[2023-03-16 09:58:17,579] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:58:17,579] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:58:17,579] [INFO] DQC Reference Directory: /var/lib/cwl/stg8359cb6d-197f-4690-9ae9-0a362b97e76a/dqc_reference
[2023-03-16 09:58:18,676] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:58:18,676] [INFO] Task started: Prodigal
[2023-03-16 09:58:18,677] [INFO] Running command: cat /var/lib/cwl/stgcfa62ddb-c894-4bbb-a5b1-206e7ec7883c/OceanDNA-b29589.fa | prodigal -d OceanDNA-b29589/cds.fna -a OceanDNA-b29589/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:58:43,533] [INFO] Task succeeded: Prodigal
[2023-03-16 09:58:43,533] [INFO] Task started: HMMsearch
[2023-03-16 09:58:43,533] [INFO] Running command: hmmsearch --tblout OceanDNA-b29589/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8359cb6d-197f-4690-9ae9-0a362b97e76a/dqc_reference/reference_markers.hmm OceanDNA-b29589/protein.faa > /dev/null
[2023-03-16 09:58:43,764] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:58:43,765] [INFO] Found 6/6 markers.
[2023-03-16 09:58:43,790] [INFO] Query marker FASTA was written to OceanDNA-b29589/markers.fasta
[2023-03-16 09:58:43,791] [INFO] Task started: Blastn
[2023-03-16 09:58:43,791] [INFO] Running command: blastn -query OceanDNA-b29589/markers.fasta -db /var/lib/cwl/stg8359cb6d-197f-4690-9ae9-0a362b97e76a/dqc_reference/reference_markers.fasta -out OceanDNA-b29589/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:58:44,682] [INFO] Task succeeded: Blastn
[2023-03-16 09:58:44,684] [INFO] Selected 18 target genomes.
[2023-03-16 09:58:44,684] [INFO] Target genome list was writen to OceanDNA-b29589/target_genomes.txt
[2023-03-16 09:58:44,694] [INFO] Task started: fastANI
[2023-03-16 09:58:44,694] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfa62ddb-c894-4bbb-a5b1-206e7ec7883c/OceanDNA-b29589.fa --refList OceanDNA-b29589/target_genomes.txt --output OceanDNA-b29589/fastani_result.tsv --threads 1
[2023-03-16 09:58:57,463] [INFO] Task succeeded: fastANI
[2023-03-16 09:58:57,463] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8359cb6d-197f-4690-9ae9-0a362b97e76a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:58:57,463] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8359cb6d-197f-4690-9ae9-0a362b97e76a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:58:57,474] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 09:58:57,474] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 09:58:57,475] [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
Palleronia marisminoris	strain=DSM 26347	GCA_900113405.1	315423	315423	type	True	81.3935	628	1342	95	below_threshold
Palleronia marisminoris	strain=CECT 7066	GCA_900172315.1	315423	315423	type	True	81.0789	608	1342	95	below_threshold
Maribius pelagius	strain=DSM 26893	GCA_900110115.1	387096	387096	type	True	79.9019	568	1342	95	below_threshold
Maribius salinus	strain=DSM 26892	GCA_900141995.1	313368	313368	type	True	79.5218	550	1342	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	79.1174	529	1342	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	78.8776	465	1342	95	below_threshold
Jannaschia formosa	strain=12N15	GCA_003340555.1	2259592	2259592	type	True	78.1139	376	1342	95	below_threshold
Hwanghaeicola aestuarii	strain=DSM 22009	GCA_003253995.1	568105	568105	type	True	78.0826	366	1342	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.8009	321	1342	95	below_threshold
Paenimaribius caenipelagi	strain=JBTF-M29	GCA_007004065.1	2489174	2489174	type	True	77.6216	284	1342	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	77.5714	319	1342	95	below_threshold
Maritimibacter alexandrii	strain=LZ-17	GCA_005871115.1	2570355	2570355	type	True	77.406	304	1342	95	below_threshold
Pseudoroseicyclus tamaricis	strain=CLL3-39	GCA_012070395.1	2705421	2705421	type	True	77.3831	277	1342	95	below_threshold
Pseudoroseicyclus tamaricis	strain=CLL3-39	GCA_010435925.1	2705421	2705421	type	True	77.3831	277	1342	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	77.3696	282	1342	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	77.3578	351	1342	95	below_threshold
