[2023-03-18 01:41:20,960] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:41:20,960] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:41:20,960] [INFO] DQC Reference Directory: /var/lib/cwl/stga33a765b-fb40-4276-9b7b-64b51392ceb4/dqc_reference
[2023-03-18 01:41:22,074] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:41:22,075] [INFO] Task started: Prodigal
[2023-03-18 01:41:22,075] [INFO] Running command: cat /var/lib/cwl/stg15de691b-70cf-4f3d-9ded-21a469f85e12/OceanDNA-b1132.fa | prodigal -d OceanDNA-b1132/cds.fna -a OceanDNA-b1132/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:41:33,977] [INFO] Task succeeded: Prodigal
[2023-03-18 01:41:33,977] [INFO] Task started: HMMsearch
[2023-03-18 01:41:33,977] [INFO] Running command: hmmsearch --tblout OceanDNA-b1132/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga33a765b-fb40-4276-9b7b-64b51392ceb4/dqc_reference/reference_markers.hmm OceanDNA-b1132/protein.faa > /dev/null
[2023-03-18 01:41:34,138] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:41:34,139] [INFO] Found 6/6 markers.
[2023-03-18 01:41:34,155] [INFO] Query marker FASTA was written to OceanDNA-b1132/markers.fasta
[2023-03-18 01:41:34,155] [INFO] Task started: Blastn
[2023-03-18 01:41:34,155] [INFO] Running command: blastn -query OceanDNA-b1132/markers.fasta -db /var/lib/cwl/stga33a765b-fb40-4276-9b7b-64b51392ceb4/dqc_reference/reference_markers.fasta -out OceanDNA-b1132/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:41:34,899] [INFO] Task succeeded: Blastn
[2023-03-18 01:41:34,900] [INFO] Selected 29 target genomes.
[2023-03-18 01:41:34,900] [INFO] Target genome list was writen to OceanDNA-b1132/target_genomes.txt
[2023-03-18 01:41:34,921] [INFO] Task started: fastANI
[2023-03-18 01:41:34,921] [INFO] Running command: fastANI --query /var/lib/cwl/stg15de691b-70cf-4f3d-9ded-21a469f85e12/OceanDNA-b1132.fa --refList OceanDNA-b1132/target_genomes.txt --output OceanDNA-b1132/fastani_result.tsv --threads 1
[2023-03-18 01:41:53,086] [INFO] Task succeeded: fastANI
[2023-03-18 01:41:53,087] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga33a765b-fb40-4276-9b7b-64b51392ceb4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:41:53,087] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga33a765b-fb40-4276-9b7b-64b51392ceb4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:41:53,092] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:41:53,092] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 01:41:53,092] [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	76.7246	120	622	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.4821	127	622	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	76.2809	83	622	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	76.0044	85	622	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	75.9811	81	622	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	75.7778	68	622	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 01:41:53,092] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1132/tc_result.tsv
[2023-03-18 01:41:53,092] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:41:53,092] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:41:53,093] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga33a765b-fb40-4276-9b7b-64b51392ceb4/dqc_reference/checkm_data
[2023-03-18 01:41:53,093] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:41:53,096] [INFO] Task started: CheckM
[2023-03-18 01:41:53,096] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1132/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1132/checkm_input OceanDNA-b1132/checkm_result
[2023-03-18 01:42:26,588] [INFO] Task succeeded: CheckM
[2023-03-18 01:42:26,588] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:42:26,590] [INFO] ===== Completeness check finished =====
[2023-03-18 01:42:26,590] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:42:26,590] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1132/markers.fasta)
[2023-03-18 01:42:26,591] [INFO] Task started: Blastn
[2023-03-18 01:42:26,591] [INFO] Running command: blastn -query OceanDNA-b1132/markers.fasta -db /var/lib/cwl/stga33a765b-fb40-4276-9b7b-64b51392ceb4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1132/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:42:27,892] [INFO] Task succeeded: Blastn
[2023-03-18 01:42:27,893] [INFO] Selected 6 target genomes.
[2023-03-18 01:42:27,893] [INFO] Target genome list was writen to OceanDNA-b1132/target_genomes_gtdb.txt
[2023-03-18 01:42:27,896] [INFO] Task started: fastANI
[2023-03-18 01:42:27,896] [INFO] Running command: fastANI --query /var/lib/cwl/stg15de691b-70cf-4f3d-9ded-21a469f85e12/OceanDNA-b1132.fa --refList OceanDNA-b1132/target_genomes_gtdb.txt --output OceanDNA-b1132/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:42:30,598] [INFO] Task succeeded: fastANI
[2023-03-18 01:42:30,602] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 01:42:30,602] [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_002687745.1	s__UBA3125 sp002687745	99.6241	538	622	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA3125	95.0	98.98	96.61	0.89	0.87	5	conclusive
GCA_002501135.1	s__UBA3125 sp002501135	90.6562	475	622	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA3125	95.0	99.79	99.79	0.86	0.86	2	-
GCA_018673475.1	s__UBA3125 sp018673475	90.1092	543	622	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_002365325.1	s__UBA3125 sp002365325	86.3972	438	622	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	81.64	458	622	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	79.0596	293	622	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 01:42:30,603] [INFO] GTDB search result was written to OceanDNA-b1132/result_gtdb.tsv
[2023-03-18 01:42:30,603] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:42:30,604] [INFO] DFAST_QC result json was written to OceanDNA-b1132/dqc_result.json
[2023-03-18 01:42:30,604] [INFO] DFAST_QC completed!
[2023-03-18 01:42:30,604] [INFO] Total running time: 0h1m10s