[2023-03-15 04:59:01,514] [INFO] DFAST_QC pipeline started.
[2023-03-15 04:59:01,514] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 04:59:01,514] [INFO] DQC Reference Directory: /var/lib/cwl/stgc6fb2f8e-3940-4a8a-9804-4425c1114745/dqc_reference
[2023-03-15 04:59:03,421] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 04:59:03,421] [INFO] Task started: Prodigal
[2023-03-15 04:59:03,422] [INFO] Running command: cat /var/lib/cwl/stg07b73301-5461-4b4d-97dd-94e13cd6dff5/OceanDNA-b13086.fa | prodigal -d OceanDNA-b13086/cds.fna -a OceanDNA-b13086/protein.faa -g 11 -q > /dev/null
[2023-03-15 04:59:24,944] [INFO] Task succeeded: Prodigal
[2023-03-15 04:59:24,945] [INFO] Task started: HMMsearch
[2023-03-15 04:59:24,945] [INFO] Running command: hmmsearch --tblout OceanDNA-b13086/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc6fb2f8e-3940-4a8a-9804-4425c1114745/dqc_reference/reference_markers.hmm OceanDNA-b13086/protein.faa > /dev/null
[2023-03-15 04:59:25,094] [INFO] Task succeeded: HMMsearch
[2023-03-15 04:59:25,095] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg07b73301-5461-4b4d-97dd-94e13cd6dff5/OceanDNA-b13086.fa]
[2023-03-15 04:59:25,121] [INFO] Query marker FASTA was written to OceanDNA-b13086/markers.fasta
[2023-03-15 04:59:25,122] [INFO] Task started: Blastn
[2023-03-15 04:59:25,122] [INFO] Running command: blastn -query OceanDNA-b13086/markers.fasta -db /var/lib/cwl/stgc6fb2f8e-3940-4a8a-9804-4425c1114745/dqc_reference/reference_markers.fasta -out OceanDNA-b13086/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:59:25,684] [INFO] Task succeeded: Blastn
[2023-03-15 04:59:25,689] [INFO] Selected 21 target genomes.
[2023-03-15 04:59:25,689] [INFO] Target genome list was writen to OceanDNA-b13086/target_genomes.txt
[2023-03-15 04:59:25,703] [INFO] Task started: fastANI
[2023-03-15 04:59:25,704] [INFO] Running command: fastANI --query /var/lib/cwl/stg07b73301-5461-4b4d-97dd-94e13cd6dff5/OceanDNA-b13086.fa --refList OceanDNA-b13086/target_genomes.txt --output OceanDNA-b13086/fastani_result.tsv --threads 1
[2023-03-15 04:59:43,062] [INFO] Task succeeded: fastANI
[2023-03-15 04:59:43,062] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc6fb2f8e-3940-4a8a-9804-4425c1114745/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 04:59:43,062] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc6fb2f8e-3940-4a8a-9804-4425c1114745/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 04:59:43,070] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 04:59:43,070] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 04:59:43,070] [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	78.1617	458	855	95	below_threshold
Rubricoccus marinus	strain=SG-29	GCA_002257665.1	716817	716817	type	True	77.6873	331	855	95	below_threshold
Rhodocaloribacter litoris	strain=ISCAR-4553	GCA_011682235.2	2558931	2558931	type	True	76.1545	133	855	95	below_threshold
Gemmatirosa kalamazoonensis	strain=KBS708	GCA_000522985.1	861299	861299	type	True	74.9563	182	855	95	below_threshold
Hymenobacter caeli	strain=9A	GCA_013294115.1	2735894	2735894	type	True	74.9393	60	855	95	below_threshold
Polyangium aurulentum	strain=SDU3-1	GCA_005144635.2	2567896	2567896	type	True	74.8369	171	855	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	74.714	90	855	95	below_threshold
Corynebacterium sphenisci	strain=DSM 44792	GCA_001941505.1	191493	191493	type	True	74.7085	72	855	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	74.6702	69	855	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	74.6623	70	855	95	below_threshold
Aromatoleum toluclasticum	strain=MF63	GCA_000378245.1	92003	92003	type	True	74.6494	54	855	95	below_threshold
Methylobacterium nodulans	strain=ORS 2060	GCA_000022085.1	114616	114616	type	True	74.6445	93	855	95	below_threshold
Aromatoleum tolulyticum	strain=ATCC 51758	GCA_900156155.1	34027	34027	type	True	74.6176	61	855	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 04:59:43,073] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13086/tc_result.tsv
[2023-03-15 04:59:43,074] [INFO] ===== Taxonomy check completed =====
[2023-03-15 04:59:43,074] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 04:59:43,074] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc6fb2f8e-3940-4a8a-9804-4425c1114745/dqc_reference/checkm_data
[2023-03-15 04:59:43,075] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 04:59:43,084] [INFO] Task started: CheckM
[2023-03-15 04:59:43,085] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13086/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13086/checkm_input OceanDNA-b13086/checkm_result
[2023-03-15 05:00:35,952] [INFO] Task succeeded: CheckM
[2023-03-15 05:00:35,952] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 48.61%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:00:36,028] [INFO] ===== Completeness check finished =====
[2023-03-15 05:00:36,028] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:00:36,028] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13086/markers.fasta)
[2023-03-15 05:00:36,029] [INFO] Task started: Blastn
[2023-03-15 05:00:36,029] [INFO] Running command: blastn -query OceanDNA-b13086/markers.fasta -db /var/lib/cwl/stgc6fb2f8e-3940-4a8a-9804-4425c1114745/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13086/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:00:36,894] [INFO] Task succeeded: Blastn
[2023-03-15 05:00:36,898] [INFO] Selected 10 target genomes.
[2023-03-15 05:00:36,898] [INFO] Target genome list was writen to OceanDNA-b13086/target_genomes_gtdb.txt
[2023-03-15 05:00:36,910] [INFO] Task started: fastANI
[2023-03-15 05:00:36,910] [INFO] Running command: fastANI --query /var/lib/cwl/stg07b73301-5461-4b4d-97dd-94e13cd6dff5/OceanDNA-b13086.fa --refList OceanDNA-b13086/target_genomes_gtdb.txt --output OceanDNA-b13086/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:00:43,986] [INFO] Task succeeded: fastANI
[2023-03-15 05:00:43,992] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 05:00:43,992] [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	78.495	446	855	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	78.1231	463	855	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	77.8811	309	855	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	77.7761	313	855	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	77.6895	330	855	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	76.8881	195	855	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__JABDIZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003285105.1	s__MEBICO9517 sp003285105	75.9824	141	855	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__MEBIC09517;g__MEBICO9517	95.0	96.96	96.85	0.95	0.94	3	-
GCA_003139545.1	s__Palsa-739 sp003139545	74.6639	59	855	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__Palsa-739	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 05:00:43,994] [INFO] GTDB search result was written to OceanDNA-b13086/result_gtdb.tsv
[2023-03-15 05:00:43,995] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:00:44,000] [INFO] DFAST_QC result json was written to OceanDNA-b13086/dqc_result.json
[2023-03-15 05:00:44,000] [INFO] DFAST_QC completed!
[2023-03-15 05:00:44,000] [INFO] Total running time: 0h1m42s