[2023-03-16 03:23:49,808] [INFO] DFAST_QC pipeline started.
[2023-03-16 03:23:49,808] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 03:23:49,808] [INFO] DQC Reference Directory: /var/lib/cwl/stg0744a097-c7d2-4af4-8858-c29d25210706/dqc_reference
[2023-03-16 03:23:50,984] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 03:23:50,984] [INFO] Task started: Prodigal
[2023-03-16 03:23:50,984] [INFO] Running command: cat /var/lib/cwl/stg18a5a0ed-49bd-4809-a969-4e6e9644638e/OceanDNA-b36167.fa | prodigal -d OceanDNA-b36167/cds.fna -a OceanDNA-b36167/protein.faa -g 11 -q > /dev/null
[2023-03-16 03:23:59,039] [INFO] Task succeeded: Prodigal
[2023-03-16 03:23:59,040] [INFO] Task started: HMMsearch
[2023-03-16 03:23:59,040] [INFO] Running command: hmmsearch --tblout OceanDNA-b36167/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0744a097-c7d2-4af4-8858-c29d25210706/dqc_reference/reference_markers.hmm OceanDNA-b36167/protein.faa > /dev/null
[2023-03-16 03:23:59,254] [INFO] Task succeeded: HMMsearch
[2023-03-16 03:23:59,254] [INFO] Found 6/6 markers.
[2023-03-16 03:23:59,270] [INFO] Query marker FASTA was written to OceanDNA-b36167/markers.fasta
[2023-03-16 03:23:59,270] [INFO] Task started: Blastn
[2023-03-16 03:23:59,270] [INFO] Running command: blastn -query OceanDNA-b36167/markers.fasta -db /var/lib/cwl/stg0744a097-c7d2-4af4-8858-c29d25210706/dqc_reference/reference_markers.fasta -out OceanDNA-b36167/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:23:59,838] [INFO] Task succeeded: Blastn
[2023-03-16 03:23:59,839] [INFO] Selected 33 target genomes.
[2023-03-16 03:23:59,839] [INFO] Target genome list was writen to OceanDNA-b36167/target_genomes.txt
[2023-03-16 03:23:59,857] [INFO] Task started: fastANI
[2023-03-16 03:23:59,857] [INFO] Running command: fastANI --query /var/lib/cwl/stg18a5a0ed-49bd-4809-a969-4e6e9644638e/OceanDNA-b36167.fa --refList OceanDNA-b36167/target_genomes.txt --output OceanDNA-b36167/fastani_result.tsv --threads 1
[2023-03-16 03:24:17,328] [INFO] Task succeeded: fastANI
[2023-03-16 03:24:17,328] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0744a097-c7d2-4af4-8858-c29d25210706/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 03:24:17,328] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0744a097-c7d2-4af4-8858-c29d25210706/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 03:24:17,332] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 03:24:17,332] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 03:24:17,332] [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
Methylophaga sulfidovorans	strain=DSM 11578	GCA_900114205.1	45496	45496	type	True	76.7274	59	465	95	below_threshold
Methylophaga aminisulfidivorans	strain=MP	GCA_000214595.2	230105	230105	type	True	76.3414	59	465	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 03:24:17,332] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36167/tc_result.tsv
[2023-03-16 03:24:17,332] [INFO] ===== Taxonomy check completed =====
[2023-03-16 03:24:17,332] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 03:24:17,332] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0744a097-c7d2-4af4-8858-c29d25210706/dqc_reference/checkm_data
[2023-03-16 03:24:17,333] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 03:24:17,339] [INFO] Task started: CheckM
[2023-03-16 03:24:17,340] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36167/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36167/checkm_input OceanDNA-b36167/checkm_result
[2023-03-16 03:24:42,917] [INFO] Task succeeded: CheckM
[2023-03-16 03:24:42,918] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.40%
Contamintation: 1.50%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-16 03:24:42,920] [INFO] ===== Completeness check finished =====
[2023-03-16 03:24:42,920] [INFO] ===== Start GTDB Search =====
[2023-03-16 03:24:42,920] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36167/markers.fasta)
[2023-03-16 03:24:42,920] [INFO] Task started: Blastn
[2023-03-16 03:24:42,920] [INFO] Running command: blastn -query OceanDNA-b36167/markers.fasta -db /var/lib/cwl/stg0744a097-c7d2-4af4-8858-c29d25210706/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36167/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:24:43,789] [INFO] Task succeeded: Blastn
[2023-03-16 03:24:43,790] [INFO] Selected 22 target genomes.
[2023-03-16 03:24:43,790] [INFO] Target genome list was writen to OceanDNA-b36167/target_genomes_gtdb.txt
[2023-03-16 03:24:44,350] [INFO] Task started: fastANI
[2023-03-16 03:24:44,351] [INFO] Running command: fastANI --query /var/lib/cwl/stg18a5a0ed-49bd-4809-a969-4e6e9644638e/OceanDNA-b36167.fa --refList OceanDNA-b36167/target_genomes_gtdb.txt --output OceanDNA-b36167/fastani_result_gtdb.tsv --threads 1
[2023-03-16 03:24:52,324] [INFO] Task succeeded: fastANI
[2023-03-16 03:24:52,333] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 03:24:52,333] [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_002400805.1	s__41-12-T18 sp002400805	82.7487	171	465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__41-12-T18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002163085.1	s__41-12-T18 sp002163085	81.9675	291	465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__41-12-T18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002163115.1	s__41-12-T18 sp002163115	79.1839	186	465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__41-12-T18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215775.1	s__GCA-002733105 sp013215775	79.1836	125	465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733105.1	s__GCA-002733105 sp002733105	77.79	92	465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215825.1	s__GCA-002733105 sp013215825	77.582	106	465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859375.1	s__GCA-002733105 sp014859375	77.376	85	465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733505.1	s__GCA-002733105 sp002733505	77.2786	70	465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706095.1	s__Methylophaga sp002706095	77.2221	51	465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	98.12	97.28	0.92	0.89	8	-
GCA_002733335.1	s__GCA-002733105 sp002733335	77.1259	82	465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003645385.1	s__GCA-002733105 sp003645385	77.1127	72	465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	98.88	98.88	0.61	0.61	2	-
GCA_002402245.1	s__GCA-002733105 sp002402245	77.1016	85	465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733715.2	s__GCA-002733105 sp002733715	77.087	83	465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011053005.1	s__GCA-002733105 sp011053005	77.0421	93	465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013139345.1	s__GCA-002733105 sp013139345	76.7353	78	465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 03:24:52,333] [INFO] GTDB search result was written to OceanDNA-b36167/result_gtdb.tsv
[2023-03-16 03:24:52,333] [INFO] ===== GTDB Search completed =====
[2023-03-16 03:24:52,334] [INFO] DFAST_QC result json was written to OceanDNA-b36167/dqc_result.json
[2023-03-16 03:24:52,334] [INFO] DFAST_QC completed!
[2023-03-16 03:24:52,334] [INFO] Total running time: 0h1m3s