[2023-03-16 02:38:04,898] [INFO] DFAST_QC pipeline started.
[2023-03-16 02:38:04,898] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 02:38:04,898] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ae76f4c-a492-48ec-8272-9cb8adf088a3/dqc_reference
[2023-03-16 02:38:06,058] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 02:38:06,064] [INFO] Task started: Prodigal
[2023-03-16 02:38:06,064] [INFO] Running command: cat /var/lib/cwl/stgcf83c454-a470-4262-a405-570c9837da59/OceanDNA-b30127.fa | prodigal -d OceanDNA-b30127/cds.fna -a OceanDNA-b30127/protein.faa -g 11 -q > /dev/null
[2023-03-16 02:38:27,922] [INFO] Task succeeded: Prodigal
[2023-03-16 02:38:27,923] [INFO] Task started: HMMsearch
[2023-03-16 02:38:27,923] [INFO] Running command: hmmsearch --tblout OceanDNA-b30127/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ae76f4c-a492-48ec-8272-9cb8adf088a3/dqc_reference/reference_markers.hmm OceanDNA-b30127/protein.faa > /dev/null
[2023-03-16 02:38:28,127] [INFO] Task succeeded: HMMsearch
[2023-03-16 02:38:28,128] [INFO] Found 6/6 markers.
[2023-03-16 02:38:28,149] [INFO] Query marker FASTA was written to OceanDNA-b30127/markers.fasta
[2023-03-16 02:38:28,149] [INFO] Task started: Blastn
[2023-03-16 02:38:28,149] [INFO] Running command: blastn -query OceanDNA-b30127/markers.fasta -db /var/lib/cwl/stg4ae76f4c-a492-48ec-8272-9cb8adf088a3/dqc_reference/reference_markers.fasta -out OceanDNA-b30127/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 02:38:29,040] [INFO] Task succeeded: Blastn
[2023-03-16 02:38:29,041] [INFO] Selected 26 target genomes.
[2023-03-16 02:38:29,041] [INFO] Target genome list was writen to OceanDNA-b30127/target_genomes.txt
[2023-03-16 02:38:29,056] [INFO] Task started: fastANI
[2023-03-16 02:38:29,056] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf83c454-a470-4262-a405-570c9837da59/OceanDNA-b30127.fa --refList OceanDNA-b30127/target_genomes.txt --output OceanDNA-b30127/fastani_result.tsv --threads 1
[2023-03-16 02:38:51,234] [INFO] Task succeeded: fastANI
[2023-03-16 02:38:51,234] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ae76f4c-a492-48ec-8272-9cb8adf088a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 02:38:51,234] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ae76f4c-a492-48ec-8272-9cb8adf088a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 02:38:51,248] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2023-03-16 02:38:51,248] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 02:38:51,248] [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
Roseovarius nubinhibens	strain=ISM	GCA_000152625.1	314263	314263	type	True	97.4827	1088	1133	95	conclusive
Roseovarius litoreus	strain=DSM 28249	GCA_900142765.1	1155722	1155722	type	True	79.0759	509	1133	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	79.0524	514	1133	95	below_threshold
Roseovarius faecimaris	strain=MME-070	GCA_009762325.1	2494550	2494550	type	True	79.0334	552	1133	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	78.9086	481	1133	95	below_threshold
Roseovarius pacificus	strain=DSM 29589	GCA_900142665.1	337701	337701	type	True	78.9005	481	1133	95	below_threshold
Roseovarius lutimaris	strain=DSM 28463	GCA_900115165.1	1005928	1005928	type	True	78.6917	474	1133	95	below_threshold
Roseovarius gaetbuli	strain=CECT 8370	GCA_900172365.1	1356575	1356575	type	True	78.65	504	1133	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	78.5432	497	1133	95	below_threshold
Roseovarius bejariae	strain=A21	GCA_009669325.1	2576383	2576383	type	True	78.5358	444	1133	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	78.4831	485	1133	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	78.4192	408	1133	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	78.3211	468	1133	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.215	454	1133	95	below_threshold
Leisingera methylohalidivorans	strain=DSM 14336; MB2	GCA_000511355.1	133924	133924	type	True	78.1866	389	1133	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	78.148	412	1133	95	below_threshold
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	78.1287	434	1133	95	below_threshold
Roseovarius aestuarii	strain=KCTC 22174	GCA_019966515.1	475083	475083	type	True	78.0612	424	1133	95	below_threshold
Salinihabitans flavidus	strain=DSM 27842	GCA_900110425.1	569882	569882	type	True	77.9928	393	1133	95	below_threshold
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	77.9436	403	1133	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	77.9132	406	1133	95	below_threshold
Shimia sediminis	strain=ZQ172	GCA_003990645.1	2497945	2497945	type	True	77.7988	319	1133	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	77.741	310	1133	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.6765	355	1133	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.5385	333	1133	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.4603	355	1133	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 02:38:51,248] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30127/tc_result.tsv
[2023-03-16 02:38:51,248] [INFO] ===== Taxonomy check completed =====
[2023-03-16 02:38:51,249] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 02:38:51,249] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ae76f4c-a492-48ec-8272-9cb8adf088a3/dqc_reference/checkm_data
[2023-03-16 02:38:51,249] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 02:38:51,285] [INFO] Task started: CheckM
[2023-03-16 02:38:51,285] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30127/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30127/checkm_input OceanDNA-b30127/checkm_result
[2023-03-16 02:39:47,935] [INFO] Task succeeded: CheckM
[2023-03-16 02:39:47,935] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 02:39:47,937] [INFO] ===== Completeness check finished =====
[2023-03-16 02:39:47,938] [INFO] ===== Start GTDB Search =====
[2023-03-16 02:39:47,938] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30127/markers.fasta)
[2023-03-16 02:39:47,938] [INFO] Task started: Blastn
[2023-03-16 02:39:47,938] [INFO] Running command: blastn -query OceanDNA-b30127/markers.fasta -db /var/lib/cwl/stg4ae76f4c-a492-48ec-8272-9cb8adf088a3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30127/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 02:39:49,649] [INFO] Task succeeded: Blastn
[2023-03-16 02:39:49,650] [INFO] Selected 26 target genomes.
