[2023-03-17 04:15:14,718] [INFO] DFAST_QC pipeline started.
[2023-03-17 04:15:14,718] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 04:15:14,718] [INFO] DQC Reference Directory: /var/lib/cwl/stg87d67cce-ddc8-4f0b-a792-cc3d10b4e851/dqc_reference
[2023-03-17 04:15:16,099] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 04:15:16,099] [INFO] Task started: Prodigal
[2023-03-17 04:15:16,099] [INFO] Running command: cat /var/lib/cwl/stgb1d69b45-6d5b-4700-9f59-ae2b75df4d3e/OceanDNA-b11431.fa | prodigal -d OceanDNA-b11431/cds.fna -a OceanDNA-b11431/protein.faa -g 11 -q > /dev/null
[2023-03-17 04:15:36,899] [INFO] Task succeeded: Prodigal
[2023-03-17 04:15:36,900] [INFO] Task started: HMMsearch
[2023-03-17 04:15:36,900] [INFO] Running command: hmmsearch --tblout OceanDNA-b11431/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg87d67cce-ddc8-4f0b-a792-cc3d10b4e851/dqc_reference/reference_markers.hmm OceanDNA-b11431/protein.faa > /dev/null
[2023-03-17 04:15:37,153] [INFO] Task succeeded: HMMsearch
[2023-03-17 04:15:37,153] [INFO] Found 6/6 markers.
[2023-03-17 04:15:37,171] [INFO] Query marker FASTA was written to OceanDNA-b11431/markers.fasta
[2023-03-17 04:15:37,171] [INFO] Task started: Blastn
[2023-03-17 04:15:37,171] [INFO] Running command: blastn -query OceanDNA-b11431/markers.fasta -db /var/lib/cwl/stg87d67cce-ddc8-4f0b-a792-cc3d10b4e851/dqc_reference/reference_markers.fasta -out OceanDNA-b11431/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:15:37,793] [INFO] Task succeeded: Blastn
[2023-03-17 04:15:37,794] [INFO] Selected 26 target genomes.
[2023-03-17 04:15:37,795] [INFO] Target genome list was writen to OceanDNA-b11431/target_genomes.txt
[2023-03-17 04:15:37,807] [INFO] Task started: fastANI
[2023-03-17 04:15:37,808] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1d69b45-6d5b-4700-9f59-ae2b75df4d3e/OceanDNA-b11431.fa --refList OceanDNA-b11431/target_genomes.txt --output OceanDNA-b11431/fastani_result.tsv --threads 1
[2023-03-17 04:15:54,199] [INFO] Task succeeded: fastANI
[2023-03-17 04:15:54,199] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg87d67cce-ddc8-4f0b-a792-cc3d10b4e851/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 04:15:54,199] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg87d67cce-ddc8-4f0b-a792-cc3d10b4e851/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 04:15:54,214] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2023-03-17 04:15:54,214] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 04:15:54,214] [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
Xanthomarina gelatinilytica	strain=AK20	GCA_000348685.1	1137281	1137281	type	True	98.3788	886	958	95	conclusive
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.9064	286	958	95	below_threshold
Bizionia myxarmorum	strain=ADA-4	GCA_008086205.1	291186	291186	type	True	77.884	268	958	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	77.8761	273	958	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	77.7244	256	958	95	below_threshold
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	77.7048	338	958	95	below_threshold
Oceanihabitans sediminis	strain=DSM 28133	GCA_003315315.1	1812012	1812012	type	True	77.6753	233	958	95	below_threshold
Tamlana haliotis	strain=B1N29	GCA_008806375.1	2614804	2614804	type	True	77.6351	155	958	95	below_threshold
Oceanihabitans sediminis	strain=S9-10	GCA_003337215.1	1812012	1812012	type	True	77.5902	230	958	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	77.5235	269	958	95	below_threshold
Changchengzhania lutea	strain=SM1355	GCA_006974145.1	2049305	2049305	type	True	77.4827	170	958	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	77.4614	180	958	95	below_threshold
Bizionia argentinensis	strain=JUB59	GCA_000224335.2	456455	456455	type	True	77.4244	249	958	95	below_threshold
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	77.3819	162	958	95	below_threshold
Tamlana agarivorans	strain=JW-26	GCA_001642835.1	481183	481183	type	True	77.3659	168	958	95	below_threshold
Tamlana carrageenivorans	strain=UJ94	GCA_002893765.1	2069432	2069432	type	True	77.3561	168	958	95	below_threshold
