[2023-03-18 03:45:10,276] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:45:10,276] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:45:10,276] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe0b049e-2ff3-4d74-995a-5e00bdf412ff/dqc_reference
[2023-03-18 03:45:12,144] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:45:12,144] [INFO] Task started: Prodigal
[2023-03-18 03:45:12,144] [INFO] Running command: cat /var/lib/cwl/stgb233cf18-97fb-4ec6-8c89-7035f9093e80/OceanDNA-b1129.fa | prodigal -d OceanDNA-b1129/cds.fna -a OceanDNA-b1129/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:45:22,431] [INFO] Task succeeded: Prodigal
[2023-03-18 03:45:22,431] [INFO] Task started: HMMsearch
[2023-03-18 03:45:22,431] [INFO] Running command: hmmsearch --tblout OceanDNA-b1129/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe0b049e-2ff3-4d74-995a-5e00bdf412ff/dqc_reference/reference_markers.hmm OceanDNA-b1129/protein.faa > /dev/null
[2023-03-18 03:45:22,662] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:45:22,662] [INFO] Found 6/6 markers.
[2023-03-18 03:45:22,674] [INFO] Query marker FASTA was written to OceanDNA-b1129/markers.fasta
[2023-03-18 03:45:22,675] [INFO] Task started: Blastn
[2023-03-18 03:45:22,675] [INFO] Running command: blastn -query OceanDNA-b1129/markers.fasta -db /var/lib/cwl/stgbe0b049e-2ff3-4d74-995a-5e00bdf412ff/dqc_reference/reference_markers.fasta -out OceanDNA-b1129/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:45:23,465] [INFO] Task succeeded: Blastn
[2023-03-18 03:45:23,465] [INFO] Selected 30 target genomes.
[2023-03-18 03:45:23,466] [INFO] Target genome list was writen to OceanDNA-b1129/target_genomes.txt
[2023-03-18 03:45:23,481] [INFO] Task started: fastANI
[2023-03-18 03:45:23,481] [INFO] Running command: fastANI --query /var/lib/cwl/stgb233cf18-97fb-4ec6-8c89-7035f9093e80/OceanDNA-b1129.fa --refList OceanDNA-b1129/target_genomes.txt --output OceanDNA-b1129/fastani_result.tsv --threads 1
[2023-03-18 03:45:46,818] [INFO] Task succeeded: fastANI
[2023-03-18 03:45:46,818] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe0b049e-2ff3-4d74-995a-5e00bdf412ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:45:46,818] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe0b049e-2ff3-4d74-995a-5e00bdf412ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:45:46,823] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:45:46,823] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 03:45:46,824] [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
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.6009	93	540	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.575	99	540	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	76.4613	59	540	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	76.0868	52	540	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	75.8126	79	540	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 03:45:46,824] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1129/tc_result.tsv
[2023-03-18 03:45:46,824] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:45:46,824] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:45:46,824] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe0b049e-2ff3-4d74-995a-5e00bdf412ff/dqc_reference/checkm_data
[2023-03-18 03:45:46,825] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:45:46,828] [INFO] Task started: CheckM
[2023-03-18 03:45:46,828] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1129/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1129/checkm_input OceanDNA-b1129/checkm_result
[2023-03-18 03:46:16,440] [INFO] Task succeeded: CheckM
[2023-03-18 03:46:16,441] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.73%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 03:46:16,443] [INFO] ===== Completeness check finished =====
[2023-03-18 03:46:16,443] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:46:16,443] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1129/markers.fasta)
[2023-03-18 03:46:16,443] [INFO] Task started: Blastn
[2023-03-18 03:46:16,443] [INFO] Running command: blastn -query OceanDNA-b1129/markers.fasta -db /var/lib/cwl/stgbe0b049e-2ff3-4d74-995a-5e00bdf412ff/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1129/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:46:17,812] [INFO] Task succeeded: Blastn
[2023-03-18 03:46:17,813] [INFO] Selected 6 target genomes.
[2023-03-18 03:46:17,813] [INFO] Target genome list was writen to OceanDNA-b1129/target_genomes_gtdb.txt
[2023-03-18 03:46:17,821] [INFO] Task started: fastANI
[2023-03-18 03:46:17,821] [INFO] Running command: fastANI --query /var/lib/cwl/stgb233cf18-97fb-4ec6-8c89-7035f9093e80/OceanDNA-b1129.fa --refList OceanDNA-b1129/target_genomes_gtdb.txt --output OceanDNA-b1129/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:46:20,304] [INFO] Task succeeded: fastANI
[2023-03-18 03:46:20,309] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 03:46:20,309] [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_002501135.1	s__UBA3125 sp002501135	99.7892	460	540	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA3125	95.0	99.79	99.79	0.86	0.86	2	conclusive
GCA_018673475.1	s__UBA3125 sp018673475	91.4724	480	540	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA3125	95.0	99.96	99.93	0.97	0.96	16	-
GCA_002687745.1	s__UBA3125 sp002687745	90.9244	440	540	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA3125	95.0	98.98	96.61	0.89	0.87	5	-
GCA_002365325.1	s__UBA3125 sp002365325	86.4535	382	540	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA3125	95.0	98.82	97.98	0.79	0.76	7	-
GCA_014381745.1	s__UBA3125 sp014381745	81.7389	436	540	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA3125	95.0	99.87	99.86	0.97	0.96	3	-
GCA_015658775.1	s__UBA3125 sp015658775	78.6314	262	540	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA3125	95.0	98.89	98.89	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2023-03-18 03:46:20,309] [INFO] GTDB search result was written to OceanDNA-b1129/result_gtdb.tsv
[2023-03-18 03:46:20,309] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:46:20,310] [INFO] DFAST_QC result json was written to OceanDNA-b1129/dqc_result.json
[2023-03-18 03:46:20,310] [INFO] DFAST_QC completed!
[2023-03-18 03:46:20,310] [INFO] Total running time: 0h1m10s