[2023-03-18 07:06:19,986] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:06:19,986] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:06:19,986] [INFO] DQC Reference Directory: /var/lib/cwl/stg41bd5ed1-49ce-4466-8cfd-3cc75fec26f2/dqc_reference
[2023-03-18 07:06:21,100] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:06:21,101] [INFO] Task started: Prodigal
[2023-03-18 07:06:21,101] [INFO] Running command: cat /var/lib/cwl/stg5cf68f23-7709-4cbd-97f4-b90ad93a6d73/OceanDNA-b10045.fa | prodigal -d OceanDNA-b10045/cds.fna -a OceanDNA-b10045/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:06:35,821] [INFO] Task succeeded: Prodigal
[2023-03-18 07:06:35,822] [INFO] Task started: HMMsearch
[2023-03-18 07:06:35,822] [INFO] Running command: hmmsearch --tblout OceanDNA-b10045/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg41bd5ed1-49ce-4466-8cfd-3cc75fec26f2/dqc_reference/reference_markers.hmm OceanDNA-b10045/protein.faa > /dev/null
[2023-03-18 07:06:36,030] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:06:36,030] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5cf68f23-7709-4cbd-97f4-b90ad93a6d73/OceanDNA-b10045.fa]
[2023-03-18 07:06:36,047] [INFO] Query marker FASTA was written to OceanDNA-b10045/markers.fasta
[2023-03-18 07:06:36,047] [INFO] Task started: Blastn
[2023-03-18 07:06:36,048] [INFO] Running command: blastn -query OceanDNA-b10045/markers.fasta -db /var/lib/cwl/stg41bd5ed1-49ce-4466-8cfd-3cc75fec26f2/dqc_reference/reference_markers.fasta -out OceanDNA-b10045/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:06:36,593] [INFO] Task succeeded: Blastn
[2023-03-18 07:06:36,594] [INFO] Selected 22 target genomes.
[2023-03-18 07:06:36,595] [INFO] Target genome list was writen to OceanDNA-b10045/target_genomes.txt
[2023-03-18 07:06:36,606] [INFO] Task started: fastANI
[2023-03-18 07:06:36,606] [INFO] Running command: fastANI --query /var/lib/cwl/stg5cf68f23-7709-4cbd-97f4-b90ad93a6d73/OceanDNA-b10045.fa --refList OceanDNA-b10045/target_genomes.txt --output OceanDNA-b10045/fastani_result.tsv --threads 1
[2023-03-18 07:06:51,872] [INFO] Task succeeded: fastANI
[2023-03-18 07:06:51,872] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg41bd5ed1-49ce-4466-8cfd-3cc75fec26f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:06:51,872] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg41bd5ed1-49ce-4466-8cfd-3cc75fec26f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:06:51,885] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:06:51,885] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 07:06:51,885] [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
Polaribacter filamentus	strain=ATCC 700397	GCA_002943715.1	53483	53483	type	True	81.5956	581	820	95	below_threshold
Polaribacter glomeratus	strain=ATCC 43844	GCA_002954665.1	102	102	type	True	81.3542	583	820	95	below_threshold
Polaribacter glomeratus	strain=ACAM 171	GCA_007997115.1	102	102	type	True	81.3199	589	820	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	80.5695	484	820	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	80.5355	537	820	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001680885.1	1774273	1774273	type	True	80.4798	551	820	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	80.4637	500	820	95	below_threshold
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	80.4624	496	820	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	80.437	543	820	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_001680875.1	996801	996801	type	True	80.3324	522	820	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	80.3299	531	820	95	below_threshold
Polaribacter atrinae	strain=KACC 17473	GCA_001640115.1	1333662	1333662	type	True	80.2726	511	820	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	80.0933	509	820	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	80.071	511	820	95	below_threshold
Polaribacter litorisediminis	strain=OITF-11	GCA_019968605.1	1908341	1908341	type	True	79.7138	521	820	95	below_threshold
Polaribacter porphyrae	strain=NBRC 108759	GCA_002954685.1	1137780	1137780	type	True	79.5308	501	820	95	below_threshold
Polaribacter porphyrae	strain=LMG 26671	GCA_020532745.1	1137780	1137780	type	True	79.5251	497	820	95	below_threshold