[2023-03-16 02:39:49,650] [INFO] Target genome list was writen to OceanDNA-b30127/target_genomes_gtdb.txt
[2023-03-16 02:39:49,956] [INFO] Task started: fastANI
[2023-03-16 02:39:49,957] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf83c454-a470-4262-a405-570c9837da59/OceanDNA-b30127.fa --refList OceanDNA-b30127/target_genomes_gtdb.txt --output OceanDNA-b30127/fastani_result_gtdb.tsv --threads 1
[2023-03-16 02:40:10,864] [INFO] Task succeeded: fastANI
[2023-03-16 02:40:10,878] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 02:40:10,878] [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_000152625.1	s__Roseovarius nubinhibens	97.4827	1088	1133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.78	96.50	0.89	0.84	4	conclusive
GCF_900142765.1	s__Roseovarius litoreus	79.0849	508	1133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	95.85	95.85	0.86	0.86	2	-
GCF_009762325.1	s__Roseovarius faecimaris	79.0331	552	1133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001441615.1	s__Roseovarius atlanticus	78.9238	496	1133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142665.1	s__Roseovarius pacificus	78.9099	480	1133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.52	95.05	0.91	0.82	3	-
GCF_009363655.1	s__Roseovarius sp009363655	78.8019	498	1133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.13	98.13	0.93	0.93	2	-
GCF_003651245.1	s__Roseovarius spongiae	78.7735	545	1133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142185.1	s__Lutimaribacter pacificus	78.7411	478	1133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900115165.1	s__Roseovarius lutimaris	78.6956	472	1133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975705.1	s__Salipiger abyssi	78.687	515	1133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018069895.1	s__Roseovarius sp018069895	78.6652	470	1133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.42	99.42	0.86	0.86	2	-
GCA_006226775.1	s__Marinovum sp006226775	78.6284	459	1133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017311415.1	s__Salipiger abyssi_A	78.5686	493	1133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009669325.1	s__Roseovarius bejariae	78.5447	443	1133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002917925.1	s__Roseovarius confluentis	78.5127	486	1133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.93	98.93	0.93	0.93	2	-
GCF_003072125.1	s__Roseovarius sediminicola	78.4947	483	1133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507595.1	s__Ruegeria marisrubri	78.3911	411	1133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153725.1	s__Salipiger bermudensis	78.3196	468	1133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.06	97.75	0.87	0.75	4	-
GCF_000473325.1	s__Leisingera caerulea	78.104	437	1133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172285.1	s__Roseovarius aestuarii	78.1023	421	1133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001678945.1	s__Pseudophaeobacter_A gallaeciensis_A	78.0509	378	1133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter_A	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900110425.1	s__Salinihabitans flavidus	78.0106	391	1133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salinihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102075.1	s__Salipiger thiooxidans	77.8932	444	1133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.34	95.88	0.90	0.85	6	-
GCA_001874255.1	s__Epibacterium sp001874255	77.87	342	1133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003990645.1	s__Shimia sediminis	77.7988	319	1133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002783145.1	s__Nioella sp002783145	77.4762	275	1133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 02:40:10,878] [INFO] GTDB search result was written to OceanDNA-b30127/result_gtdb.tsv
[2023-03-16 02:40:10,878] [INFO] ===== GTDB Search completed =====
[2023-03-16 02:40:10,881] [INFO] DFAST_QC result json was written to OceanDNA-b30127/dqc_result.json
[2023-03-16 02:40:10,881] [INFO] DFAST_QC completed!
[2023-03-16 02:40:10,881] [INFO] Total running time: 0h2m6s