[2023-03-18 09:15:00,470] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:15:00,470] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:15:00,470] [INFO] DQC Reference Directory: /var/lib/cwl/stg6a24b922-7a1b-437a-aff4-aeb8a475e08e/dqc_reference
[2023-03-18 09:15:02,035] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:15:02,035] [INFO] Task started: Prodigal
[2023-03-18 09:15:02,036] [INFO] Running command: cat /var/lib/cwl/stg4ff21a77-bab7-42ef-b349-593308e6af9a/OceanDNA-b36330.fa | prodigal -d OceanDNA-b36330/cds.fna -a OceanDNA-b36330/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:15:18,865] [INFO] Task succeeded: Prodigal
[2023-03-18 09:15:18,866] [INFO] Task started: HMMsearch
[2023-03-18 09:15:18,866] [INFO] Running command: hmmsearch --tblout OceanDNA-b36330/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6a24b922-7a1b-437a-aff4-aeb8a475e08e/dqc_reference/reference_markers.hmm OceanDNA-b36330/protein.faa > /dev/null
[2023-03-18 09:15:19,060] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:15:19,061] [INFO] Found 6/6 markers.
[2023-03-18 09:15:19,079] [INFO] Query marker FASTA was written to OceanDNA-b36330/markers.fasta
[2023-03-18 09:15:19,080] [INFO] Task started: Blastn
[2023-03-18 09:15:19,080] [INFO] Running command: blastn -query OceanDNA-b36330/markers.fasta -db /var/lib/cwl/stg6a24b922-7a1b-437a-aff4-aeb8a475e08e/dqc_reference/reference_markers.fasta -out OceanDNA-b36330/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:15:19,689] [INFO] Task succeeded: Blastn
[2023-03-18 09:15:19,696] [INFO] Selected 18 target genomes.
[2023-03-18 09:15:19,696] [INFO] Target genome list was writen to OceanDNA-b36330/target_genomes.txt
[2023-03-18 09:15:19,707] [INFO] Task started: fastANI
[2023-03-18 09:15:19,707] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ff21a77-bab7-42ef-b349-593308e6af9a/OceanDNA-b36330.fa --refList OceanDNA-b36330/target_genomes.txt --output OceanDNA-b36330/fastani_result.tsv --threads 1
[2023-03-18 09:15:30,295] [INFO] Task succeeded: fastANI
[2023-03-18 09:15:30,296] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6a24b922-7a1b-437a-aff4-aeb8a475e08e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:15:30,296] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6a24b922-7a1b-437a-aff4-aeb8a475e08e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:15:30,303] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:15:30,303] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 09:15:30,303] [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 nitratireducenticrescens	strain=JAM1	GCA_000260985.3	754476	754476	type	True	82.9175	643	953	95	below_threshold
Methylophaga pinxianii	strain=TMB456	GCA_020447225.1	2881052	2881052	type	True	81.9177	631	953	95	below_threshold
Methylophaga sulfidovorans	strain=DSM 11578	GCA_900114205.1	45496	45496	type	True	76.6836	131	953	95	below_threshold
Methylophaga aminisulfidivorans	strain=MP	GCA_000214595.2	230105	230105	type	True	76.5736	139	953	95	below_threshold
Methylophaga thiooxydans	strain=DMS010	GCA_000156355.1	392484	392484	type	True	76.5076	129	953	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 09:15:30,305] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36330/tc_result.tsv
[2023-03-18 09:15:30,307] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:15:30,307] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:15:30,307] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6a24b922-7a1b-437a-aff4-aeb8a475e08e/dqc_reference/checkm_data
[2023-03-18 09:15:30,307] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:15:30,315] [INFO] Task started: CheckM
[2023-03-18 09:15:30,315] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36330/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36330/checkm_input OceanDNA-b36330/checkm_result
[2023-03-18 09:16:14,652] [INFO] Task succeeded: CheckM
[2023-03-18 09:16:14,653] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 09:16:14,655] [INFO] ===== Completeness check finished =====
[2023-03-18 09:16:14,655] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:16:14,656] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36330/markers.fasta)
[2023-03-18 09:16:14,657] [INFO] Task started: Blastn
[2023-03-18 09:16:14,657] [INFO] Running command: blastn -query OceanDNA-b36330/markers.fasta -db /var/lib/cwl/stg6a24b922-7a1b-437a-aff4-aeb8a475e08e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36330/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:16:15,658] [INFO] Task succeeded: Blastn
[2023-03-18 09:16:15,794] [INFO] Selected 5 target genomes.
[2023-03-18 09:16:15,795] [INFO] Target genome list was writen to OceanDNA-b36330/target_genomes_gtdb.txt
[2023-03-18 09:16:15,800] [INFO] Task started: fastANI
[2023-03-18 09:16:15,800] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ff21a77-bab7-42ef-b349-593308e6af9a/OceanDNA-b36330.fa --refList OceanDNA-b36330/target_genomes_gtdb.txt --output OceanDNA-b36330/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:16:19,574] [INFO] Task succeeded: fastANI
[2023-03-18 09:16:19,578] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 09:16:19,578] [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_002363955.1	s__Methylophaga sp002363955	98.7952	900	953	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	98.95	98.64	0.94	0.91	14	conclusive
GCF_001720165.1	s__Methylophaga muralis	83.4391	677	953	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	97.83	97.83	0.96	0.96	2	-
GCA_002354555.1	s__Methylophaga sp002354555	83.4232	629	953	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	98.87	98.17	0.91	0.88	3	-
GCA_002696735.1	s__Methylophaga sp002696735	83.1572	693	953	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	98.51	97.89	0.93	0.90	20	-
GCF_000260985.4	s__Methylophaga nitratireducenticrescens	82.9063	645	953	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	99.21	99.21	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-03-18 09:16:19,579] [INFO] GTDB search result was written to OceanDNA-b36330/result_gtdb.tsv
[2023-03-18 09:16:19,579] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:16:19,580] [INFO] DFAST_QC result json was written to OceanDNA-b36330/dqc_result.json
[2023-03-18 09:16:19,580] [INFO] DFAST_QC completed!
[2023-03-18 09:16:19,580] [INFO] Total running time: 0h1m19s