[2023-03-17 02:45:48,877] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:45:48,878] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:45:48,878] [INFO] DQC Reference Directory: /var/lib/cwl/stg57b8a7d9-2634-4885-9597-63dff517a4e5/dqc_reference
[2023-03-17 02:45:50,398] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:45:50,399] [INFO] Task started: Prodigal
[2023-03-17 02:45:50,399] [INFO] Running command: cat /var/lib/cwl/stg21b7846a-df94-47f0-a1e8-c074f987d476/OceanDNA-b6262.fa | prodigal -d OceanDNA-b6262/cds.fna -a OceanDNA-b6262/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:46:01,964] [INFO] Task succeeded: Prodigal
[2023-03-17 02:46:01,964] [INFO] Task started: HMMsearch
[2023-03-17 02:46:01,964] [INFO] Running command: hmmsearch --tblout OceanDNA-b6262/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg57b8a7d9-2634-4885-9597-63dff517a4e5/dqc_reference/reference_markers.hmm OceanDNA-b6262/protein.faa > /dev/null
[2023-03-17 02:46:02,144] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:46:02,144] [INFO] Found 6/6 markers.
[2023-03-17 02:46:02,160] [INFO] Query marker FASTA was written to OceanDNA-b6262/markers.fasta
[2023-03-17 02:46:02,161] [INFO] Task started: Blastn
[2023-03-17 02:46:02,161] [INFO] Running command: blastn -query OceanDNA-b6262/markers.fasta -db /var/lib/cwl/stg57b8a7d9-2634-4885-9597-63dff517a4e5/dqc_reference/reference_markers.fasta -out OceanDNA-b6262/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:46:02,737] [INFO] Task succeeded: Blastn
[2023-03-17 02:46:02,738] [INFO] Selected 22 target genomes.
[2023-03-17 02:46:02,738] [INFO] Target genome list was writen to OceanDNA-b6262/target_genomes.txt
[2023-03-17 02:46:02,768] [INFO] Task started: fastANI
[2023-03-17 02:46:02,768] [INFO] Running command: fastANI --query /var/lib/cwl/stg21b7846a-df94-47f0-a1e8-c074f987d476/OceanDNA-b6262.fa --refList OceanDNA-b6262/target_genomes.txt --output OceanDNA-b6262/fastani_result.tsv --threads 1
[2023-03-17 02:46:15,986] [INFO] Task succeeded: fastANI
[2023-03-17 02:46:15,986] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg57b8a7d9-2634-4885-9597-63dff517a4e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:46:15,987] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg57b8a7d9-2634-4885-9597-63dff517a4e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:46:15,996] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 02:46:15,996] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 02:46:15,996] [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 oceani	strain=JCM30924	GCA_003426875.1	1853311	1853311	type	True	78.0294	246	538	95	below_threshold
Lutibacter oceani	strain=325-5	GCA_003384935.1	1853311	1853311	type	True	77.9864	244	538	95	below_threshold
Lutibacter maritimus	strain=DSM 24450	GCA_900116115.1	593133	593133	type	True	77.9749	227	538	95	below_threshold
Lutibacter agarilyticus	strain=DSM 29150	GCA_900188235.1	1109740	1109740	type	True	77.9065	216	538	95	below_threshold
Lutibacter flavus	strain=DSM 27993	GCA_900188355.1	691689	691689	type	True	77.8494	222	538	95	below_threshold
Lutibacter profundi	strain=LP1	GCA_001543325.1	1622118	1622118	type	True	77.5514	225	538	95	below_threshold
Lutibacter oricola	strain=DSM 24956	GCA_900106565.1	762486	762486	type	True	77.5239	200	538	95	below_threshold
Lutibacter citreus	strain=1KV19	GCA_003260195.1	2138210	2138210	type	True	77.413	207	538	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	76.3614	80	538	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001680885.1	1774273	1774273	type	True	76.337	81	538	95	below_threshold
Tenacibaculum ovolyticum	strain=DSM 18103	GCA_000430545.1	104270	104270	type	True	76.1778	62	538	95	below_threshold
Aureivirga marina	strain=LMG 26721	GCA_015767265.1	1182451	1182451	type	True	75.9402	67	538	95	below_threshold
Tenacibaculum gallaicum	strain=DSM 18841	GCA_003387615.1	561505	561505	type	True	75.9366	73	538	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	75.744	50	538	95	below_threshold
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	75.6248	84	538	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 02:46:15,996] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6262/tc_result.tsv