Snuella sedimenti	strain=CAU 1569	GCA_016428595.1	2798802	2798802	type	True	77.3121	160	958	95	below_threshold
Aestuariivivens insulae	strain=AH-MY3	GCA_022662195.1	1621988	1621988	type	True	77.3107	203	958	95	below_threshold
Flavivirga eckloniae	strain=ECD14	GCA_002886045.1	1803846	1803846	type	True	77.2607	191	958	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.2359	144	958	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	77.2217	170	958	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	77.2217	170	958	95	below_threshold
Confluentibacter sediminis	strain=DSL-48	GCA_003258355.1	2219045	2219045	type	True	77.1022	208	958	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.997	203	958	95	below_threshold
Algibacter onchidii	strain=XY-114	GCA_004804355.1	2562860	2562860	type	True	76.9912	148	958	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	76.9498	158	958	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 04:15:54,214] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11431/tc_result.tsv
[2023-03-17 04:15:54,214] [INFO] ===== Taxonomy check completed =====
[2023-03-17 04:15:54,214] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 04:15:54,215] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg87d67cce-ddc8-4f0b-a792-cc3d10b4e851/dqc_reference/checkm_data
[2023-03-17 04:15:54,215] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 04:15:54,219] [INFO] Task started: CheckM
[2023-03-17 04:15:54,219] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11431/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11431/checkm_input OceanDNA-b11431/checkm_result
[2023-03-17 04:16:46,993] [INFO] Task succeeded: CheckM
[2023-03-17 04:16:46,993] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 04:16:46,996] [INFO] ===== Completeness check finished =====
[2023-03-17 04:16:46,996] [INFO] ===== Start GTDB Search =====
[2023-03-17 04:16:46,996] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11431/markers.fasta)
[2023-03-17 04:16:46,996] [INFO] Task started: Blastn
[2023-03-17 04:16:46,996] [INFO] Running command: blastn -query OceanDNA-b11431/markers.fasta -db /var/lib/cwl/stg87d67cce-ddc8-4f0b-a792-cc3d10b4e851/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11431/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:16:47,855] [INFO] Task succeeded: Blastn
[2023-03-17 04:16:47,856] [INFO] Selected 7 target genomes.
[2023-03-17 04:16:47,856] [INFO] Target genome list was writen to OceanDNA-b11431/target_genomes_gtdb.txt
[2023-03-17 04:16:47,922] [INFO] Task started: fastANI
[2023-03-17 04:16:47,922] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1d69b45-6d5b-4700-9f59-ae2b75df4d3e/OceanDNA-b11431.fa --refList OceanDNA-b11431/target_genomes_gtdb.txt --output OceanDNA-b11431/fastani_result_gtdb.tsv --threads 1
[2023-03-17 04:16:52,677] [INFO] Task succeeded: fastANI
[2023-03-17 04:16:52,682] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 04:16:52,683] [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_000348685.1	s__Xanthomarina gelatinilytica	98.3788	886	958	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	98.37	98.31	0.90	0.88	4	conclusive
GCF_008084905.1	s__Xanthomarina maritima	80.5141	569	958	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148645.1	s__Xanthomarina spongicola	80.4805	611	958	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003144015.1	s__Xanthomarina sp003144015	80.4665	619	958	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638915.1	s__Xanthomarina arctica	79.9257	595	958	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002366675.1	s__Xanthomarina sp002366675	79.6519	391	958	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860825.1	s__Oceanihabitans sp018860825	77.8993	266	958	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 04:16:52,683] [INFO] GTDB search result was written to OceanDNA-b11431/result_gtdb.tsv
[2023-03-17 04:16:52,683] [INFO] ===== GTDB Search completed =====
[2023-03-17 04:16:52,685] [INFO] DFAST_QC result json was written to OceanDNA-b11431/dqc_result.json
[2023-03-17 04:16:52,685] [INFO] DFAST_QC completed!
[2023-03-17 04:16:52,685] [INFO] Total running time: 0h1m38s