[2023-06-18 18:10:12,378] [INFO] DFAST_QC pipeline started.
[2023-06-18 18:10:12,380] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 18:10:12,381] [INFO] DQC Reference Directory: /var/lib/cwl/stg42dbb7ea-aade-4f0a-b9d2-3bb4d987671e/dqc_reference
[2023-06-18 18:10:15,136] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 18:10:15,138] [INFO] Task started: Prodigal
[2023-06-18 18:10:15,138] [INFO] Running command: gunzip -c /var/lib/cwl/stge2e89a77-e41e-4e64-9418-7837e45132ce/GCA_018657205.1_ASM1865720v1_genomic.fna.gz | prodigal -d GCA_018657205.1_ASM1865720v1_genomic.fna/cds.fna -a GCA_018657205.1_ASM1865720v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 18:10:21,433] [INFO] Task succeeded: Prodigal
[2023-06-18 18:10:21,433] [INFO] Task started: HMMsearch
[2023-06-18 18:10:21,433] [INFO] Running command: hmmsearch --tblout GCA_018657205.1_ASM1865720v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg42dbb7ea-aade-4f0a-b9d2-3bb4d987671e/dqc_reference/reference_markers.hmm GCA_018657205.1_ASM1865720v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 18:10:21,660] [INFO] Task succeeded: HMMsearch
[2023-06-18 18:10:21,665] [INFO] Found 6/6 markers.
[2023-06-18 18:10:21,698] [INFO] Query marker FASTA was written to GCA_018657205.1_ASM1865720v1_genomic.fna/markers.fasta
[2023-06-18 18:10:21,699] [INFO] Task started: Blastn
[2023-06-18 18:10:21,699] [INFO] Running command: blastn -query GCA_018657205.1_ASM1865720v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg42dbb7ea-aade-4f0a-b9d2-3bb4d987671e/dqc_reference/reference_markers.fasta -out GCA_018657205.1_ASM1865720v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:10:22,375] [INFO] Task succeeded: Blastn
[2023-06-18 18:10:22,405] [INFO] Selected 35 target genomes.
[2023-06-18 18:10:22,406] [INFO] Target genome list was writen to GCA_018657205.1_ASM1865720v1_genomic.fna/target_genomes.txt
[2023-06-18 18:10:22,418] [INFO] Task started: fastANI
[2023-06-18 18:10:22,418] [INFO] Running command: fastANI --query /var/lib/cwl/stge2e89a77-e41e-4e64-9418-7837e45132ce/GCA_018657205.1_ASM1865720v1_genomic.fna.gz --refList GCA_018657205.1_ASM1865720v1_genomic.fna/target_genomes.txt --output GCA_018657205.1_ASM1865720v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 18:10:46,900] [INFO] Task succeeded: fastANI
[2023-06-18 18:10:46,900] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg42dbb7ea-aade-4f0a-b9d2-3bb4d987671e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 18:10:46,901] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg42dbb7ea-aade-4f0a-b9d2-3bb4d987671e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 18:10:46,917] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 18:10:46,917] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 18:10:46,918] [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 lutimaris	strain=DSM 28463	GCA_900115165.1	1005928	1005928	type	True	76.6123	66	662	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	76.3949	52	662	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	76.3475	61	662	95	below_threshold
Ruegeria atlantica	strain=CECT 4292	GCA_001458195.1	81569	81569	suspected-type	True	76.3227	50	662	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	76.246	58	662	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	76.246	58	662	95	below_threshold
Roseovarius litorisediminis	strain=CECT 8287	GCA_900172295.1	1312363	1312363	type	True	76.1907	56	662	95	below_threshold
Roseovarius gahaiensis	strain=GH877	GCA_011601345.1	2716691	2716691	type	True	76.0509	60	662	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	75.9392	55	662	95	below_threshold
Pseudoprimorskyibacter insulae	strain=CECT 8871	GCA_900302505.1	1695997	1695997	type	True	75.5948	69	662	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 18:10:46,919] [INFO] DFAST Taxonomy check result was written to GCA_018657205.1_ASM1865720v1_genomic.fna/tc_result.tsv
[2023-06-18 18:10:46,922] [INFO] ===== Taxonomy check completed =====
[2023-06-18 18:10:46,922] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 18:10:46,922] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg42dbb7ea-aade-4f0a-b9d2-3bb4d987671e/dqc_reference/checkm_data
