[2023-03-18 01:08:39,250] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:08:39,250] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:08:39,250] [INFO] DQC Reference Directory: /var/lib/cwl/stg2382ead8-7d4d-495e-b724-dc5c5bc8ef05/dqc_reference
[2023-03-18 01:08:40,373] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:08:40,373] [INFO] Task started: Prodigal
[2023-03-18 01:08:40,373] [INFO] Running command: cat /var/lib/cwl/stg864cde6a-6870-4da9-acb2-96d2c3acdb84/OceanDNA-b6278.fa | prodigal -d OceanDNA-b6278/cds.fna -a OceanDNA-b6278/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:08:54,287] [INFO] Task succeeded: Prodigal
[2023-03-18 01:08:54,287] [INFO] Task started: HMMsearch
[2023-03-18 01:08:54,287] [INFO] Running command: hmmsearch --tblout OceanDNA-b6278/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2382ead8-7d4d-495e-b724-dc5c5bc8ef05/dqc_reference/reference_markers.hmm OceanDNA-b6278/protein.faa > /dev/null
[2023-03-18 01:08:54,473] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:08:54,473] [INFO] Found 6/6 markers.
[2023-03-18 01:08:54,488] [INFO] Query marker FASTA was written to OceanDNA-b6278/markers.fasta
[2023-03-18 01:08:54,489] [INFO] Task started: Blastn
[2023-03-18 01:08:54,489] [INFO] Running command: blastn -query OceanDNA-b6278/markers.fasta -db /var/lib/cwl/stg2382ead8-7d4d-495e-b724-dc5c5bc8ef05/dqc_reference/reference_markers.fasta -out OceanDNA-b6278/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:08:55,089] [INFO] Task succeeded: Blastn
[2023-03-18 01:08:55,090] [INFO] Selected 24 target genomes.
[2023-03-18 01:08:55,090] [INFO] Target genome list was writen to OceanDNA-b6278/target_genomes.txt
[2023-03-18 01:08:55,105] [INFO] Task started: fastANI
[2023-03-18 01:08:55,105] [INFO] Running command: fastANI --query /var/lib/cwl/stg864cde6a-6870-4da9-acb2-96d2c3acdb84/OceanDNA-b6278.fa --refList OceanDNA-b6278/target_genomes.txt --output OceanDNA-b6278/fastani_result.tsv --threads 1
[2023-03-18 01:09:08,969] [INFO] Task succeeded: fastANI
[2023-03-18 01:09:08,970] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2382ead8-7d4d-495e-b724-dc5c5bc8ef05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:09:08,970] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2382ead8-7d4d-495e-b724-dc5c5bc8ef05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:09:08,984] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:09:08,984] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 01:09:08,985] [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 pacificus	strain=CGMCC 1.15763	GCA_014643655.1	1775173	1775173	type	True	78.6561	324	723	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	78.5243	337	723	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	78.4468	335	723	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	78.4055	353	723	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	78.3797	339	723	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	78.3664	333	723	95	below_threshold
Polaribacter aquimarinus	strain=ZY113	GCA_003129485.1	2100726	2100726	type	True	78.3595	307	723	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_001680875.1	996801	996801	type	True	78.3378	322	723	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	78.3288	339	723	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	78.292	331	723	95	below_threshold
Polaribacter glomeratus	strain=ACAM 171	GCA_007997115.1	102	102	type	True	78.1535	301	723	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	78.144	315	723	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	78.1326	309	723	95	below_threshold
Polaribacter glomeratus	strain=ATCC 43844	GCA_002954665.1	102	102	type	True	78.0908	305	723	95	below_threshold
Polaribacter filamentus	strain=ATCC 700397	GCA_002943715.1	53483	53483	type	True	77.9074	313	723	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	77.8826	317	723	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	77.8606	265	723	95	below_threshold
Polaribacter porphyrae	strain=LMG 26671	GCA_020532745.1	1137780	1137780	type	True	77.8197	304	723	95	below_threshold
Tenacibaculum ovolyticum	strain=DSM 18103	GCA_000430545.1	104270	104270	type	True	77.6693	273	723	95	below_threshold
Tenacibaculum finnmarkense	strain=TNO006	GCA_900239185.1	2781243	2781243	type	True	77.4467	226	723	95	below_threshold
Tenacibaculum singaporense	strain=DSM 106434	GCA_003867015.1	2358479	2358479	type	True	77.3733	235	723	95	below_threshold
Tenacibaculum mesophilum	strain=DSM 13764	GCA_003867075.1	104268	104268	type	True	77.2875	231	723	95	below_threshold
Tenacibaculum mesophilum	strain=DSM 13764	GCA_900129475.1	104268	104268	type	True	77.2299	236	723	95	below_threshold
Tenacibaculum mesophilum	strain=DSM 13764	GCA_009362255.1	104268	104268	type	True	77.2002	238	723	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 01:09:08,985] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6278/tc_result.tsv
