[2023-03-15 11:22:20,468] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:22:20,468] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:22:20,468] [INFO] DQC Reference Directory: /var/lib/cwl/stgea2b011e-ecb0-450f-b1b0-4e6eb6893082/dqc_reference
[2023-03-15 11:22:21,953] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:22:21,953] [INFO] Task started: Prodigal
[2023-03-15 11:22:21,953] [INFO] Running command: cat /var/lib/cwl/stg7043dbcf-78d7-4164-be0a-24c7c361e0fb/OceanDNA-b6205.fa | prodigal -d OceanDNA-b6205/cds.fna -a OceanDNA-b6205/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:22:44,246] [INFO] Task succeeded: Prodigal
[2023-03-15 11:22:44,247] [INFO] Task started: HMMsearch
[2023-03-15 11:22:44,247] [INFO] Running command: hmmsearch --tblout OceanDNA-b6205/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea2b011e-ecb0-450f-b1b0-4e6eb6893082/dqc_reference/reference_markers.hmm OceanDNA-b6205/protein.faa > /dev/null
[2023-03-15 11:22:44,442] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:22:44,443] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7043dbcf-78d7-4164-be0a-24c7c361e0fb/OceanDNA-b6205.fa]
[2023-03-15 11:22:44,464] [INFO] Query marker FASTA was written to OceanDNA-b6205/markers.fasta
[2023-03-15 11:22:44,465] [INFO] Task started: Blastn
[2023-03-15 11:22:44,465] [INFO] Running command: blastn -query OceanDNA-b6205/markers.fasta -db /var/lib/cwl/stgea2b011e-ecb0-450f-b1b0-4e6eb6893082/dqc_reference/reference_markers.fasta -out OceanDNA-b6205/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:22:45,054] [INFO] Task succeeded: Blastn
[2023-03-15 11:22:45,054] [INFO] Selected 25 target genomes.
[2023-03-15 11:22:45,055] [INFO] Target genome list was writen to OceanDNA-b6205/target_genomes.txt
[2023-03-15 11:22:45,067] [INFO] Task started: fastANI
[2023-03-15 11:22:45,068] [INFO] Running command: fastANI --query /var/lib/cwl/stg7043dbcf-78d7-4164-be0a-24c7c361e0fb/OceanDNA-b6205.fa --refList OceanDNA-b6205/target_genomes.txt --output OceanDNA-b6205/fastani_result.tsv --threads 1
[2023-03-15 11:22:59,224] [INFO] Task succeeded: fastANI
[2023-03-15 11:22:59,224] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea2b011e-ecb0-450f-b1b0-4e6eb6893082/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:22:59,224] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea2b011e-ecb0-450f-b1b0-4e6eb6893082/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:22:59,229] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:22:59,230] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 11:22:59,230] [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
Leptobacterium flavescens	strain=KCTC 22160	GCA_010671605.1	472055	472055	type	True	76.3539	98	1120	95	below_threshold
Abyssalbus ytuae	strain=MT3330	GCA_022807975.1	2926907	2926907	type	True	76.1163	103	1120	95	below_threshold
Cellulophaga fucicola	strain=DSM 24786	GCA_900119145.1	76595	76595	type	True	75.7515	60	1120	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001673755.1	1836467	1836467	type	True	75.6603	55	1120	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001913155.1	1836467	1836467	type	True	75.6376	56	1120	95	below_threshold
Maribacter litoralis	strain=SDRB-Phe2	GCA_003075045.1	2059726	2059726	type	True	75.5267	58	1120	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:22:59,230] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6205/tc_result.tsv
[2023-03-15 11:22:59,230] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:22:59,230] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:22:59,230] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea2b011e-ecb0-450f-b1b0-4e6eb6893082/dqc_reference/checkm_data
[2023-03-15 11:22:59,231] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:22:59,236] [INFO] Task started: CheckM
[2023-03-15 11:22:59,236] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6205/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6205/checkm_input OceanDNA-b6205/checkm_result
[2023-03-15 11:23:55,846] [INFO] Task succeeded: CheckM
[2023-03-15 11:23:55,847] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:23:55,849] [INFO] ===== Completeness check finished =====
[2023-03-15 11:23:55,849] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:23:55,849] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6205/markers.fasta)
[2023-03-15 11:23:55,850] [INFO] Task started: Blastn
[2023-03-15 11:23:55,850] [INFO] Running command: blastn -query OceanDNA-b6205/markers.fasta -db /var/lib/cwl/stgea2b011e-ecb0-450f-b1b0-4e6eb6893082/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6205/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:23:56,773] [INFO] Task succeeded: Blastn
[2023-03-15 11:23:56,774] [INFO] Selected 27 target genomes.
[2023-03-15 11:23:56,774] [INFO] Target genome list was writen to OceanDNA-b6205/target_genomes_gtdb.txt
[2023-03-15 11:23:56,790] [INFO] Task started: fastANI
[2023-03-15 11:23:56,790] [INFO] Running command: fastANI --query /var/lib/cwl/stg7043dbcf-78d7-4164-be0a-24c7c361e0fb/OceanDNA-b6205.fa --refList OceanDNA-b6205/target_genomes_gtdb.txt --output OceanDNA-b6205/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:24:12,746] [INFO] Task succeeded: fastANI
[2023-03-15 11:24:12,752] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:24:12,752] [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_009901575.1	s__Leptobacterium sp009901575	76.4075	108	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leptobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010671605.1	s__Leptobacterium flavescens	76.3539	98	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leptobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900312815.1	s__Aquimarina sp900312815	75.8064	52	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900299535.1	s__Aquimarina sp900299535	75.757	66	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	95.11	95.11	0.81	0.81	2	-
GCF_900119145.1	s__Cellulophaga fucicola	75.7515	60	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009796805.1	s__Algibacter sp009796805	75.7149	59	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001913155.1	s__Maribacter hydrothermalis	75.6376	56	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002094855.1	s__Zunongwangia atlantica	75.5561	54	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zunongwangia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003075045.1	s__Maribacter litoralis	75.5267	58	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	97.43	97.43	0.90	0.90	2	-
GCF_002846555.1	s__Aquimarina sp002846555	75.5197	69	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:24:12,753] [INFO] GTDB search result was written to OceanDNA-b6205/result_gtdb.tsv
[2023-03-15 11:24:12,753] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:24:12,754] [INFO] DFAST_QC result json was written to OceanDNA-b6205/dqc_result.json
[2023-03-15 11:24:12,754] [INFO] DFAST_QC completed!
[2023-03-15 11:24:12,754] [INFO] Total running time: 0h1m52s