[2023-03-19 01:50:01,575] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:50:01,575] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:50:01,575] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb5101af-79e5-459b-ab00-f6353a0fa6ea/dqc_reference
[2023-03-19 01:50:02,679] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:50:02,679] [INFO] Task started: Prodigal
[2023-03-19 01:50:02,679] [INFO] Running command: cat /var/lib/cwl/stgeabb7692-1bfd-425f-83bc-f51b2d790782/OceanDNA-b6709.fa | prodigal -d OceanDNA-b6709/cds.fna -a OceanDNA-b6709/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:50:36,037] [INFO] Task succeeded: Prodigal
[2023-03-19 01:50:36,037] [INFO] Task started: HMMsearch
[2023-03-19 01:50:36,037] [INFO] Running command: hmmsearch --tblout OceanDNA-b6709/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb5101af-79e5-459b-ab00-f6353a0fa6ea/dqc_reference/reference_markers.hmm OceanDNA-b6709/protein.faa > /dev/null
[2023-03-19 01:50:36,267] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:50:36,268] [INFO] Found 6/6 markers.
[2023-03-19 01:50:36,291] [INFO] Query marker FASTA was written to OceanDNA-b6709/markers.fasta
[2023-03-19 01:50:36,292] [INFO] Task started: Blastn
[2023-03-19 01:50:36,293] [INFO] Running command: blastn -query OceanDNA-b6709/markers.fasta -db /var/lib/cwl/stgbb5101af-79e5-459b-ab00-f6353a0fa6ea/dqc_reference/reference_markers.fasta -out OceanDNA-b6709/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:50:36,838] [INFO] Task succeeded: Blastn
[2023-03-19 01:50:36,838] [INFO] Selected 29 target genomes.
[2023-03-19 01:50:36,839] [INFO] Target genome list was writen to OceanDNA-b6709/target_genomes.txt
[2023-03-19 01:50:36,857] [INFO] Task started: fastANI
[2023-03-19 01:50:36,858] [INFO] Running command: fastANI --query /var/lib/cwl/stgeabb7692-1bfd-425f-83bc-f51b2d790782/OceanDNA-b6709.fa --refList OceanDNA-b6709/target_genomes.txt --output OceanDNA-b6709/fastani_result.tsv --threads 1
[2023-03-19 01:50:54,211] [INFO] Task succeeded: fastANI
[2023-03-19 01:50:54,212] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb5101af-79e5-459b-ab00-f6353a0fa6ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:50:54,212] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb5101af-79e5-459b-ab00-f6353a0fa6ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:50:54,222] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:50:54,222] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 01:50:54,223] [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
Muricauda alvinocaridis	strain=SCR12	GCA_004916895.1	2530200	2530200	type	True	76.8816	160	1368	95	below_threshold
Muricauda algicola	strain=AsT0115	GCA_005937185.1	2583815	2583815	type	True	76.649	175	1368	95	below_threshold
Muricauda aquimarina	strain=JCM11811	GCA_003992675.1	254955	254955	type	True	76.6459	136	1368	95	below_threshold
Muricauda beolgyonensis	strain=KCTC 23501	GCA_003992615.1	864064	864064	type	True	76.5772	143	1368	95	below_threshold
Muricauda amphidinii	strain=LMIT004	GCA_013090115.1	2735167	2735167	type	True	76.5713	153	1368	95	below_threshold
Muricauda ochracea	strain=JGD-17	GCA_009903685.1	2696472	2696472	type	True	76.5384	146	1368	95	below_threshold
Muricauda onchidii	strain=XY-359	GCA_004804315.1	2562684	2562684	type	True	76.5158	133	1368	95	below_threshold
Muricauda profundi	strain=BC31-3-A3	GCA_017313275.1	2915620	2915620	type	True	76.4566	137	1368	95	below_threshold
Croceitalea dokdonensis	strain=DOKDO 023	GCA_001306415.1	346188	346188	type	True	76.4025	143	1368	95	below_threshold
Muricauda olearia	strain=CL-SS4	GCA_009184425.1	552546	552546	type	True	76.339	175	1368	95	below_threshold
Muricauda lutaonensis	strain=CC-HSB-11	GCA_000963865.1	516051	516051	type	True	76.3278	119	1368	95	below_threshold
Muricauda hymeniacidonis	strain=176CP4-71	GCA_004296335.1	2517819	2517819	type	True	76.3074	154	1368	95	below_threshold
Muricauda parva	strain=DSM 25885	GCA_900215465.1	1247520	1247520	type	True	76.2912	175	1368	95	below_threshold
Muricauda amoyensis	strain=GCL-11	GCA_003058265.1	2169401	2169401	type	True	76.2519	132	1368	95	below_threshold
Muricauda flava	strain=DSM 22638	GCA_900129665.1	570519	570519	type	True	76.2307	151	1368	95	below_threshold
Arenibacter catalasegens	strain=P308H10	GCA_002909235.1	2056779	2056779	type	True	75.9994	78	1368	95	below_threshold
Maribacter algicola	strain=PoM-212	GCA_003933245.1	2498892	2498892	type	True	75.8902	95	1368	95	below_threshold
Aggregatimonas sangjinii	strain=F202Z8	GCA_005943945.1	2583587	2583587	type	True	75.7158	64	1368	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 01:50:54,223] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6709/tc_result.tsv
