[2023-03-19 05:00:56,910] [INFO] DFAST_QC pipeline started.
[2023-03-19 05:00:56,910] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 05:00:56,910] [INFO] DQC Reference Directory: /var/lib/cwl/stgb48aa558-bf8e-4da9-8bb8-f260f71bf118/dqc_reference
[2023-03-19 05:00:57,996] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 05:00:57,996] [INFO] Task started: Prodigal
[2023-03-19 05:00:57,997] [INFO] Running command: cat /var/lib/cwl/stg692c629e-2291-4a76-8d5f-349dd63e0c45/OceanDNA-b7996.fa | prodigal -d OceanDNA-b7996/cds.fna -a OceanDNA-b7996/protein.faa -g 11 -q > /dev/null
[2023-03-19 05:01:07,164] [INFO] Task succeeded: Prodigal
[2023-03-19 05:01:07,164] [INFO] Task started: HMMsearch
[2023-03-19 05:01:07,164] [INFO] Running command: hmmsearch --tblout OceanDNA-b7996/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb48aa558-bf8e-4da9-8bb8-f260f71bf118/dqc_reference/reference_markers.hmm OceanDNA-b7996/protein.faa > /dev/null
[2023-03-19 05:01:07,351] [INFO] Task succeeded: HMMsearch
[2023-03-19 05:01:07,351] [INFO] Found 6/6 markers.
[2023-03-19 05:01:07,364] [INFO] Query marker FASTA was written to OceanDNA-b7996/markers.fasta
[2023-03-19 05:01:07,365] [INFO] Task started: Blastn
[2023-03-19 05:01:07,365] [INFO] Running command: blastn -query OceanDNA-b7996/markers.fasta -db /var/lib/cwl/stgb48aa558-bf8e-4da9-8bb8-f260f71bf118/dqc_reference/reference_markers.fasta -out OceanDNA-b7996/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:01:07,996] [INFO] Task succeeded: Blastn
[2023-03-19 05:01:07,996] [INFO] Selected 28 target genomes.
[2023-03-19 05:01:07,997] [INFO] Target genome list was writen to OceanDNA-b7996/target_genomes.txt
[2023-03-19 05:01:08,012] [INFO] Task started: fastANI
[2023-03-19 05:01:08,012] [INFO] Running command: fastANI --query /var/lib/cwl/stg692c629e-2291-4a76-8d5f-349dd63e0c45/OceanDNA-b7996.fa --refList OceanDNA-b7996/target_genomes.txt --output OceanDNA-b7996/fastani_result.tsv --threads 1
[2023-03-19 05:01:22,663] [INFO] Task succeeded: fastANI
[2023-03-19 05:01:22,664] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb48aa558-bf8e-4da9-8bb8-f260f71bf118/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 05:01:22,664] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb48aa558-bf8e-4da9-8bb8-f260f71bf118/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 05:01:22,669] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 05:01:22,670] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 05:01:22,670] [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
Lutibacter flavus	strain=DSM 27993	GCA_900188355.1	691689	691689	type	True	76.0191	59	518	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	75.9712	51	518	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_001680875.1	996801	996801	type	True	75.6635	52	518	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	75.5518	51	518	95	below_threshold
Aureibaculum flavum	strain=A20	GCA_016406085.1	2795986	2795986	type	True	75.5424	50	518	95	below_threshold
Aquimarina latercula	strain=DSM 2041	GCA_000430645.1	987	987	type	True	75.4692	51	518	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 05:01:22,670] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7996/tc_result.tsv
[2023-03-19 05:01:22,670] [INFO] ===== Taxonomy check completed =====
[2023-03-19 05:01:22,670] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 05:01:22,670] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb48aa558-bf8e-4da9-8bb8-f260f71bf118/dqc_reference/checkm_data
[2023-03-19 05:01:22,671] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 05:01:22,674] [INFO] Task started: CheckM
[2023-03-19 05:01:22,674] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7996/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7996/checkm_input OceanDNA-b7996/checkm_result
[2023-03-19 05:01:49,972] [INFO] Task succeeded: CheckM
[2023-03-19 05:01:49,973] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 05:01:49,974] [INFO] ===== Completeness check finished =====
[2023-03-19 05:01:49,975] [INFO] ===== Start GTDB Search =====
[2023-03-19 05:01:49,975] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7996/markers.fasta)
[2023-03-19 05:01:49,976] [INFO] Task started: Blastn
[2023-03-19 05:01:49,976] [INFO] Running command: blastn -query OceanDNA-b7996/markers.fasta -db /var/lib/cwl/stgb48aa558-bf8e-4da9-8bb8-f260f71bf118/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7996/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:01:50,693] [INFO] Task succeeded: Blastn
[2023-03-19 05:01:50,693] [INFO] Selected 11 target genomes.
[2023-03-19 05:01:50,693] [INFO] Target genome list was writen to OceanDNA-b7996/target_genomes_gtdb.txt
[2023-03-19 05:01:50,707] [INFO] Task started: fastANI
[2023-03-19 05:01:50,708] [INFO] Running command: fastANI --query /var/lib/cwl/stg692c629e-2291-4a76-8d5f-349dd63e0c45/OceanDNA-b7996.fa --refList OceanDNA-b7996/target_genomes_gtdb.txt --output OceanDNA-b7996/fastani_result_gtdb.tsv --threads 1
[2023-03-19 05:01:54,266] [INFO] Task succeeded: fastANI
[2023-03-19 05:01:54,273] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 05:01:54,273] [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_012959395.1	s__MAG-121220-bin8 sp012959395	97.7474	398	518	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	97.96	97.81	0.81	0.77	13	conclusive
GCA_905181625.1	s__MAG-121220-bin8 sp905181625	81.6859	367	518	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239275.1	s__MAG-121220-bin8 sp014239275	81.577	295	518	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.08	98.67	0.74	0.67	4	-
GCA_902511755.1	s__MAG-121220-bin8 sp902511755	79.6587	226	518	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.22	98.71	0.74	0.72	3	-
GCA_905181705.1	s__MAG-121220-bin8 sp905181705	79.0027	234	518	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002702895.1	s__MAG-121220-bin8 sp002702895	78.8775	272	518	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003331265.1	s__MAG-121220-bin8 sp003331265	78.3047	221	518	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018662905.1	s__MAG-121220-bin8 sp018662905	78.2861	121	518	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.06	99.06	0.75	0.75	2	-
GCA_905182765.1	s__MAG-121220-bin8 sp905182765	78.124	192	518	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902559035.1	s__MAG-121220-bin8 sp902559035	78.0296	174	518	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	96.40	96.04	0.82	0.79	6	-
GCA_905479415.1	s__MAG-121220-bin8 sp905479415	77.9947	180	518	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	98.94	98.70	0.82	0.77	8	-
--------------------------------------------------------------------------------
[2023-03-19 05:01:54,273] [INFO] GTDB search result was written to OceanDNA-b7996/result_gtdb.tsv
[2023-03-19 05:01:54,274] [INFO] ===== GTDB Search completed =====
[2023-03-19 05:01:54,275] [INFO] DFAST_QC result json was written to OceanDNA-b7996/dqc_result.json
[2023-03-19 05:01:54,275] [INFO] DFAST_QC completed!
[2023-03-19 05:01:54,275] [INFO] Total running time: 0h0m57s