[2023-03-16 02:38:04,741] [INFO] DFAST_QC pipeline started.
[2023-03-16 02:38:04,741] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 02:38:04,741] [INFO] DQC Reference Directory: /var/lib/cwl/stg994e094f-fdf1-4abf-a110-0aa043b9df66/dqc_reference
[2023-03-16 02:38:05,899] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 02:38:05,901] [INFO] Task started: Prodigal
[2023-03-16 02:38:05,901] [INFO] Running command: cat /var/lib/cwl/stga6785eca-6261-40b7-8fab-545f8af0011f/OceanDNA-b13088.fa | prodigal -d OceanDNA-b13088/cds.fna -a OceanDNA-b13088/protein.faa -g 11 -q > /dev/null
[2023-03-16 02:38:40,162] [INFO] Task succeeded: Prodigal
[2023-03-16 02:38:40,162] [INFO] Task started: HMMsearch
[2023-03-16 02:38:40,162] [INFO] Running command: hmmsearch --tblout OceanDNA-b13088/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg994e094f-fdf1-4abf-a110-0aa043b9df66/dqc_reference/reference_markers.hmm OceanDNA-b13088/protein.faa > /dev/null
[2023-03-16 02:38:40,371] [INFO] Task succeeded: HMMsearch
[2023-03-16 02:38:40,371] [INFO] Found 6/6 markers.
[2023-03-16 02:38:40,399] [INFO] Query marker FASTA was written to OceanDNA-b13088/markers.fasta
[2023-03-16 02:38:40,399] [INFO] Task started: Blastn
[2023-03-16 02:38:40,399] [INFO] Running command: blastn -query OceanDNA-b13088/markers.fasta -db /var/lib/cwl/stg994e094f-fdf1-4abf-a110-0aa043b9df66/dqc_reference/reference_markers.fasta -out OceanDNA-b13088/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 02:38:41,084] [INFO] Task succeeded: Blastn
[2023-03-16 02:38:41,085] [INFO] Selected 23 target genomes.
[2023-03-16 02:38:41,085] [INFO] Target genome list was writen to OceanDNA-b13088/target_genomes.txt
[2023-03-16 02:38:41,095] [INFO] Task started: fastANI
[2023-03-16 02:38:41,095] [INFO] Running command: fastANI --query /var/lib/cwl/stga6785eca-6261-40b7-8fab-545f8af0011f/OceanDNA-b13088.fa --refList OceanDNA-b13088/target_genomes.txt --output OceanDNA-b13088/fastani_result.tsv --threads 1
[2023-03-16 02:39:01,911] [INFO] Task succeeded: fastANI
[2023-03-16 02:39:01,912] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg994e094f-fdf1-4abf-a110-0aa043b9df66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 02:39:01,912] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg994e094f-fdf1-4abf-a110-0aa043b9df66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 02:39:01,923] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 02:39:01,923] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 02:39:01,923] [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
Rubrivirga marina	strain=SAORIC-28	GCA_002283365.1	1196024	1196024	type	True	82.277	939	1457	95	below_threshold
Rubricoccus marinus	strain=SG-29	GCA_002257665.1	716817	716817	type	True	78.6855	554	1457	95	below_threshold
Rhodocaloribacter litoris	strain=ISCAR-4553	GCA_011682235.2	2558931	2558931	type	True	76.3479	248	1457	95	below_threshold
Salinibacter ruber	strain=DSM 13855; M31	GCA_000013045.1	146919	146919	type	True	75.6378	123	1457	95	below_threshold
Salinibacter altiplanensis	strain=AN15	GCA_002894645.1	1803181	1803181	type	True	75.5588	94	1457	95	below_threshold
Longibacter salinarum	strain=KCTC 52045	GCA_002554795.1	1850348	1850348	type	True	75.4659	53	1457	95	below_threshold
Salisaeta longa	strain=DSM 21114	GCA_000419585.1	503170	503170	type	True	75.322	84	1457	95	below_threshold
Lysobacter aestuarii	strain=JCM 31130	GCA_006546775.1	1706195	1706195	type	True	75.0707	91	1457	95	below_threshold
Hymenobacter gummosus	strain=KCTC 52166	GCA_003970915.1	1776032	1776032	type	True	75.0217	120	1457	95	below_threshold
Aureimonas leprariae	strain=YIM 132180	GCA_008802405.1	2615207	2615207	type	True	74.9574	143	1457	95	below_threshold
Hymenobacter busanensis	strain=MA3	GCA_008727865.1	2607656	2607656	type	True	74.9232	64	1457	95	below_threshold
Roseomonas aerilata	strain=DSM 19363	GCA_000711725.1	452982	452982	type	True	74.8906	159	1457	95	below_threshold
Rubellimicrobium mesophilum	strain=DSM 19309	GCA_000600335.2	1123067	1123067	type	True	74.8626	154	1457	95	below_threshold
Mangrovactinospora gilvigriseus	strain=MUSC 26	GCA_001879105.1	1428644	1428644	type	True	74.8371	245	1457	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	74.8062	155	1457	95	below_threshold
