102] [INFO] Task started: HMMsearch
[2023-03-16 04:52:40,102] [INFO] Running command: hmmsearch --tblout OceanDNA-b6781/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg111c41ea-32e5-4da3-9212-57af7f879ab0/dqc_reference/reference_markers.hmm OceanDNA-b6781/protein.faa > /dev/null
[2023-03-16 04:52:40,294] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:52:40,294] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg74b52109-4a72-459e-aa69-827a7daac514/OceanDNA-b6781.fa]
[2023-03-16 04:52:40,313] [INFO] Query marker FASTA was written to OceanDNA-b6781/markers.fasta
[2023-03-16 04:52:40,313] [INFO] Task started: Blastn
[2023-03-16 04:52:40,313] [INFO] Running command: blastn -query OceanDNA-b6781/markers.fasta -db /var/lib/cwl/stg111c41ea-32e5-4da3-9212-57af7f879ab0/dqc_reference/reference_markers.fasta -out OceanDNA-b6781/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:52:40,918] [INFO] Task succeeded: Blastn
[2023-03-16 04:52:40,919] [INFO] Selected 19 target genomes.
[2023-03-16 04:52:40,919] [INFO] Target genome list was writen to OceanDNA-b6781/target_genomes.txt
[2023-03-16 04:52:40,929] [INFO] Task started: fastANI
[2023-03-16 04:52:40,929] [INFO] Running command: fastANI --query /var/lib/cwl/stg74b52109-4a72-459e-aa69-827a7daac514/OceanDNA-b6781.fa --refList OceanDNA-b6781/target_genomes.txt --output OceanDNA-b6781/fastani_result.tsv --threads 1
[2023-03-16 04:52:54,805] [INFO] Task succeeded: fastANI
[2023-03-16 04:52:54,805] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg111c41ea-32e5-4da3-9212-57af7f879ab0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:52:54,806] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg111c41ea-32e5-4da3-9212-57af7f879ab0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:52:54,816] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:52:54,816] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:52:54,816] [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
Flavobacterium kayseriense	strain=F-47	GCA_014305095.1	2764714	2764714	type	True	87.3774	788	977	95	below_threshold
Flavobacterium muglaense	strain=F-60	GCA_014305155.1	2764716	2764716	type	True	82.3633	462	977	95	below_threshold
Flavobacterium frigidarium	strain=DSM 17623	GCA_000425505.1	99286	99286	type	True	80.1424	405	977	95	below_threshold
Flavobacterium gillisiae	strain=DSM 22376	GCA_900107635.1	150146	150146	type	True	78.9833	418	977	95	below_threshold
Flavobacterium degerlachei	strain=DSM 15718	GCA_900106645.1	229203	229203	type	True	78.9219	399	977	95	below_threshold
Flavobacterium granuli	strain=DSM 19729	GCA_900129705.1	280093	280093	type	True	78.7137	340	977	95	below_threshold
Flavobacterium granuli	strain=DSM 17797	GCA_003003155.1	280093	280093	type	True	78.7002	343	977	95	below_threshold
Flavobacterium flabelliforme	strain=P4023	GCA_017948675.1	2816119	2816119	type	True	78.5572	345	977	95	below_threshold
Flavobacterium commune	strain=PK15	GCA_001857965.1	1306519	1306519	type	True	78.543	293	977	95	below_threshold
Flavobacterium xinjiangense	strain=CGMCC 1.2749	GCA_900142885.1	178356	178356	type	True	78.5175	345	977	95	below_threshold
Flavobacterium faecale	strain=WV33	GCA_003076455.1	1355330	1355330	type	True	78.5062	306	977	95	below_threshold
Flavobacterium flevense	strain=DSM 1076	GCA_900142775.1	983	983	type	True	78.382	305	977	95	below_threshold
Flavobacterium flevense	strain=NBRC 14960	GCA_006539745.1	983	983	type	True	78.3671	301	977	95	below_threshold
Flavobacterium palustre	strain=CGMCC 1.12811	GCA_014639535.1	1476463	1476463	type	True	78.271	284	977	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	77.7129	258	977	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	77.7109	270	977	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	77.6825	290	977	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	77.4901	276	977	95	below_threshold
Flavobacterium oreochromis	strain=Costa Rica 04-02-TN	GCA_019565455.1	2906078	2906078	type	True	76.4387	91	977	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:52:54,817] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6781/tc_result.tsv
