[2023-03-18 21:15:24,360] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:15:24,361] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:15:24,361] [INFO] DQC Reference Directory: /var/lib/cwl/stga29d3b1a-bdc5-4cdf-bca4-a43f2714e786/dqc_reference
[2023-03-18 21:15:25,496] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:15:25,496] [INFO] Task started: Prodigal
[2023-03-18 21:15:25,496] [INFO] Running command: cat /var/lib/cwl/stg49e6de3f-12c0-442e-84aa-c331cfe53203/OceanDNA-b17441.fa | prodigal -d OceanDNA-b17441/cds.fna -a OceanDNA-b17441/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:15:39,247] [INFO] Task succeeded: Prodigal
[2023-03-18 21:15:39,247] [INFO] Task started: HMMsearch
[2023-03-18 21:15:39,247] [INFO] Running command: hmmsearch --tblout OceanDNA-b17441/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga29d3b1a-bdc5-4cdf-bca4-a43f2714e786/dqc_reference/reference_markers.hmm OceanDNA-b17441/protein.faa > /dev/null
[2023-03-18 21:15:39,415] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:15:39,416] [INFO] Found 6/6 markers.
[2023-03-18 21:15:39,431] [INFO] Query marker FASTA was written to OceanDNA-b17441/markers.fasta
[2023-03-18 21:15:39,432] [INFO] Task started: Blastn
[2023-03-18 21:15:39,432] [INFO] Running command: blastn -query OceanDNA-b17441/markers.fasta -db /var/lib/cwl/stga29d3b1a-bdc5-4cdf-bca4-a43f2714e786/dqc_reference/reference_markers.fasta -out OceanDNA-b17441/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:15:39,926] [INFO] Task succeeded: Blastn
[2023-03-18 21:15:39,926] [INFO] Selected 14 target genomes.
[2023-03-18 21:15:39,927] [INFO] Target genome list was writen to OceanDNA-b17441/target_genomes.txt
[2023-03-18 21:15:39,988] [INFO] Task started: fastANI
[2023-03-18 21:15:39,989] [INFO] Running command: fastANI --query /var/lib/cwl/stg49e6de3f-12c0-442e-84aa-c331cfe53203/OceanDNA-b17441.fa --refList OceanDNA-b17441/target_genomes.txt --output OceanDNA-b17441/fastani_result.tsv --threads 1
[2023-03-18 21:15:47,686] [INFO] Task succeeded: fastANI
[2023-03-18 21:15:47,687] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga29d3b1a-bdc5-4cdf-bca4-a43f2714e786/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:15:47,687] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga29d3b1a-bdc5-4cdf-bca4-a43f2714e786/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:15:47,687] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:15:47,687] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 21:15:47,687] [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 21:15:47,687] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17441/tc_result.tsv
[2023-03-18 21:15:47,687] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:15:47,687] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:15:47,688] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga29d3b1a-bdc5-4cdf-bca4-a43f2714e786/dqc_reference/checkm_data
[2023-03-18 21:15:47,690] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:15:47,694] [INFO] Task started: CheckM
[2023-03-18 21:15:47,694] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17441/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17441/checkm_input OceanDNA-b17441/checkm_result
[2023-03-18 21:16:25,958] [INFO] Task succeeded: CheckM
[2023-03-18 21:16:25,958] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.74%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 21:16:25,960] [INFO] ===== Completeness check finished =====
[2023-03-18 21:16:25,961] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:16:25,961] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17441/markers.fasta)
[2023-03-18 21:16:25,961] [INFO] Task started: Blastn
[2023-03-18 21:16:25,961] [INFO] Running command: blastn -query OceanDNA-b17441/markers.fasta -db /var/lib/cwl/stga29d3b1a-bdc5-4cdf-bca4-a43f2714e786/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17441/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:16:26,679] [INFO] Task succeeded: Blastn
[2023-03-18 21:16:26,680] [INFO] Selected 13 target genomes.
[2023-03-18 21:16:26,680] [INFO] Target genome list was writen to OceanDNA-b17441/target_genomes_gtdb.txt
[2023-03-18 21:16:26,689] [INFO] Task started: fastANI
[2023-03-18 21:16:26,689] [INFO] Running command: fastANI --query /var/lib/cwl/stg49e6de3f-12c0-442e-84aa-c331cfe53203/OceanDNA-b17441.fa --refList OceanDNA-b17441/target_genomes_gtdb.txt --output OceanDNA-b17441/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:16:34,463] [INFO] Task succeeded: fastANI
[2023-03-18 21:16:34,467] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 21:16:34,467] [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_002311875.1	s__UBA1138 sp002311875	99.6914	733	770	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA1138	95.0	99.17	99.17	0.96	0.96	2	conclusive
GCA_002313925.1	s__UBA1138 sp002313925	82.217	532	770	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA1138	95.0	96.15	95.66	0.87	0.85	5	-
GCA_012960225.1	s__UBA1138 sp012960225	82.0429	604	770	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA1138	95.0	99.89	99.89	0.95	0.95	2	-
GCA_002501085.1	s__UBA1138 sp002501085	81.4274	524	770	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA1138	95.0	98.27	98.27	0.83	0.83	2	-
GCA_002724575.1	s__UBA1138 sp002724575	79.5971	419	770	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA1138	95.0	96.61	95.09	0.77	0.73	4	-
--------------------------------------------------------------------------------
[2023-03-18 21:16:34,467] [INFO] GTDB search result was written to OceanDNA-b17441/result_gtdb.tsv
[2023-03-18 21:16:34,468] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:16:34,468] [INFO] DFAST_QC result json was written to OceanDNA-b17441/dqc_result.json
[2023-03-18 21:16:34,468] [INFO] DFAST_QC completed!
[2023-03-18 21:16:34,468] [INFO] Total running time: 0h1m10s