[2023-03-18 01:09:08,985] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:09:08,985] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:09:08,985] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2382ead8-7d4d-495e-b724-dc5c5bc8ef05/dqc_reference/checkm_data
[2023-03-18 01:09:08,986] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:09:08,991] [INFO] Task started: CheckM
[2023-03-18 01:09:08,992] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6278/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6278/checkm_input OceanDNA-b6278/checkm_result
[2023-03-18 01:09:46,986] [INFO] Task succeeded: CheckM
[2023-03-18 01:09:46,987] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:09:46,991] [INFO] ===== Completeness check finished =====
[2023-03-18 01:09:46,991] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:09:46,991] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6278/markers.fasta)
[2023-03-18 01:09:46,992] [INFO] Task started: Blastn
[2023-03-18 01:09:46,992] [INFO] Running command: blastn -query OceanDNA-b6278/markers.fasta -db /var/lib/cwl/stg2382ead8-7d4d-495e-b724-dc5c5bc8ef05/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6278/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:09:47,861] [INFO] Task succeeded: Blastn
[2023-03-18 01:09:47,862] [INFO] Selected 21 target genomes.
[2023-03-18 01:09:47,862] [INFO] Target genome list was writen to OceanDNA-b6278/target_genomes_gtdb.txt
[2023-03-18 01:09:47,883] [INFO] Task started: fastANI
[2023-03-18 01:09:47,883] [INFO] Running command: fastANI --query /var/lib/cwl/stg864cde6a-6870-4da9-acb2-96d2c3acdb84/OceanDNA-b6278.fa --refList OceanDNA-b6278/target_genomes_gtdb.txt --output OceanDNA-b6278/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:10:00,989] [INFO] Task succeeded: fastANI
[2023-03-18 01:10:01,002] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 01:10:01,002] [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_013373385.1	s__Polaribacter_A sp013373385	79.4059	425	723	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016763595.1	s__Polaribacter_A sp016763595	79.2273	265	723	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000766795.1	s__Polaribacter sp000766795	78.7538	343	723	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643655.1	s__Polaribacter_A pacificus	78.6561	324	723	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163835.1	s__Polaribacter sp002163835	78.6116	350	723	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001889045.1	s__Tenacibaculum_A todarodis	78.5241	337	723	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827455.1	s__VISM01 sp007827455	78.5149	338	723	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__VISM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954605.1	s__Polaribacter butkevichii	78.4079	336	723	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	78.4012	354	723	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003129485.1	s__Polaribacter sp003129485	78.3726	306	723	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001640115.1	s__Polaribacter atrinae	78.2957	319	723	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	78.2265	309	723	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105145.1	s__Polaribacter sp900105145	78.2261	364	723	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018861005.1	s__Polaribacter vadi_A	78.2172	334	723	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001693415.1	s__Tenacibaculum soleae	78.0767	268	723	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002943715.1	s__Polaribacter filamentus	77.9074	313	723	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900239345.1	s__Tenacibaculum dicentrarchi	77.7606	237	723	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	98.61	97.94	0.93	0.91	10	-
GCF_000430545.1	s__Tenacibaculum ovolyticum	77.6693	273	723	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.63	97.63	0.88	0.88	2	-
GCA_905480405.1	s__Polaribacter sp905480405	77.6009	298	723	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003867015.1	s__Tenacibaculum singaporense	77.3617	236	723	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	96.88	96.88	0.91	0.91	2	-
GCF_003867075.1	s__Tenacibaculum mesophilum	77.275	232	723	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	99.18	98.30	0.96	0.93	5	-
--------------------------------------------------------------------------------
[2023-03-18 01:10:01,002] [INFO] GTDB search result was written to OceanDNA-b6278/result_gtdb.tsv
[2023-03-18 01:10:01,002] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:10:01,005] [INFO] DFAST_QC result json was written to OceanDNA-b6278/dqc_result.json
[2023-03-18 01:10:01,005] [INFO] DFAST_QC completed!
[2023-03-18 01:10:01,005] [INFO] Total running time: 0h1m22s