[2023-03-16 02:38:04,615] [INFO] DFAST_QC pipeline started.
[2023-03-16 02:38:04,615] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 02:38:04,615] [INFO] DQC Reference Directory: /var/lib/cwl/stgd36b1c57-8d32-441d-8a0e-18f92ff88379/dqc_reference
[2023-03-16 02:38:05,900] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 02:38:05,901] [INFO] Task started: Prodigal
[2023-03-16 02:38:05,902] [INFO] Running command: cat /var/lib/cwl/stg4b321ce5-1642-4244-b15a-374dbb8ae82c/OceanDNA-b36419.fa | prodigal -d OceanDNA-b36419/cds.fna -a OceanDNA-b36419/protein.faa -g 11 -q > /dev/null
[2023-03-16 02:38:14,804] [INFO] Task succeeded: Prodigal
[2023-03-16 02:38:14,804] [INFO] Task started: HMMsearch
[2023-03-16 02:38:14,804] [INFO] Running command: hmmsearch --tblout OceanDNA-b36419/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd36b1c57-8d32-441d-8a0e-18f92ff88379/dqc_reference/reference_markers.hmm OceanDNA-b36419/protein.faa > /dev/null
[2023-03-16 02:38:14,962] [INFO] Task succeeded: HMMsearch
[2023-03-16 02:38:14,963] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4b321ce5-1642-4244-b15a-374dbb8ae82c/OceanDNA-b36419.fa]
[2023-03-16 02:38:14,980] [INFO] Query marker FASTA was written to OceanDNA-b36419/markers.fasta
[2023-03-16 02:38:14,980] [INFO] Task started: Blastn
[2023-03-16 02:38:14,980] [INFO] Running command: blastn -query OceanDNA-b36419/markers.fasta -db /var/lib/cwl/stgd36b1c57-8d32-441d-8a0e-18f92ff88379/dqc_reference/reference_markers.fasta -out OceanDNA-b36419/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 02:38:15,626] [INFO] Task succeeded: Blastn
[2023-03-16 02:38:15,627] [INFO] Selected 6 target genomes.
[2023-03-16 02:38:15,627] [INFO] Target genome list was writen to OceanDNA-b36419/target_genomes.txt
[2023-03-16 02:38:15,629] [INFO] Task started: fastANI
[2023-03-16 02:38:15,629] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b321ce5-1642-4244-b15a-374dbb8ae82c/OceanDNA-b36419.fa --refList OceanDNA-b36419/target_genomes.txt --output OceanDNA-b36419/fastani_result.tsv --threads 1
[2023-03-16 02:38:19,754] [INFO] Task succeeded: fastANI
[2023-03-16 02:38:19,755] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd36b1c57-8d32-441d-8a0e-18f92ff88379/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 02:38:19,755] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd36b1c57-8d32-441d-8a0e-18f92ff88379/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 02:38:19,760] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2023-03-16 02:38:19,760] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 02:38:19,760] [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
Alcanivorax venustensis	strain=ISO4	GCA_015356855.1	172371	172371	type	True	95.1622	390	404	95	conclusive
Alcanivorax profundimaris	strain=ST75FaO-1	GCA_015265435.1	2735259	2735259	type	True	85.3555	354	404	95	below_threshold
Alcanivorax gelatiniphagus	strain=MEBiC 08158	GCA_005938655.1	1194167	1194167	type	True	84.9034	344	404	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	84.8052	339	404	95	below_threshold
Alcanivorax mobilis	strain=MT13131	GCA_002864685.1	2019569	2019569	type	True	82.444	316	404	95	below_threshold
Alcanivorax xenomutans	strain=JC109	GCA_900217905.1	1094342	1094342	type	True	79.9971	268	404	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 02:38:19,760] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36419/tc_result.tsv
[2023-03-16 02:38:19,760] [INFO] ===== Taxonomy check completed =====
[2023-03-16 02:38:19,760] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 02:38:19,761] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd36b1c57-8d32-441d-8a0e-18f92ff88379/dqc_reference/checkm_data
[2023-03-16 02:38:19,761] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 02:38:19,765] [INFO] Task started: CheckM
[2023-03-16 02:38:19,765] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36419/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36419/checkm_input OceanDNA-b36419/checkm_result
[2023-03-16 02:38:46,351] [INFO] Task succeeded: CheckM
[2023-03-16 02:38:46,351] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.77%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 02:38:46,353] [INFO] ===== Completeness check finished =====
[2023-03-16 02:38:46,353] [INFO] ===== Start GTDB Search =====
[2023-03-16 02:38:46,353] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36419/markers.fasta)
[2023-03-16 02:38:46,354] [INFO] Task started: Blastn
[2023-03-16 02:38:46,354] [INFO] Running command: blastn -query OceanDNA-b36419/markers.fasta -db /var/lib/cwl/stgd36b1c57-8d32-441d-8a0e-18f92ff88379/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36419/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 02:38:47,350] [INFO] Task succeeded: Blastn
[2023-03-16 02:38:47,350] [INFO] Selected 8 target genomes.
[2023-03-16 02:38:47,350] [INFO] Target genome list was writen to OceanDNA-b36419/target_genomes_gtdb.txt
[2023-03-16 02:38:47,433] [INFO] Task started: fastANI
[2023-03-16 02:38:47,433] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b321ce5-1642-4244-b15a-374dbb8ae82c/OceanDNA-b36419.fa --refList OceanDNA-b36419/target_genomes_gtdb.txt --output OceanDNA-b36419/fastani_result_gtdb.tsv --threads 1
[2023-03-16 02:38:52,883] [INFO] Task succeeded: fastANI
[2023-03-16 02:38:52,888] [INFO] Found 7 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-16 02:38:52,888] [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_017794945.1	s__Alcanivorax sp009711585	96.6166	369	404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	96.99	96.99	0.93	0.93	2	inconclusive
GCF_015356855.1	s__Alcanivorax venustensis	95.1622	390	404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.73	95.38	0.91	0.87	46	inconclusive
GCA_002389055.1	s__Alcanivorax sp002389055	91.9493	354	404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	96.98	96.27	0.78	0.74	3	-
GCF_015265435.1	s__Alcanivorax profundimaris	85.3555	354	404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.49	97.23	0.85	0.77	11	-
GCF_016906305.1	s__Alcanivorax marinus_B	84.9276	350	404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938655.1	s__Alcanivorax gelatiniphagus	84.873	345	404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.53	98.53	0.93	0.93	3	-
GCF_002864685.1	s__Alcanivorax mobilis	82.4565	316	404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.57	98.57	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-03-16 02:38:52,888] [INFO] GTDB search result was written to OceanDNA-b36419/result_gtdb.tsv
[2023-03-16 02:38:52,888] [INFO] ===== GTDB Search completed =====
[2023-03-16 02:38:52,889] [INFO] DFAST_QC result json was written to OceanDNA-b36419/dqc_result.json
[2023-03-16 02:38:52,889] [INFO] DFAST_QC completed!
[2023-03-16 02:38:52,889] [INFO] Total running time: 0h0m48s