[2023-03-16 04:52:54,817] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:52:54,817] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:52:54,817] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg111c41ea-32e5-4da3-9212-57af7f879ab0/dqc_reference/checkm_data
[2023-03-16 04:52:54,818] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:52:54,822] [INFO] Task started: CheckM
[2023-03-16 04:52:54,822] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6781/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6781/checkm_input OceanDNA-b6781/checkm_result
[2023-03-16 04:53:43,524] [INFO] Task succeeded: CheckM
[2023-03-16 04:53:43,524] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 48.84%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:53:43,526] [INFO] ===== Completeness check finished =====
[2023-03-16 04:53:43,527] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:53:43,527] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6781/markers.fasta)
[2023-03-16 04:53:43,527] [INFO] Task started: Blastn
[2023-03-16 04:53:43,527] [INFO] Running command: blastn -query OceanDNA-b6781/markers.fasta -db /var/lib/cwl/stg111c41ea-32e5-4da3-9212-57af7f879ab0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6781/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:53:44,496] [INFO] Task succeeded: Blastn
[2023-03-16 04:53:44,497] [INFO] Selected 16 target genomes.
[2023-03-16 04:53:44,497] [INFO] Target genome list was writen to OceanDNA-b6781/target_genomes_gtdb.txt
[2023-03-16 04:53:44,507] [INFO] Task started: fastANI
[2023-03-16 04:53:44,507] [INFO] Running command: fastANI --query /var/lib/cwl/stg74b52109-4a72-459e-aa69-827a7daac514/OceanDNA-b6781.fa --refList OceanDNA-b6781/target_genomes_gtdb.txt --output OceanDNA-b6781/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:53:55,042] [INFO] Task succeeded: fastANI
[2023-03-16 04:53:55,052] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:53:55,052] [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_014305095.1	s__Flavobacterium kayseriense	87.3774	788	977	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.16	98.32	0.96	0.92	3	-
GCF_014305155.1	s__Flavobacterium sp014305155	82.3927	460	977	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000425505.1	s__Flavobacterium frigidarium	80.1564	404	977	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013294005.1	s__Flavobacterium sp013294005	80.0517	461	977	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.41	97.36	0.86	0.85	3	-
GCF_900106645.1	s__Flavobacterium degerlachei	78.9276	398	977	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129705.1	s__Flavobacterium granuli	78.7137	340	977	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000744835.1	s__Flavobacterium sp000744835	78.5743	331	977	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280815.1	s__Flavobacterium sp002280815	78.5638	276	977	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014281985.1	s__Flavobacterium sp014281985	78.5449	334	977	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.07	98.07	0.91	0.91	2	-
GCF_001857965.1	s__Flavobacterium commune	78.5341	293	977	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.64	97.64	0.89	0.89	2	-
GCF_900142885.1	s__Flavobacterium xinjiangense	78.5175	345	977	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634825.1	s__Flavobacterium sp003634825	78.5034	287	977	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004016525.1	s__Flavobacterium sufflavum	78.3902	308	977	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000695795.1	s__Flavobacterium seoulense	78.3885	297	977	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142775.1	s__Flavobacterium flevense	78.3801	305	977	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014639535.1	s__Flavobacterium palustre	78.271	284	977	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:53:55,052] [INFO] GTDB search result was written to OceanDNA-b6781/result_gtdb.tsv
[2023-03-16 04:53:55,052] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:53:55,054] [INFO] DFAST_QC result json was written to OceanDNA-b6781/dqc_result.json
[2023-03-16 04:53:55,054] [INFO] DFAST_QC completed!
[2023-03-16 04:53:55,054] [INFO] Total running time: 0h1m35s