[2023-03-18 23:56:04,491] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:56:04,491] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:56:04,492] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ad4e6f8-4629-4cf6-9cdf-08129a6502e9/dqc_reference
[2023-03-18 23:56:05,628] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:56:05,628] [INFO] Task started: Prodigal
[2023-03-18 23:56:05,628] [INFO] Running command: cat /var/lib/cwl/stgdb30987e-5032-49b2-8fb7-264d71c4a6bb/OceanDNA-b44268.fa | prodigal -d OceanDNA-b44268/cds.fna -a OceanDNA-b44268/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:56:18,090] [INFO] Task succeeded: Prodigal
[2023-03-18 23:56:18,091] [INFO] Task started: HMMsearch
[2023-03-18 23:56:18,091] [INFO] Running command: hmmsearch --tblout OceanDNA-b44268/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ad4e6f8-4629-4cf6-9cdf-08129a6502e9/dqc_reference/reference_markers.hmm OceanDNA-b44268/protein.faa > /dev/null
[2023-03-18 23:56:18,262] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:56:18,263] [INFO] Found 6/6 markers.
[2023-03-18 23:56:18,278] [INFO] Query marker FASTA was written to OceanDNA-b44268/markers.fasta
[2023-03-18 23:56:18,279] [INFO] Task started: Blastn
[2023-03-18 23:56:18,279] [INFO] Running command: blastn -query OceanDNA-b44268/markers.fasta -db /var/lib/cwl/stg0ad4e6f8-4629-4cf6-9cdf-08129a6502e9/dqc_reference/reference_markers.fasta -out OceanDNA-b44268/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:56:18,885] [INFO] Task succeeded: Blastn
[2023-03-18 23:56:18,886] [INFO] Selected 35 target genomes.
[2023-03-18 23:56:18,886] [INFO] Target genome list was writen to OceanDNA-b44268/target_genomes.txt
[2023-03-18 23:56:18,907] [INFO] Task started: fastANI
[2023-03-18 23:56:18,907] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb30987e-5032-49b2-8fb7-264d71c4a6bb/OceanDNA-b44268.fa --refList OceanDNA-b44268/target_genomes.txt --output OceanDNA-b44268/fastani_result.tsv --threads 1
[2023-03-18 23:56:38,364] [INFO] Task succeeded: fastANI
[2023-03-18 23:56:38,364] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ad4e6f8-4629-4cf6-9cdf-08129a6502e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:56:38,364] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ad4e6f8-4629-4cf6-9cdf-08129a6502e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:56:38,364] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:56:38,365] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 23:56:38,365] [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 23:56:38,365] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44268/tc_result.tsv
[2023-03-18 23:56:38,365] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:56:38,365] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:56:38,365] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ad4e6f8-4629-4cf6-9cdf-08129a6502e9/dqc_reference/checkm_data
[2023-03-18 23:56:38,368] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:56:38,372] [INFO] Task started: CheckM
[2023-03-18 23:56:38,372] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44268/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44268/checkm_input OceanDNA-b44268/checkm_result
[2023-03-18 23:57:13,602] [INFO] Task succeeded: CheckM
[2023-03-18 23:57:13,603] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:57:13,605] [INFO] ===== Completeness check finished =====
[2023-03-18 23:57:13,605] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:57:13,605] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44268/markers.fasta)
[2023-03-18 23:57:13,606] [INFO] Task started: Blastn
[2023-03-18 23:57:13,606] [INFO] Running command: blastn -query OceanDNA-b44268/markers.fasta -db /var/lib/cwl/stg0ad4e6f8-4629-4cf6-9cdf-08129a6502e9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44268/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:57:14,618] [INFO] Task succeeded: Blastn
[2023-03-18 23:57:14,619] [INFO] Selected 21 target genomes.
[2023-03-18 23:57:14,619] [INFO] Target genome list was writen to OceanDNA-b44268/target_genomes_gtdb.txt
[2023-03-18 23:57:14,636] [INFO] Task started: fastANI
[2023-03-18 23:57:14,636] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb30987e-5032-49b2-8fb7-264d71c4a6bb/OceanDNA-b44268.fa --refList OceanDNA-b44268/target_genomes_gtdb.txt --output OceanDNA-b44268/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:57:25,977] [INFO] Task succeeded: fastANI
[2023-03-18 23:57:25,982] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 23:57:25,982] [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_018648825.1	s__Thiopontia sp018648825	78.4505	286	680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCF-002020875;f__GCF-002020875;g__Thiopontia	95.0	99.74	99.68	0.85	0.80	15	-
GCA_013349825.1	s__Thiopontia sp013349825	77.8704	191	680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCF-002020875;f__GCF-002020875;g__Thiopontia	95.0	99.78	99.58	0.88	0.82	21	-
GCA_014384675.1	s__Thiopontia autotrophica	77.2639	103	680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCF-002020875;f__GCF-002020875;g__Thiopontia	95.0	99.91	99.91	0.96	0.96	2	-
GCA_018671205.1	s__Thiopontia sp018671205	77.0089	136	680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCF-002020875;f__GCF-002020875;g__Thiopontia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013343005.1	s__Reidiella endopervernicosa	76.2351	68	680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCF-013343005;f__GCF-013343005;g__Reidiella	95.0	99.22	99.22	0.89	0.89	2	-
GCF_001007875.1	s__Sedimenticola thiotaurini	76.1898	50	680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Sedimenticola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:57:25,983] [INFO] GTDB search result was written to OceanDNA-b44268/result_gtdb.tsv
[2023-03-18 23:57:25,983] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:57:25,984] [INFO] DFAST_QC result json was written to OceanDNA-b44268/dqc_result.json
[2023-03-18 23:57:25,984] [INFO] DFAST_QC completed!
[2023-03-18 23:57:25,984] [INFO] Total running time: 0h1m21s