Pyxidicoccus fallax	strain=DSM 14698	GCA_012933655.1	394095	394095	type	True	74.7964	283	1457	95	below_threshold
Polyangium aurulentum	strain=SDU3-1	GCA_005144635.2	2567896	2567896	type	True	74.7852	337	1457	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	74.7658	208	1457	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	74.7394	199	1457	95	below_threshold
Virgisporangium ochraceum	strain=NBRC 16418	GCA_016863655.1	65505	65505	type	True	74.7382	414	1457	95	below_threshold
Halegenticoccus soli	strain=SYSU A9-0	GCA_002844195.1	1985678	1985678	type	True	74.658	186	1457	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 02:39:01,924] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13088/tc_result.tsv
[2023-03-16 02:39:01,924] [INFO] ===== Taxonomy check completed =====
[2023-03-16 02:39:01,924] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 02:39:01,924] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg994e094f-fdf1-4abf-a110-0aa043b9df66/dqc_reference/checkm_data
[2023-03-16 02:39:01,925] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 02:39:01,930] [INFO] Task started: CheckM
[2023-03-16 02:39:01,930] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13088/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13088/checkm_input OceanDNA-b13088/checkm_result
[2023-03-16 02:40:20,768] [INFO] Task succeeded: CheckM
[2023-03-16 02:40:20,769] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 02:40:20,772] [INFO] ===== Completeness check finished =====
[2023-03-16 02:40:20,772] [INFO] ===== Start GTDB Search =====
[2023-03-16 02:40:20,772] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13088/markers.fasta)
[2023-03-16 02:40:20,772] [INFO] Task started: Blastn
[2023-03-16 02:40:20,772] [INFO] Running command: blastn -query OceanDNA-b13088/markers.fasta -db /var/lib/cwl/stg994e094f-fdf1-4abf-a110-0aa043b9df66/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13088/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 02:40:21,905] [INFO] Task succeeded: Blastn
[2023-03-16 02:40:21,905] [INFO] Selected 7 target genomes.
[2023-03-16 02:40:21,906] [INFO] Target genome list was writen to OceanDNA-b13088/target_genomes_gtdb.txt
[2023-03-16 02:40:22,015] [INFO] Task started: fastANI
[2023-03-16 02:40:22,016] [INFO] Running command: fastANI --query /var/lib/cwl/stga6785eca-6261-40b7-8fab-545f8af0011f/OceanDNA-b13088.fa --refList OceanDNA-b13088/target_genomes_gtdb.txt --output OceanDNA-b13088/fastani_result_gtdb.tsv --threads 1
[2023-03-16 02:40:28,440] [INFO] Task succeeded: fastANI
[2023-03-16 02:40:28,445] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 02:40:28,445] [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_002283555.1	s__Rubrivirga sp002283555	82.4438	911	1457	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubrivirga	95.0	98.32	98.29	0.93	0.92	3	-
GCF_002283365.1	s__Rubrivirga marina	82.2798	941	1457	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubrivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012269805.1	s__Rubrivirga sp012269805	82.0442	613	1457	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubrivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012960515.1	s__Rubricoccus sp012960515	79.0307	553	1457	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002257665.1	s__Rubricoccus marinus	78.6877	553	1457	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013003465.1	s__JABDIZ01 sp013003465	77.8747	267	1457	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__JABDIZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018122625.2	s__Coralloluteibacterium stylophorae	74.8322	215	1457	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Coralloluteibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 02:40:28,445] [INFO] GTDB search result was written to OceanDNA-b13088/result_gtdb.tsv
[2023-03-16 02:40:28,445] [INFO] ===== GTDB Search completed =====
[2023-03-16 02:40:28,447] [INFO] DFAST_QC result json was written to OceanDNA-b13088/dqc_result.json
[2023-03-16 02:40:28,447] [INFO] DFAST_QC completed!
[2023-03-16 02:40:28,447] [INFO] Total running time: 0h2m24s