[2023-03-19 01:33:27,246] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:33:27,246] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:33:27,246] [INFO] DQC Reference Directory: /var/lib/cwl/stg352a2167-329c-4b3c-818c-368776126c53/dqc_reference
[2023-03-19 01:33:28,388] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:33:28,389] [INFO] Task started: Prodigal
[2023-03-19 01:33:28,389] [INFO] Running command: cat /var/lib/cwl/stg75fbe721-e0e2-4114-9bcb-68bb2b07ddf7/OceanDNA-b39208.fa | prodigal -d OceanDNA-b39208/cds.fna -a OceanDNA-b39208/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:33:37,050] [INFO] Task succeeded: Prodigal
[2023-03-19 01:33:37,051] [INFO] Task started: HMMsearch
[2023-03-19 01:33:37,051] [INFO] Running command: hmmsearch --tblout OceanDNA-b39208/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg352a2167-329c-4b3c-818c-368776126c53/dqc_reference/reference_markers.hmm OceanDNA-b39208/protein.faa > /dev/null
[2023-03-19 01:33:37,225] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:33:37,225] [INFO] Found 6/6 markers.
[2023-03-19 01:33:37,237] [INFO] Query marker FASTA was written to OceanDNA-b39208/markers.fasta
[2023-03-19 01:33:37,238] [INFO] Task started: Blastn
[2023-03-19 01:33:37,238] [INFO] Running command: blastn -query OceanDNA-b39208/markers.fasta -db /var/lib/cwl/stg352a2167-329c-4b3c-818c-368776126c53/dqc_reference/reference_markers.fasta -out OceanDNA-b39208/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:33:37,934] [INFO] Task succeeded: Blastn
[2023-03-19 01:33:37,935] [INFO] Selected 40 target genomes.
[2023-03-19 01:33:37,935] [INFO] Target genome list was writen to OceanDNA-b39208/target_genomes.txt
[2023-03-19 01:33:37,962] [INFO] Task started: fastANI
[2023-03-19 01:33:37,962] [INFO] Running command: fastANI --query /var/lib/cwl/stg75fbe721-e0e2-4114-9bcb-68bb2b07ddf7/OceanDNA-b39208.fa --refList OceanDNA-b39208/target_genomes.txt --output OceanDNA-b39208/fastani_result.tsv --threads 1
[2023-03-19 01:34:01,561] [INFO] Task succeeded: fastANI
[2023-03-19 01:34:01,561] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg352a2167-329c-4b3c-818c-368776126c53/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:34:01,561] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg352a2167-329c-4b3c-818c-368776126c53/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:34:01,568] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:34:01,568] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 01:34:01,568] [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
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	75.9587	54	477	95	below_threshold
Pseudomonas oryzae	strain=KCTC 32247	GCA_900104805.1	1392877	1392877	type	True	75.9016	70	477	95	below_threshold
Microbulbifer marinus	strain=CGMCC 1.10657	GCA_900107725.1	658218	658218	type	True	75.8835	51	477	95	below_threshold
Pseudomonas citronellolis	strain=LMG 18378	GCA_900112375.1	53408	53408	type	True	75.7296	68	477	95	below_threshold
Pseudomonas citronellolis	strain=NBRC 103043	GCA_002091555.1	53408	53408	type	True	75.7257	68	477	95	below_threshold
Pseudomonas citronellolis	strain=DSM 50332	GCA_004745455.1	53408	53408	type	True	75.7098	69	477	95	below_threshold
Pseudomonas flexibilis	strain=ATCC 29606	GCA_900155995.1	706570	706570	type	True	75.6556	51	477	95	below_threshold
Pseudomonas flexibilis	strain=ATCC 29606	GCA_000802425.1	706570	706570	type	True	75.507	53	477	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 01:34:01,568] [INFO] DFAST Taxonomy check result was written to OceanDNA-b39208/tc_result.tsv
[2023-03-19 01:34:01,568] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:34:01,568] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:34:01,568] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg352a2167-329c-4b3c-818c-368776126c53/dqc_reference/checkm_data
[2023-03-19 01:34:01,569] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:34:01,613] [INFO] Task started: CheckM
[2023-03-19 01:34:01,613] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b39208/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b39208/checkm_input OceanDNA-b39208/checkm_result
[2023-03-19 01:34:27,754] [INFO] Task succeeded: CheckM
[2023-03-19 01:34:27,754] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:34:27,756] [INFO] ===== Completeness check finished =====
[2023-03-19 01:34:27,756] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:34:27,756] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b39208/markers.fasta)
[2023-03-19 01:34:27,757] [INFO] Task started: Blastn
[2023-03-19 01:34:27,757] [INFO] Running command: blastn -query OceanDNA-b39208/markers.fasta -db /var/lib/cwl/stg352a2167-329c-4b3c-818c-368776126c53/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b39208/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:34:28,965] [INFO] Task succeeded: Blastn
[2023-03-19 01:34:28,966] [INFO] Selected 30 target genomes.
[2023-03-19 01:34:28,966] [INFO] Target genome list was writen to OceanDNA-b39208/target_genomes_gtdb.txt
[2023-03-19 01:34:29,023] [INFO] Task started: fastANI
[2023-03-19 01:34:29,024] [INFO] Running command: fastANI --query /var/lib/cwl/stg75fbe721-e0e2-4114-9bcb-68bb2b07ddf7/OceanDNA-b39208.fa --refList OceanDNA-b39208/target_genomes_gtdb.txt --output OceanDNA-b39208/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:34:45,134] [INFO] Task succeeded: fastANI
[2023-03-19 01:34:45,138] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 01:34:45,138] [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_004535795.1	s__LSUCC0057 sp004535795	97.2538	462	477	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__LSUCC0057	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900105885.1	s__Pseudomonas_K guangdongensis	76.2166	57	477	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	98.99	98.99	0.99	0.99	2	-
GCF_900107725.1	s__Microbulbifer marinus	75.8835	51	477	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003696305.1	s__Pseudomonas_E sp003696305	75.7425	59	477	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112375.1	s__Pseudomonas citronellolis	75.7296	68	477	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.078	97.44	97.08	0.86	0.82	26	-
GCF_900100495.1	s__Pseudomonas_E benzenivorans	75.4113	54	477	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 01:34:45,139] [INFO] GTDB search result was written to OceanDNA-b39208/result_gtdb.tsv
[2023-03-19 01:34:45,139] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:34:45,140] [INFO] DFAST_QC result json was written to OceanDNA-b39208/dqc_result.json
[2023-03-19 01:34:45,140] [INFO] DFAST_QC completed!
[2023-03-19 01:34:45,140] [INFO] Total running time: 0h1m18s