[2023-03-15 06:50:51,566] [INFO] DFAST_QC pipeline started.
[2023-03-15 06:50:51,570] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 06:50:51,570] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d58f5fe-2759-49df-9254-ecc1af9302b1/dqc_reference
[2023-03-15 06:50:53,467] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 06:50:53,468] [INFO] Task started: Prodigal
[2023-03-15 06:50:53,469] [INFO] Running command: cat /var/lib/cwl/stg74acd23d-8c76-4388-a663-7e30a4aad70f/OceanDNA-b11031.fa | prodigal -d OceanDNA-b11031/cds.fna -a OceanDNA-b11031/protein.faa -g 11 -q > /dev/null
[2023-03-15 06:51:14,168] [INFO] Task succeeded: Prodigal
[2023-03-15 06:51:14,168] [INFO] Task started: HMMsearch
[2023-03-15 06:51:14,168] [INFO] Running command: hmmsearch --tblout OceanDNA-b11031/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d58f5fe-2759-49df-9254-ecc1af9302b1/dqc_reference/reference_markers.hmm OceanDNA-b11031/protein.faa > /dev/null
[2023-03-15 06:51:14,336] [INFO] Task succeeded: HMMsearch
[2023-03-15 06:51:14,337] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg74acd23d-8c76-4388-a663-7e30a4aad70f/OceanDNA-b11031.fa]
[2023-03-15 06:51:14,375] [INFO] Query marker FASTA was written to OceanDNA-b11031/markers.fasta
[2023-03-15 06:51:14,376] [INFO] Task started: Blastn
[2023-03-15 06:51:14,376] [INFO] Running command: blastn -query OceanDNA-b11031/markers.fasta -db /var/lib/cwl/stg7d58f5fe-2759-49df-9254-ecc1af9302b1/dqc_reference/reference_markers.fasta -out OceanDNA-b11031/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:51:14,890] [INFO] Task succeeded: Blastn
[2023-03-15 06:51:14,924] [INFO] Selected 17 target genomes.
[2023-03-15 06:51:14,924] [INFO] Target genome list was writen to OceanDNA-b11031/target_genomes.txt
[2023-03-15 06:51:14,936] [INFO] Task started: fastANI
[2023-03-15 06:51:14,936] [INFO] Running command: fastANI --query /var/lib/cwl/stg74acd23d-8c76-4388-a663-7e30a4aad70f/OceanDNA-b11031.fa --refList OceanDNA-b11031/target_genomes.txt --output OceanDNA-b11031/fastani_result.tsv --threads 1
[2023-03-15 06:51:25,696] [INFO] Task succeeded: fastANI
[2023-03-15 06:51:25,696] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d58f5fe-2759-49df-9254-ecc1af9302b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 06:51:25,696] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d58f5fe-2759-49df-9254-ecc1af9302b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 06:51:25,707] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 06:51:25,707] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 06:51:25,707] [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
Flavicella marina	strain=2A-7	GCA_009193215.1	1475951	1475951	type	True	78.5729	300	1063	95	below_threshold
Flavicella sediminum	strain=ALS 84	GCA_006381105.1	2585141	2585141	type	True	78.2352	318	1063	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	77.16	136	1063	95	below_threshold
Polaribacter filamentus	strain=ATCC 700397	GCA_002943715.1	53483	53483	type	True	77.0642	138	1063	95	below_threshold
Lutibacter agarilyticus	strain=DSM 29150	GCA_900188235.1	1109740	1109740	type	True	76.6569	134	1063	95	below_threshold
Polaribacter glomeratus	strain=ATCC 43844	GCA_002954665.1	102	102	type	True	76.6428	142	1063	95	below_threshold
Tenacibaculum finnmarkense	strain=TNO006	GCA_900239185.1	2781243	2781243	type	True	76.6386	92	1063	95	below_threshold
Polaribacter aquimarinus	strain=ZY113	GCA_003129485.1	2100726	2100726	type	True	76.6315	115	1063	95	below_threshold
Polaribacter glomeratus	strain=ACAM 171	GCA_007997115.1	102	102	type	True	76.5744	137	1063	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	76.4491	147	1063	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	76.402	129	1063	95	below_threshold
Tenacibaculum skagerrakense	strain=DSM 14836	GCA_004345825.1	186571	186571	type	True	76.2527	84	1063	95	below_threshold
Urechidicola croceus	strain=LPB0138	GCA_001761325.1	1850246	1850246	type	True	76.2142	106	1063	95	below_threshold
Polaribacter pacificus	strain=CGMCC 1.15763	GCA_014643655.1	1775173	1775173	type	True	76.205	83	1063	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	76.2021	112	1063	95	below_threshold
Polaribacter litorisediminis	strain=OITF-11	GCA_019968605.1	1908341	1908341	type	True	75.9203	98	1063	95	below_threshold
