[2023-03-16 10:06:33,509] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:06:33,509] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:06:33,509] [INFO] DQC Reference Directory: /var/lib/cwl/stg48c6e927-aba4-4a35-9027-7f5d3a6d465a/dqc_reference
[2023-03-16 10:06:34,665] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:06:34,666] [INFO] Task started: Prodigal
[2023-03-16 10:06:34,666] [INFO] Running command: cat /var/lib/cwl/stg2f044af8-a52b-4023-a124-7b96fb80efc2/OceanDNA-b27614.fa | prodigal -d OceanDNA-b27614/cds.fna -a OceanDNA-b27614/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:06:54,742] [INFO] Task succeeded: Prodigal
[2023-03-16 10:06:54,743] [INFO] Task started: HMMsearch
[2023-03-16 10:06:54,743] [INFO] Running command: hmmsearch --tblout OceanDNA-b27614/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg48c6e927-aba4-4a35-9027-7f5d3a6d465a/dqc_reference/reference_markers.hmm OceanDNA-b27614/protein.faa > /dev/null
[2023-03-16 10:06:54,927] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:06:54,927] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2f044af8-a52b-4023-a124-7b96fb80efc2/OceanDNA-b27614.fa]
[2023-03-16 10:06:54,946] [INFO] Query marker FASTA was written to OceanDNA-b27614/markers.fasta
[2023-03-16 10:06:54,948] [INFO] Task started: Blastn
[2023-03-16 10:06:54,948] [INFO] Running command: blastn -query OceanDNA-b27614/markers.fasta -db /var/lib/cwl/stg48c6e927-aba4-4a35-9027-7f5d3a6d465a/dqc_reference/reference_markers.fasta -out OceanDNA-b27614/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:06:55,615] [INFO] Task succeeded: Blastn
[2023-03-16 10:06:55,615] [INFO] Selected 26 target genomes.
[2023-03-16 10:06:55,616] [INFO] Target genome list was writen to OceanDNA-b27614/target_genomes.txt
[2023-03-16 10:06:55,629] [INFO] Task started: fastANI
[2023-03-16 10:06:55,629] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f044af8-a52b-4023-a124-7b96fb80efc2/OceanDNA-b27614.fa --refList OceanDNA-b27614/target_genomes.txt --output OceanDNA-b27614/fastani_result.tsv --threads 1
[2023-03-16 10:07:13,596] [INFO] Task succeeded: fastANI
[2023-03-16 10:07:13,597] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg48c6e927-aba4-4a35-9027-7f5d3a6d465a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:07:13,597] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg48c6e927-aba4-4a35-9027-7f5d3a6d465a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:07:13,611] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:07:13,611] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 10:07:13,611] [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
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	77.8565	319	1019	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	77.8127	387	1019	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	77.6237	337	1019	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	77.5544	289	1019	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	77.4115	302	1019	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	77.3939	348	1019	95	below_threshold
Ruegeria marina	strain=CGMCC 1.9108	GCA_900101475.1	639004	639004	type	True	77.3639	316	1019	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	77.3325	320	1019	95	below_threshold
Falsiruegeria litorea	strain=CECT 7639	GCA_900172225.1	1280831	1280831	type	True	77.3315	266	1019	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	77.3047	325	1019	95	below_threshold
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	77.2763	263	1019	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	77.2285	284	1019	95	below_threshold
Aliishimia ponticola	strain=MYP11	GCA_004803475.1	2499833	2499833	type	True	77.1251	248	1019	95	below_threshold
Chachezhania sediminis	strain=CAU 1508	GCA_009765275.1	2599291	2599291	type	True	77.0069	232	1019	95	below_threshold
Ruegeria faecimaris	strain=DSM 28009	GCA_900182615.1	686389	686389	type	True	76.9732	193	1019	95	below_threshold
Phaeobacter porticola	strain=P97	GCA_001888185.1	1844006	1844006	type	True	76.9692	204	1019	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	76.8005	182	1019	95	below_threshold
Phaeobacter inhibens	strain=DSM 16374	GCA_000473105.1	221822	221822	type	True	76.7743	235	1019	95	below_threshold
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	76.7735	179	1019	95	below_threshold
Rhodovulum robiginosum	strain=DSM 12329	GCA_003944755.1	68292	68292	type	True	76.7473	190	1019	95	below_threshold
Shimia isoporae	strain=DSM 26433	GCA_004346865.1	647720	647720	type	True	76.5624	118	1019	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	76.5415	189	1019	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.5104	206	1019	95	below_threshold
Rhabdonatronobacter sediminivivens	strain=IM2376	GCA_013415485.1	2743469	2743469	type	True	76.3894	154	1019	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	76.3557	162	1019	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 10:07:13,611] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27614/tc_result.tsv
[2023-03-16 10:07:13,611] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:07:13,611] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:07:13,611] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg48c6e927-aba4-4a35-9027-7f5d3a6d465a/dqc_reference/checkm_data
[2023-03-16 10:07:13,612] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:07:13,616] [INFO] Task started: CheckM
[2023-03-16 10:07:13,616] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27614/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27614/checkm_input OceanDNA-b27614/checkm_result
[2023-03-16 10:08:06,903] [INFO] Task succeeded: CheckM
[2023-03-16 10:08:06,903] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:08:06,905] [INFO] ===== Completeness check finished =====
[2023-03-16 10:08:06,905] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:08:06,906] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27614/markers.fasta)
[2023-03-16 10:08:06,907] [INFO] Task started: Blastn
[2023-03-16 10:08:06,907] [INFO] Running command: blastn -query OceanDNA-b27614/markers.fasta -db /var/lib/cwl/stg48c6e927-aba4-4a35-9027-7f5d3a6d465a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27614/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:08:07,942] [INFO] Task succeeded: Blastn
[2023-03-16 10:08:07,943] [INFO] Selected 27 target genomes.