Polaribacter aquimarinus	strain=ZY113	GCA_003129485.1	2100726	2100726	type	True	79.4891	465	820	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	79.4081	468	820	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	79.3039	366	820	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	79.1318	447	820	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	78.9469	365	820	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 07:06:51,886] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10045/tc_result.tsv
[2023-03-18 07:06:51,886] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:06:51,886] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:06:51,886] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg41bd5ed1-49ce-4466-8cfd-3cc75fec26f2/dqc_reference/checkm_data
[2023-03-18 07:06:51,887] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:06:51,891] [INFO] Task started: CheckM
[2023-03-18 07:06:51,891] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10045/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10045/checkm_input OceanDNA-b10045/checkm_result
[2023-03-18 07:07:31,006] [INFO] Task succeeded: CheckM
[2023-03-18 07:07:31,007] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.92%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 07:07:31,009] [INFO] ===== Completeness check finished =====
[2023-03-18 07:07:31,009] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:07:31,009] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10045/markers.fasta)
[2023-03-18 07:07:31,010] [INFO] Task started: Blastn
[2023-03-18 07:07:31,010] [INFO] Running command: blastn -query OceanDNA-b10045/markers.fasta -db /var/lib/cwl/stg41bd5ed1-49ce-4466-8cfd-3cc75fec26f2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10045/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:07:31,808] [INFO] Task succeeded: Blastn
[2023-03-18 07:07:31,809] [INFO] Selected 16 target genomes.
[2023-03-18 07:07:31,809] [INFO] Target genome list was writen to OceanDNA-b10045/target_genomes_gtdb.txt
[2023-03-18 07:07:31,900] [INFO] Task started: fastANI
[2023-03-18 07:07:31,900] [INFO] Running command: fastANI --query /var/lib/cwl/stg5cf68f23-7709-4cbd-97f4-b90ad93a6d73/OceanDNA-b10045.fa --refList OceanDNA-b10045/target_genomes_gtdb.txt --output OceanDNA-b10045/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:07:43,057] [INFO] Task succeeded: fastANI
[2023-03-18 07:07:43,067] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 07:07:43,067] [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_000981625.1	s__Polaribacter sp000981625	99.5875	667	820	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900106075.1	s__Polaribacter sp900106075	83.6957	613	820	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	98.66	98.45	0.96	0.92	5	-
GCF_900105145.1	s__Polaribacter sp900105145	81.6756	581	820	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163675.1	s__Polaribacter sp002163675	81.5693	530	820	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954665.1	s__Polaribacter glomeratus	81.3445	585	820	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.98	99.98	1.00	1.00	2	-
GCF_002163835.1	s__Polaribacter sp002163835	81.2359	535	820	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000766795.1	s__Polaribacter sp000766795	81.2133	537	820	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181765.1	s__Polaribacter sp905181765	80.7343	374	820	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	96.49	96.49	0.69	0.69	2	-
GCF_009796785.1	s__Polaribacter sp009796785	80.5907	503	820	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002831685.1	s__Polaribacter sp002831685	80.538	513	820	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001761365.1	s__Polaribacter vadi	80.5223	539	820	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014352875.1	s__Polaribacter sp014352875	80.437	543	820	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016858305.2	s__Polaribacter sp016858305	80.392	506	820	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997075.1	s__Polaribacter sp007997075	80.2783	503	820	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002005425.1	s__Polaribacter sp002005425	79.5633	457	820	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	96.81	96.81	0.92	0.92	2	-
GCF_002954685.1	s__Polaribacter porphyrae	79.5512	499	820	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 07:07:43,067] [INFO] GTDB search result was written to OceanDNA-b10045/result_gtdb.tsv
[2023-03-18 07:07:43,067] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:07:43,069] [INFO] DFAST_QC result json was written to OceanDNA-b10045/dqc_result.json
[2023-03-18 07:07:43,070] [INFO] DFAST_QC completed!
[2023-03-18 07:07:43,070] [INFO] Total running time: 0h1m23s