[2023-03-17 02:46:15,996] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:46:15,997] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:46:15,997] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg57b8a7d9-2634-4885-9597-63dff517a4e5/dqc_reference/checkm_data
[2023-03-17 02:46:15,997] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:46:16,076] [INFO] Task started: CheckM
[2023-03-17 02:46:16,076] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6262/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6262/checkm_input OceanDNA-b6262/checkm_result
[2023-03-17 02:46:48,699] [INFO] Task succeeded: CheckM
[2023-03-17 02:46:48,699] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 02:46:48,703] [INFO] ===== Completeness check finished =====
[2023-03-17 02:46:48,703] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:46:48,703] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6262/markers.fasta)
[2023-03-17 02:46:48,704] [INFO] Task started: Blastn
[2023-03-17 02:46:48,704] [INFO] Running command: blastn -query OceanDNA-b6262/markers.fasta -db /var/lib/cwl/stg57b8a7d9-2634-4885-9597-63dff517a4e5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6262/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:46:49,514] [INFO] Task succeeded: Blastn
[2023-03-17 02:46:49,516] [INFO] Selected 20 target genomes.
[2023-03-17 02:46:49,516] [INFO] Target genome list was writen to OceanDNA-b6262/target_genomes_gtdb.txt
[2023-03-17 02:46:49,809] [INFO] Task started: fastANI
[2023-03-17 02:46:49,809] [INFO] Running command: fastANI --query /var/lib/cwl/stg21b7846a-df94-47f0-a1e8-c074f987d476/OceanDNA-b6262.fa --refList OceanDNA-b6262/target_genomes_gtdb.txt --output OceanDNA-b6262/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:47:01,378] [INFO] Task succeeded: fastANI
[2023-03-17 02:47:01,388] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 02:47:01,389] [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_012524075.1	s__Lutibacter sp012524075	78.0744	254	538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003384935.1	s__Lutibacter oceani	77.9864	244	538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900116115.1	s__Lutibacter maritimus	77.9749	227	538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188235.1	s__Lutibacter agarilyticus	77.9223	215	538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013139515.1	s__Lutibacter sp013139515	77.8508	201	538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188355.1	s__Lutibacter flavus	77.8343	223	538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016342705.1	s__Lutibacter sp016342705	77.6829	234	538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001543325.1	s__Lutibacter profundi	77.5514	225	538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106565.1	s__Lutibacter oricola	77.5239	200	538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003260195.1	s__Lutibacter citreus	77.4273	206	538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004121075.1	s__Lutibacter sp004121075	77.3469	203	538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004195315.1	s__Lutibacter sp004195315	77.2298	164	538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013041805.1	s__Lutibacter sp013041805	77.2129	206	538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	100.00	100.00	0.99	0.99	2	-
GCA_002390165.1	s__Lutibacter sp002390165	77.2038	155	538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001800975.1	s__Lutibacter sp001800975	77.081	164	538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997385.1	s__Seonamhaeicola algicola	75.6248	84	538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000789235.1	s__Wocania ichthyoenteri	75.5025	66	538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002441545.1	s__Yeosuana sp002441545	75.3892	60	538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 02:47:01,389] [INFO] GTDB search result was written to OceanDNA-b6262/result_gtdb.tsv
[2023-03-17 02:47:01,390] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:47:01,393] [INFO] DFAST_QC result json was written to OceanDNA-b6262/dqc_result.json
[2023-03-17 02:47:01,393] [INFO] DFAST_QC completed!
[2023-03-17 02:47:01,393] [INFO] Total running time: 0h1m13s