Tenacibaculum agarivorans	strain=HZ1	GCA_001936575.1	1908389	1908389	type	True	75.6667	76	1063	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 06:51:25,710] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11031/tc_result.tsv
[2023-03-15 06:51:25,715] [INFO] ===== Taxonomy check completed =====
[2023-03-15 06:51:25,715] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 06:51:25,715] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d58f5fe-2759-49df-9254-ecc1af9302b1/dqc_reference/checkm_data
[2023-03-15 06:51:25,716] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 06:51:25,814] [INFO] Task started: CheckM
[2023-03-15 06:51:25,814] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11031/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11031/checkm_input OceanDNA-b11031/checkm_result
[2023-03-15 06:52:18,642] [INFO] Task succeeded: CheckM
[2023-03-15 06:52:18,642] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 06:52:18,804] [INFO] ===== Completeness check finished =====
[2023-03-15 06:52:18,805] [INFO] ===== Start GTDB Search =====
[2023-03-15 06:52:18,805] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11031/markers.fasta)
[2023-03-15 06:52:18,806] [INFO] Task started: Blastn
[2023-03-15 06:52:18,806] [INFO] Running command: blastn -query OceanDNA-b11031/markers.fasta -db /var/lib/cwl/stg7d58f5fe-2759-49df-9254-ecc1af9302b1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11031/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:52:19,509] [INFO] Task succeeded: Blastn
[2023-03-15 06:52:19,579] [INFO] Selected 16 target genomes.
[2023-03-15 06:52:19,579] [INFO] Target genome list was writen to OceanDNA-b11031/target_genomes_gtdb.txt
[2023-03-15 06:52:19,932] [INFO] Task started: fastANI
[2023-03-15 06:52:19,932] [INFO] Running command: fastANI --query /var/lib/cwl/stg74acd23d-8c76-4388-a663-7e30a4aad70f/OceanDNA-b11031.fa --refList OceanDNA-b11031/target_genomes_gtdb.txt --output OceanDNA-b11031/fastani_result_gtdb.tsv --threads 1
[2023-03-15 06:52:29,022] [INFO] Task succeeded: fastANI
[2023-03-15 06:52:29,031] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 06:52:29,032] [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_009193215.1	s__Flavicella marina	78.5729	300	1063	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006381105.1	s__Flavicella sediminum	78.2358	318	1063	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954605.1	s__Polaribacter butkevichii	77.1999	134	1063	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	76.9491	155	1063	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	76.9117	138	1063	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163835.1	s__Polaribacter sp002163835	76.8386	146	1063	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	76.8069	169	1063	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	76.7833	125	1063	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	76.6588	141	1063	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.98	99.98	1.00	1.00	2	-
GCF_900188235.1	s__Lutibacter agarilyticus	76.6569	134	1063	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480405.1	s__Polaribacter sp905480405	76.5958	116	1063	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018054895.1	s__Lutibacter sp018054895	76.5829	94	1063	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105145.1	s__Polaribacter sp900105145	76.4907	162	1063	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001761325.1	s__Urechidicola croceus	76.2142	106	1063	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Urechidicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017498485.1	s__Polaribacter sp017498485	76.2021	112	1063	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	76.1366	90	1063	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	96.49	96.49	0.69	0.69	2	-
--------------------------------------------------------------------------------
[2023-03-15 06:52:29,056] [INFO] GTDB search result was written to OceanDNA-b11031/result_gtdb.tsv
[2023-03-15 06:52:29,095] [INFO] ===== GTDB Search completed =====
[2023-03-15 06:52:29,122] [INFO] DFAST_QC result json was written to OceanDNA-b11031/dqc_result.json
[2023-03-15 06:52:29,122] [INFO] DFAST_QC completed!
[2023-03-15 06:52:29,122] [INFO] Total running time: 0h1m38s