[2023-06-18 18:10:46,923] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 18:10:46,954] [INFO] Task started: CheckM
[2023-06-18 18:10:46,954] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018657205.1_ASM1865720v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018657205.1_ASM1865720v1_genomic.fna/checkm_input GCA_018657205.1_ASM1865720v1_genomic.fna/checkm_result
[2023-06-18 18:11:12,288] [INFO] Task succeeded: CheckM
[2023-06-18 18:11:12,289] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.75%
Contamintation: 2.23%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 18:11:12,318] [INFO] ===== Completeness check finished =====
[2023-06-18 18:11:12,319] [INFO] ===== Start GTDB Search =====
[2023-06-18 18:11:12,319] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018657205.1_ASM1865720v1_genomic.fna/markers.fasta)
[2023-06-18 18:11:12,320] [INFO] Task started: Blastn
[2023-06-18 18:11:12,320] [INFO] Running command: blastn -query GCA_018657205.1_ASM1865720v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg42dbb7ea-aade-4f0a-b9d2-3bb4d987671e/dqc_reference/reference_markers_gtdb.fasta -out GCA_018657205.1_ASM1865720v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:11:13,429] [INFO] Task succeeded: Blastn
[2023-06-18 18:11:13,437] [INFO] Selected 25 target genomes.
[2023-06-18 18:11:13,437] [INFO] Target genome list was writen to GCA_018657205.1_ASM1865720v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 18:11:13,455] [INFO] Task started: fastANI
[2023-06-18 18:11:13,455] [INFO] Running command: fastANI --query /var/lib/cwl/stge2e89a77-e41e-4e64-9418-7837e45132ce/GCA_018657205.1_ASM1865720v1_genomic.fna.gz --refList GCA_018657205.1_ASM1865720v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018657205.1_ASM1865720v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 18:11:27,121] [INFO] Task succeeded: fastANI
[2023-06-18 18:11:27,133] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 18:11:27,133] [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
GCA_902512685.1	s__CABZJG01 sp902512685	98.0562	403	662	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CABZJG01	95.0	97.75	97.42	0.59	0.54	7	conclusive
GCA_902525995.1	s__CABZJG01 sp902525995	85.8916	273	662	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CABZJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002726375.1	s__CABZJG01 sp002726375	85.8545	379	662	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CABZJG01	95.0	97.70	96.98	0.64	0.64	3	-
GCA_001642945.1	s__LGRT01 sp001642945	77.4209	90	662	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__LGRT01	95.0	99.21	98.81	0.97	0.88	20	-
GCA_001510135.1	s__LFER01 sp001510135	76.5761	58	662	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__LFER01	95.0	98.63	96.26	0.85	0.78	7	-
GCF_002222635.1	s__Ascidiaceihabitans pseudonitzschiae_A	76.4361	60	662	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.92	99.92	0.96	0.96	2	-
GCF_013032505.1	s__Ruegeria atlantica_F	76.2879	51	662	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458195.1	s__Ruegeria atlantica	76.2858	51	662	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	95.59	95.51	0.84	0.83	3	-
GCF_900172295.1	s__Roseovarius litorisediminis	76.1907	56	662	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016019955.1	s__Shimia sp016019955	76.0927	57	662	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	99.56	99.56	0.93	0.93	2	-
GCF_017744095.1	s__Shimia sp017744095	75.8668	61	662	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900302505.1	s__Pseudoprimorskyibacter insulae	75.5948	69	662	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudoprimorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 18:11:27,135] [INFO] GTDB search result was written to GCA_018657205.1_ASM1865720v1_genomic.fna/result_gtdb.tsv
[2023-06-18 18:11:27,135] [INFO] ===== GTDB Search completed =====
[2023-06-18 18:11:27,143] [INFO] DFAST_QC result json was written to GCA_018657205.1_ASM1865720v1_genomic.fna/dqc_result.json
[2023-06-18 18:11:27,143] [INFO] DFAST_QC completed!
[2023-06-18 18:11:27,144] [INFO] Total running time: 0h1m15s