[2023-03-19 01:50:54,223] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:50:54,223] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:50:54,223] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb5101af-79e5-459b-ab00-f6353a0fa6ea/dqc_reference/checkm_data
[2023-03-19 01:50:54,224] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:50:54,229] [INFO] Task started: CheckM
[2023-03-19 01:50:54,229] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6709/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6709/checkm_input OceanDNA-b6709/checkm_result
[2023-03-19 01:52:18,343] [INFO] Task succeeded: CheckM
[2023-03-19 01:52:18,343] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.90%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 01:52:18,346] [INFO] ===== Completeness check finished =====
[2023-03-19 01:52:18,346] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:52:18,347] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6709/markers.fasta)
[2023-03-19 01:52:18,348] [INFO] Task started: Blastn
[2023-03-19 01:52:18,348] [INFO] Running command: blastn -query OceanDNA-b6709/markers.fasta -db /var/lib/cwl/stgbb5101af-79e5-459b-ab00-f6353a0fa6ea/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6709/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:52:19,102] [INFO] Task succeeded: Blastn
[2023-03-19 01:52:19,103] [INFO] Selected 25 target genomes.
[2023-03-19 01:52:19,103] [INFO] Target genome list was writen to OceanDNA-b6709/target_genomes_gtdb.txt
[2023-03-19 01:52:19,121] [INFO] Task started: fastANI
[2023-03-19 01:52:19,121] [INFO] Running command: fastANI --query /var/lib/cwl/stgeabb7692-1bfd-425f-83bc-f51b2d790782/OceanDNA-b6709.fa --refList OceanDNA-b6709/target_genomes_gtdb.txt --output OceanDNA-b6709/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:52:34,203] [INFO] Task succeeded: fastANI
[2023-03-19 01:52:34,213] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 01:52:34,213] [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_009797885.1	s__Croceivirga sp009797885	77.9324	385	1368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004916895.1	s__Muricauda alvinocaridis	76.8827	159	1368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214065.1	s__DT-32 sp013214065	76.6632	144	1368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__DT-32	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013090115.1	s__Muricauda amphidinii	76.5713	153	1368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013407935.1	s__Muricauda sp013407935	76.5585	136	1368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.58	96.50	0.87	0.86	8	-
GCF_000745185.1	s__Muricauda sp000745185	76.5574	143	1368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017313225.1	s__Muricauda sp017313225	76.5551	162	1368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385855.1	s__Muricauda sp003385855	76.544	164	1368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	97.98	97.98	0.89	0.89	2	-
GCF_004804315.1	s__Muricauda sp004804315	76.5158	133	1368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012272815.1	s__Croceivirga sp012272815	76.5123	188	1368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008040165.1	s__Muricauda hymeniacidonis	76.491	143	1368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001413955.1	s__Muricauda eckloniae	76.4706	164	1368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001306415.1	s__Croceitalea dokdonensis	76.4025	143	1368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002742265.1	s__Maribacter sp002742265	76.3708	84	1368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000963865.1	s__Muricauda_A lutaonensis	76.3278	119	1368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda_A	95.0	97.74	97.69	0.86	0.85	5	-
GCF_900215465.1	s__Muricauda pacifica_A	76.2912	175	1368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813125.1	s__Muricauda sp002813125	76.2579	143	1368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003058265.1	s__Muricauda sp003058265	76.2484	131	1368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129665.1	s__Muricauda flava	76.2307	151	1368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 01:52:34,214] [INFO] GTDB search result was written to OceanDNA-b6709/result_gtdb.tsv
[2023-03-19 01:52:34,214] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:52:34,216] [INFO] DFAST_QC result json was written to OceanDNA-b6709/dqc_result.json
[2023-03-19 01:52:34,216] [INFO] DFAST_QC completed!
[2023-03-19 01:52:34,216] [INFO] Total running time: 0h2m33s