[2023-03-19 04:29:39,721] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:29:39,721] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:29:39,721] [INFO] DQC Reference Directory: /var/lib/cwl/stg0700706d-dc22-4237-b902-5d0f21476035/dqc_reference
[2023-03-19 04:29:40,804] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:29:40,804] [INFO] Task started: Prodigal
[2023-03-19 04:29:40,805] [INFO] Running command: cat /var/lib/cwl/stgfa52a847-9c12-4fe3-98d2-d25505424c50/OceanDNA-b13083.fa | prodigal -d OceanDNA-b13083/cds.fna -a OceanDNA-b13083/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:30:03,535] [INFO] Task succeeded: Prodigal
[2023-03-19 04:30:03,535] [INFO] Task started: HMMsearch
[2023-03-19 04:30:03,535] [INFO] Running command: hmmsearch --tblout OceanDNA-b13083/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0700706d-dc22-4237-b902-5d0f21476035/dqc_reference/reference_markers.hmm OceanDNA-b13083/protein.faa > /dev/null
[2023-03-19 04:30:03,717] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:30:03,717] [INFO] Found 6/6 markers.
[2023-03-19 04:30:03,736] [INFO] Query marker FASTA was written to OceanDNA-b13083/markers.fasta
[2023-03-19 04:30:03,737] [INFO] Task started: Blastn
[2023-03-19 04:30:03,737] [INFO] Running command: blastn -query OceanDNA-b13083/markers.fasta -db /var/lib/cwl/stg0700706d-dc22-4237-b902-5d0f21476035/dqc_reference/reference_markers.fasta -out OceanDNA-b13083/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:30:04,387] [INFO] Task succeeded: Blastn
[2023-03-19 04:30:04,388] [INFO] Selected 23 target genomes.
[2023-03-19 04:30:04,388] [INFO] Target genome list was writen to OceanDNA-b13083/target_genomes.txt
[2023-03-19 04:30:04,400] [INFO] Task started: fastANI
[2023-03-19 04:30:04,400] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa52a847-9c12-4fe3-98d2-d25505424c50/OceanDNA-b13083.fa --refList OceanDNA-b13083/target_genomes.txt --output OceanDNA-b13083/fastani_result.tsv --threads 1
[2023-03-19 04:30:20,538] [INFO] Task succeeded: fastANI
[2023-03-19 04:30:20,538] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0700706d-dc22-4237-b902-5d0f21476035/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:30:20,538] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0700706d-dc22-4237-b902-5d0f21476035/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:30:20,548] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:30:20,548] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 04:30:20,548] [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	81.3183	729	974	95	below_threshold
Rubricoccus marinus	strain=SG-29	GCA_002257665.1	716817	716817	type	True	78.0478	421	974	95	below_threshold
Rhodocaloribacter litoris	strain=ISCAR-4553	GCA_011682235.2	2558931	2558931	type	True	75.9819	182	974	95	below_threshold
Salinibacter altiplanensis	strain=AN15	GCA_002894645.1	1803181	1803181	type	True	75.6327	66	974	95	below_threshold
Salinibacter ruber	strain=DSM 13855; M31	GCA_000013045.1	146919	146919	type	True	75.3493	97	974	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	75.0656	61	974	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	74.8881	333	974	95	below_threshold
Lysobacter spongiae	strain=119BY6-57	GCA_014145325.1	2025720	2025720	type	True	74.8811	78	974	95	below_threshold
Lutibaculum baratangense	strain=AMV1	GCA_000496075.1	1358440	1358440	type	True	74.8205	80	974	95	below_threshold
Pyxidicoccus trucidator	strain=CA060A	GCA_010894435.1	2709662	2709662	type	True	74.7943	151	974	95	below_threshold
Egicoccus halophilus	strain=CGMCC 1.14988	GCA_014640475.1	1670830	1670830	type	True	74.7768	131	974	95	below_threshold
Nocardioides albidus	strain=CCTCC AB 2015297	GCA_006335005.1	1517589	1517589	type	True	74.7745	142	974	95	below_threshold
Egicoccus halophilus	strain=EGI 80432	GCA_004300825.1	1670830	1670830	type	True	74.7736	133	974	95	below_threshold
Nocardioides halotolerans	strain=DSM 19273	GCA_000422805.1	433660	433660	type	True	74.6985	165	974	95	below_threshold
Halobellus limi	strain=CGMCC 1.10331	GCA_900108165.1	699433	699433	type	True	74.679	108	974	95	below_threshold
Halobellus limi	strain=CGMCC 1.10331	GCA_004799685.1	699433	699433	type	True	74.6748	110	974	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:30:20,548] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13083/tc_result.tsv
[2023-03-19 04:30:20,548] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:30:20,548] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:30:20,548] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0700706d-dc22-4237-b902-5d0f21476035/dqc_reference/checkm_data
[2023-03-19 04:30:20,549] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:30:20,553] [INFO] Task started: CheckM
[2023-03-19 04:30:20,553] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13083/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13083/checkm_input OceanDNA-b13083/checkm_result
[2023-03-19 04:31:15,537] [INFO] Task succeeded: CheckM
[2023-03-19 04:31:15,537] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:31:15,539] [INFO] ===== Completeness check finished =====
[2023-03-19 04:31:15,540] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:31:15,540] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13083/markers.fasta)
[2023-03-19 04:31:15,541] [INFO] Task started: Blastn
[2023-03-19 04:31:15,541] [INFO] Running command: blastn -query OceanDNA-b13083/markers.fasta -db /var/lib/cwl/stg0700706d-dc22-4237-b902-5d0f21476035/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13083/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:31:16,566] [INFO] Task succeeded: Blastn
[2023-03-19 04:31:16,567] [INFO] Selected 9 target genomes.
[2023-03-19 04:31:16,567] [INFO] Target genome list was writen to OceanDNA-b13083/target_genomes_gtdb.txt
[2023-03-19 04:31:17,159] [INFO] Task started: fastANI
[2023-03-19 04:31:17,159] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa52a847-9c12-4fe3-98d2-d25505424c50/OceanDNA-b13083.fa --refList OceanDNA-b13083/target_genomes_gtdb.txt --output OceanDNA-b13083/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:31:24,115] [INFO] Task succeeded: fastANI
[2023-03-19 04:31:24,121] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:31:24,121] [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_002283365.1	s__Rubrivirga marina	81.3939	720	974	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	81.3146	499	974	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubrivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002283555.1	s__Rubrivirga sp002283555	80.1618	638	974	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubrivirga	95.0	98.32	98.29	0.93	0.92	3	-
GCA_012960515.1	s__Rubricoccus sp012960515	78.3008	411	974	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	78.0291	424	974	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	77.3639	232	974	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__JABDIZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009908885.1	s__JAAAOL01 sp009908885	76.2904	148	974	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__JAAAOL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003285105.1	s__MEBICO9517 sp003285105	76.2046	195	974	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__MEBIC09517;g__MEBICO9517	95.0	96.96	96.85	0.95	0.94	3	-
GCF_006335005.1	s__Nocardioides albidus	74.7725	145	974	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:31:24,121] [INFO] GTDB search result was written to OceanDNA-b13083/result_gtdb.tsv
[2023-03-19 04:31:24,121] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:31:24,123] [INFO] DFAST_QC result json was written to OceanDNA-b13083/dqc_result.json
[2023-03-19 04:31:24,123] [INFO] DFAST_QC completed!
[2023-03-19 04:31:24,123] [INFO] Total running time: 0h1m44s