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	77.3377	356	1342	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.329	363	1342	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 09:58:57,476] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29589/tc_result.tsv
[2023-03-16 09:58:57,476] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:58:57,476] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:58:57,476] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8359cb6d-197f-4690-9ae9-0a362b97e76a/dqc_reference/checkm_data
[2023-03-16 09:58:57,477] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:58:57,711] [INFO] Task started: CheckM
[2023-03-16 09:58:57,711] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29589/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29589/checkm_input OceanDNA-b29589/checkm_result
[2023-03-16 09:59:59,204] [INFO] Task succeeded: CheckM
[2023-03-16 09:59:59,205] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.95%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 09:59:59,209] [INFO] ===== Completeness check finished =====
[2023-03-16 09:59:59,209] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:59:59,209] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29589/markers.fasta)
[2023-03-16 09:59:59,211] [INFO] Task started: Blastn
[2023-03-16 09:59:59,211] [INFO] Running command: blastn -query OceanDNA-b29589/markers.fasta -db /var/lib/cwl/stg8359cb6d-197f-4690-9ae9-0a362b97e76a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29589/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:00:01,088] [INFO] Task succeeded: Blastn
[2023-03-16 10:00:01,090] [INFO] Selected 14 target genomes.
[2023-03-16 10:00:01,090] [INFO] Target genome list was writen to OceanDNA-b29589/target_genomes_gtdb.txt
[2023-03-16 10:00:01,106] [INFO] Task started: fastANI
[2023-03-16 10:00:01,106] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfa62ddb-c894-4bbb-a5b1-206e7ec7883c/OceanDNA-b29589.fa --refList OceanDNA-b29589/target_genomes_gtdb.txt --output OceanDNA-b29589/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:00:11,598] [INFO] Task succeeded: fastANI
[2023-03-16 10:00:11,606] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 10:00:11,607] [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_900302445.1	s__Palleronia abyssalis	99.6792	1210	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900172315.1	s__Palleronia marisminoris	81.0649	610	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900110115.1	s__Palleronia pelagia	79.8922	569	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	96.3515	N/A	N/A	N/A	N/A	1	-
GCF_900141995.1	s__Palleronia salina	79.5366	548	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	96.3515	N/A	N/A	N/A	N/A	1	-
GCF_000743715.1	s__Palleronia rufa	79.1217	528	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363795.1	s__Palleronia sp900609015	79.075	517	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016412875.1	s__Palleronia pontilimi	79.0216	522	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358695.1	s__Palleronia sp004358695	78.8548	467	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003340555.1	s__Jannaschia formosa	78.1046	377	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003253995.1	s__Palleronia aestuarii	78.0912	364	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975705.1	s__Salipiger abyssi	77.8255	335	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358185.1	s__Antarcticimicrobium luteum	77.563	320	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744955.1	s__Actibacterium sp000744955	77.54	318	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012070395.1	s__CLL3-39 sp012070395	77.4041	275	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CLL3-39	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-16 10:00:11,607] [INFO] GTDB search result was written to OceanDNA-b29589/result_gtdb.tsv
[2023-03-16 10:00:11,608] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:00:11,611] [INFO] DFAST_QC result json was written to OceanDNA-b29589/dqc_result.json
[2023-03-16 10:00:11,611] [INFO] DFAST_QC completed!
[2023-03-16 10:00:11,611] [INFO] Total running time: 0h1m54s