[2023-03-18 21:47:30,487] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:47:30,488] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:47:30,488] [INFO] DQC Reference Directory: /var/lib/cwl/stg4cefefea-4d89-42af-a453-5f0a069f4661/dqc_reference
[2023-03-18 21:47:31,565] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:47:31,565] [INFO] Task started: Prodigal
[2023-03-18 21:47:31,566] [INFO] Running command: cat /var/lib/cwl/stg69033f31-c141-4442-8f93-7c6520fe2c26/OceanDNA-b22761.fa | prodigal -d OceanDNA-b22761/cds.fna -a OceanDNA-b22761/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:47:47,881] [INFO] Task succeeded: Prodigal
[2023-03-18 21:47:47,882] [INFO] Task started: HMMsearch
[2023-03-18 21:47:47,882] [INFO] Running command: hmmsearch --tblout OceanDNA-b22761/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4cefefea-4d89-42af-a453-5f0a069f4661/dqc_reference/reference_markers.hmm OceanDNA-b22761/protein.faa > /dev/null
[2023-03-18 21:47:48,080] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:47:48,081] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg69033f31-c141-4442-8f93-7c6520fe2c26/OceanDNA-b22761.fa]
[2023-03-18 21:47:48,108] [INFO] Query marker FASTA was written to OceanDNA-b22761/markers.fasta
[2023-03-18 21:47:48,109] [INFO] Task started: Blastn
[2023-03-18 21:47:48,109] [INFO] Running command: blastn -query OceanDNA-b22761/markers.fasta -db /var/lib/cwl/stg4cefefea-4d89-42af-a453-5f0a069f4661/dqc_reference/reference_markers.fasta -out OceanDNA-b22761/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:47:48,651] [INFO] Task succeeded: Blastn
[2023-03-18 21:47:48,657] [INFO] Selected 15 target genomes.
[2023-03-18 21:47:48,657] [INFO] Target genome list was writen to OceanDNA-b22761/target_genomes.txt
[2023-03-18 21:47:48,667] [INFO] Task started: fastANI
[2023-03-18 21:47:48,667] [INFO] Running command: fastANI --query /var/lib/cwl/stg69033f31-c141-4442-8f93-7c6520fe2c26/OceanDNA-b22761.fa --refList OceanDNA-b22761/target_genomes.txt --output OceanDNA-b22761/fastani_result.tsv --threads 1
[2023-03-18 21:48:04,036] [INFO] Task succeeded: fastANI
[2023-03-18 21:48:04,037] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4cefefea-4d89-42af-a453-5f0a069f4661/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:48:04,037] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4cefefea-4d89-42af-a453-5f0a069f4661/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:48:04,037] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:48:04,037] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 21:48:04,037] [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
--------------------------------------------------------------------------------
[2023-03-18 21:48:04,065] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22761/tc_result.tsv
[2023-03-18 21:48:04,134] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:48:04,135] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:48:04,135] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4cefefea-4d89-42af-a453-5f0a069f4661/dqc_reference/checkm_data
[2023-03-18 21:48:04,138] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:48:04,190] [INFO] Task started: CheckM
[2023-03-18 21:48:04,190] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22761/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22761/checkm_input OceanDNA-b22761/checkm_result
[2023-03-18 21:48:47,760] [INFO] Task succeeded: CheckM
[2023-03-18 21:48:47,761] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.15%
Contamintation: 2.08%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-18 21:48:47,790] [INFO] ===== Completeness check finished =====
[2023-03-18 21:48:47,790] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:48:47,790] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22761/markers.fasta)
[2023-03-18 21:48:47,791] [INFO] Task started: Blastn
[2023-03-18 21:48:47,791] [INFO] Running command: blastn -query OceanDNA-b22761/markers.fasta -db /var/lib/cwl/stg4cefefea-4d89-42af-a453-5f0a069f4661/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22761/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:48:48,584] [INFO] Task succeeded: Blastn
[2023-03-18 21:48:48,585] [INFO] Selected 14 target genomes.
[2023-03-18 21:48:48,585] [INFO] Target genome list was writen to OceanDNA-b22761/target_genomes_gtdb.txt
[2023-03-18 21:48:48,600] [INFO] Task started: fastANI
[2023-03-18 21:48:48,600] [INFO] Running command: fastANI --query /var/lib/cwl/stg69033f31-c141-4442-8f93-7c6520fe2c26/OceanDNA-b22761.fa --refList OceanDNA-b22761/target_genomes_gtdb.txt --output OceanDNA-b22761/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:48:56,811] [INFO] Task succeeded: fastANI
[2023-03-18 21:48:56,819] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 21:48:56,819] [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_016779265.1	s__M30B53 sp016779265	99.3391	767	829	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__M30B53	95.0	99.26	99.20	0.88	0.86	5	conclusive
GCA_018401745.1	s__M30B53 sp018401745	79.0571	342	829	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__M30B53	95.0	96.02	95.94	0.68	0.66	3	-
GCA_903919035.1	s__QWPN01 sp903919035	77.1799	85	829	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	99.57	99.56	0.90	0.89	5	-
GCA_014192425.1	s__QWPN01 sp014192425	76.8202	118	829	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018970605.1	s__QWPN01 sp018970605	76.7947	110	829	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903958265.1	s__QWPN01 sp903958265	76.6928	91	829	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	98.26	98.26	0.80	0.80	2	-
GCA_903885565.1	s__CAISJI01 sp903885565	76.6224	110	829	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__CAISJI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003671185.1	s__QWPN01 sp003671185	76.4675	94	829	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903951635.1	s__QWOP01 sp903951635	76.3987	111	829	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWOP01	95.0	99.54	99.51	0.90	0.90	3	-
GCA_003669605.1	s__QWOP01 sp003669605	76.3375	72	829	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWOP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903949225.1	s__QWOP01 sp903949225	76.3187	101	829	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWOP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903917235.1	s__QWPN01 sp903917235	76.3026	113	829	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	98.02	96.87	0.85	0.84	3	-
--------------------------------------------------------------------------------
[2023-03-18 21:48:56,819] [INFO] GTDB search result was written to OceanDNA-b22761/result_gtdb.tsv
[2023-03-18 21:48:56,819] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:48:56,820] [INFO] DFAST_QC result json was written to OceanDNA-b22761/dqc_result.json
[2023-03-18 21:48:56,820] [INFO] DFAST_QC completed!
[2023-03-18 21:48:56,820] [INFO] Total running time: 0h1m26s