[2023-03-16 10:08:07,943] [INFO] Target genome list was writen to OceanDNA-b27614/target_genomes_gtdb.txt
[2023-03-16 10:08:07,969] [INFO] Task started: fastANI
[2023-03-16 10:08:07,969] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f044af8-a52b-4023-a124-7b96fb80efc2/OceanDNA-b27614.fa --refList OceanDNA-b27614/target_genomes_gtdb.txt --output OceanDNA-b27614/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:08:27,359] [INFO] Task succeeded: fastANI
[2023-03-16 10:08:27,374] [INFO] Found 27 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 10:08:27,374] [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_900129345.1	s__Ruegeria intermedia	77.8401	320	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001262635.1	s__Aestuariivita boseongensis	77.6333	336	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348975.1	s__Antarcticimicrobium sediminis	77.5447	314	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002786325.1	s__Pseudooceanicola_C lipolyticus	77.4168	299	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003008555.2	s__Pukyongiella litopenaei	77.4142	310	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pukyongiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358185.1	s__Antarcticimicrobium luteum	77.3939	348	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109035.1	s__Cribrihabitans marinus	77.3416	319	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000473325.1	s__Leisingera caerulea	77.2763	263	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000743705.1	s__Ruegeria halocynthiae_B	77.2413	256	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216475.1	s__GCA-004216475 sp004216475	77.2386	260	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__GCA-004216475	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108275.1	s__Jhaorihella thermophila	77.1333	302	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jhaorihella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172365.1	s__Roseovarius gaetbuli	77.0962	251	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013317235.1	s__Leisingera sp013317235	77.0814	253	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013032025.1	s__Ruegeria atlantica_C	77.0759	237	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	100.00	100.00	0.99	0.99	2	-
GCF_009765275.1	s__Chachezhania sp009765275	76.9867	234	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Chachezhania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001888185.1	s__Phaeobacter porticola	76.9692	204	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001238295.1	s__Ruegeria sp001238295	76.947	195	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001679925.1	s__Leisingera sp001679925	76.9398	255	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003217735.2	s__Marinibacterium sp003217735	76.9031	295	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	98.81	98.75	0.89	0.89	3	-
GCF_003646465.1	s__Chachezhania antarctica	76.8801	239	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Chachezhania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789075.1	s__Pseudooceanicola pacificus	76.8683	179	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210105.1	s__Pseudooceanicola sp002210105	76.8351	228	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473105.1	s__Phaeobacter inhibens	76.7743	235	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter	95.0	97.82	97.14	0.94	0.90	26	-
GCF_001969385.1	s__Salipiger profundus	76.7606	180	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.85	99.64	0.97	0.94	5	-
GCF_003944755.1	s__Rhodovulum robiginosum	76.7473	190	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004346865.1	s__Shimia isoporae	76.5624	118	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018678075.1	s__Epibacterium ulvae_A	76.4403	147	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 10:08:27,375] [INFO] GTDB search result was written to OceanDNA-b27614/result_gtdb.tsv
[2023-03-16 10:08:27,375] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:08:27,377] [INFO] DFAST_QC result json was written to OceanDNA-b27614/dqc_result.json
[2023-03-16 10:08:27,377] [INFO] DFAST_QC completed!
[2023-03-16 10:08:27,378] [INFO] Total running time: 0h1m54s