[2023-03-15 11:10:12,559] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:10:12,559] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:10:12,559] [INFO] DQC Reference Directory: /var/lib/cwl/stg110f1938-cee3-4db4-90ab-85fb5e3a508d/dqc_reference
[2023-03-15 11:10:13,659] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:10:13,660] [INFO] Task started: Prodigal
[2023-03-15 11:10:13,660] [INFO] Running command: cat /var/lib/cwl/stg68511be4-1ded-4249-96bb-d46222da6752/OceanDNA-b960.fa | prodigal -d OceanDNA-b960/cds.fna -a OceanDNA-b960/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:10:32,879] [INFO] Task succeeded: Prodigal
[2023-03-15 11:10:32,879] [INFO] Task started: HMMsearch
[2023-03-15 11:10:32,879] [INFO] Running command: hmmsearch --tblout OceanDNA-b960/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg110f1938-cee3-4db4-90ab-85fb5e3a508d/dqc_reference/reference_markers.hmm OceanDNA-b960/protein.faa > /dev/null
[2023-03-15 11:10:33,039] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:10:33,040] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg68511be4-1ded-4249-96bb-d46222da6752/OceanDNA-b960.fa]
[2023-03-15 11:10:33,064] [INFO] Query marker FASTA was written to OceanDNA-b960/markers.fasta
[2023-03-15 11:10:33,065] [INFO] Task started: Blastn
[2023-03-15 11:10:33,065] [INFO] Running command: blastn -query OceanDNA-b960/markers.fasta -db /var/lib/cwl/stg110f1938-cee3-4db4-90ab-85fb5e3a508d/dqc_reference/reference_markers.fasta -out OceanDNA-b960/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:10:33,833] [INFO] Task succeeded: Blastn
[2023-03-15 11:10:33,838] [INFO] Selected 18 target genomes.
[2023-03-15 11:10:33,839] [INFO] Target genome list was writen to OceanDNA-b960/target_genomes.txt
[2023-03-15 11:10:33,849] [INFO] Task started: fastANI
[2023-03-15 11:10:33,849] [INFO] Running command: fastANI --query /var/lib/cwl/stg68511be4-1ded-4249-96bb-d46222da6752/OceanDNA-b960.fa --refList OceanDNA-b960/target_genomes.txt --output OceanDNA-b960/fastani_result.tsv --threads 1
[2023-03-15 11:10:45,469] [INFO] Task succeeded: fastANI
[2023-03-15 11:10:45,470] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg110f1938-cee3-4db4-90ab-85fb5e3a508d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:10:45,470] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg110f1938-cee3-4db4-90ab-85fb5e3a508d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:10:45,479] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:10:45,479] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 11:10:45,479] [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
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	77.5532	234	731	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	77.3428	255	731	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	76.9445	158	731	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	76.3977	203	731	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	76.3172	165	731	95	below_threshold
Glycomyces tenuis	strain=NRRL B-16895	GCA_000715885.1	58116	58116	type	True	75.4098	131	731	95	below_threshold
Nocardioides litoris	strain=DSM 103718	GCA_006346315.1	1926648	1926648	type	True	75.3761	179	731	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	75.3583	65	731	95	below_threshold
Streptosporangium becharense	strain=DSM 46887	GCA_014204985.1	1816182	1816182	type	True	75.3404	136	731	95	below_threshold
Streptosporangium becharense	strain=CECT 8961	GCA_014191075.1	1816182	1816182	type	True	75.3358	137	731	95	below_threshold
Nonomuraea ceibae	strain=KCTC 39826	GCA_019396325.1	1935170	1935170	type	True	75.3191	176	731	95	below_threshold
Kocuria sediminis	strain=JCM 17929	GCA_009735315.1	1038857	1038857	type	True	75.272	86	731	95	below_threshold
Kocuria turfanensis	strain=HO-9042	GCA_001580365.1	388357	388357	type	True	75.1257	100	731	95	below_threshold
Kocuria dechangensis	strain=CGMCC 1.12187	GCA_014636775.1	1176249	1176249	type	True	75.0716	84	731	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:10:45,482] [INFO] DFAST Taxonomy check result was written to OceanDNA-b960/tc_result.tsv
[2023-03-15 11:10:45,486] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:10:45,486] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:10:45,486] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg110f1938-cee3-4db4-90ab-85fb5e3a508d/dqc_reference/checkm_data
[2023-03-15 11:10:45,487] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:10:45,507] [INFO] Task started: CheckM
[2023-03-15 11:10:45,507] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b960/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b960/checkm_input OceanDNA-b960/checkm_result
[2023-03-15 11:11:29,035] [INFO] Task succeeded: CheckM
[2023-03-15 11:11:29,036] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.35%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:11:29,068] [INFO] ===== Completeness check finished =====
[2023-03-15 11:11:29,068] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:11:29,068] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b960/markers.fasta)
[2023-03-15 11:11:29,070] [INFO] Task started: Blastn
[2023-03-15 11:11:29,070] [INFO] Running command: blastn -query OceanDNA-b960/markers.fasta -db /var/lib/cwl/stg110f1938-cee3-4db4-90ab-85fb5e3a508d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b960/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:11:30,351] [INFO] Task succeeded: Blastn
[2023-03-15 11:11:30,351] [INFO] Selected 7 target genomes.
[2023-03-15 11:11:30,351] [INFO] Target genome list was writen to OceanDNA-b960/target_genomes_gtdb.txt
[2023-03-15 11:11:30,358] [INFO] Task started: fastANI
[2023-03-15 11:11:30,358] [INFO] Running command: fastANI --query /var/lib/cwl/stg68511be4-1ded-4249-96bb-d46222da6752/OceanDNA-b960.fa --refList OceanDNA-b960/target_genomes_gtdb.txt --output OceanDNA-b960/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:11:34,317] [INFO] Task succeeded: fastANI
[2023-03-15 11:11:34,322] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 11:11:34,322] [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_002346745.1	s__S20-B6 sp002346745	99.8783	594	731	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	97.72	96.97	0.85	0.81	8	conclusive
GCA_002699725.1	s__S20-B6 sp002699725	82.3895	499	731	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	98.58	98.41	0.87	0.86	3	-
GCA_002329075.1	s__S20-B6 sp002329075	82.3253	500	731	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	98.53	97.43	0.90	0.85	7	-
GCA_014381945.1	s__S20-B6 sp014381945	82.2308	525	731	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016845305.1	s__UBA9410 sp016845305	81.2207	460	731	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012961035.1	s__UBA9410 sp012961035	79.1582	359	731	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	99.67	99.67	0.93	0.93	2	-
GCA_014237715.1	s__UBA9410 sp014237715	78.9586	322	731	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	98.52	98.52	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-03-15 11:11:34,325] [INFO] GTDB search result was written to OceanDNA-b960/result_gtdb.tsv
[2023-03-15 11:11:34,326] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:11:34,328] [INFO] DFAST_QC result json was written to OceanDNA-b960/dqc_result.json
[2023-03-15 11:11:34,328] [INFO] DFAST_QC completed!
[2023-03-15 11:11:34,328] [INFO] Total running time: 0h1m22s