[2023-03-18 20:13:32,795] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:13:32,795] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:13:32,795] [INFO] DQC Reference Directory: /var/lib/cwl/stg194682d1-38a5-4df2-97b8-fc76aa38e712/dqc_reference
[2023-03-18 20:13:34,558] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:13:34,558] [INFO] Task started: Prodigal
[2023-03-18 20:13:34,558] [INFO] Running command: cat /var/lib/cwl/stgefffce90-07f4-43fd-b36f-5d55690b5ed2/OceanDNA-b12230.fa | prodigal -d OceanDNA-b12230/cds.fna -a OceanDNA-b12230/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:13:49,725] [INFO] Task succeeded: Prodigal
[2023-03-18 20:13:49,725] [INFO] Task started: HMMsearch
[2023-03-18 20:13:49,725] [INFO] Running command: hmmsearch --tblout OceanDNA-b12230/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg194682d1-38a5-4df2-97b8-fc76aa38e712/dqc_reference/reference_markers.hmm OceanDNA-b12230/protein.faa > /dev/null
[2023-03-18 20:13:49,923] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:13:49,924] [INFO] Found 6/6 markers.
[2023-03-18 20:13:49,939] [INFO] Query marker FASTA was written to OceanDNA-b12230/markers.fasta
[2023-03-18 20:13:49,940] [INFO] Task started: Blastn
[2023-03-18 20:13:49,940] [INFO] Running command: blastn -query OceanDNA-b12230/markers.fasta -db /var/lib/cwl/stg194682d1-38a5-4df2-97b8-fc76aa38e712/dqc_reference/reference_markers.fasta -out OceanDNA-b12230/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:13:50,474] [INFO] Task succeeded: Blastn
[2023-03-18 20:13:50,475] [INFO] Selected 28 target genomes.
[2023-03-18 20:13:50,475] [INFO] Target genome list was writen to OceanDNA-b12230/target_genomes.txt
[2023-03-18 20:13:50,488] [INFO] Task started: fastANI
[2023-03-18 20:13:50,488] [INFO] Running command: fastANI --query /var/lib/cwl/stgefffce90-07f4-43fd-b36f-5d55690b5ed2/OceanDNA-b12230.fa --refList OceanDNA-b12230/target_genomes.txt --output OceanDNA-b12230/fastani_result.tsv --threads 1
[2023-03-18 20:14:06,003] [INFO] Task succeeded: fastANI
[2023-03-18 20:14:06,003] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg194682d1-38a5-4df2-97b8-fc76aa38e712/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:14:06,003] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg194682d1-38a5-4df2-97b8-fc76aa38e712/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:14:06,004] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 20:14:06,004] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 20:14:06,004] [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
--------------------------------------------------------------------------------
[2023-03-18 20:14:06,004] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12230/tc_result.tsv
[2023-03-18 20:14:06,004] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:14:06,004] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:14:06,004] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg194682d1-38a5-4df2-97b8-fc76aa38e712/dqc_reference/checkm_data
[2023-03-18 20:14:06,006] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:14:06,010] [INFO] Task started: CheckM
[2023-03-18 20:14:06,010] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12230/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12230/checkm_input OceanDNA-b12230/checkm_result
[2023-03-18 20:14:46,647] [INFO] Task succeeded: CheckM
[2023-03-18 20:14:46,647] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 20:14:46,649] [INFO] ===== Completeness check finished =====
[2023-03-18 20:14:46,649] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:14:46,650] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12230/markers.fasta)
[2023-03-18 20:14:46,650] [INFO] Task started: Blastn
[2023-03-18 20:14:46,650] [INFO] Running command: blastn -query OceanDNA-b12230/markers.fasta -db /var/lib/cwl/stg194682d1-38a5-4df2-97b8-fc76aa38e712/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12230/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:14:47,357] [INFO] Task succeeded: Blastn
[2023-03-18 20:14:47,358] [INFO] Selected 27 target genomes.
[2023-03-18 20:14:47,358] [INFO] Target genome list was writen to OceanDNA-b12230/target_genomes_gtdb.txt
[2023-03-18 20:14:48,092] [INFO] Task started: fastANI
[2023-03-18 20:14:48,092] [INFO] Running command: fastANI --query /var/lib/cwl/stgefffce90-07f4-43fd-b36f-5d55690b5ed2/OceanDNA-b12230.fa --refList OceanDNA-b12230/target_genomes_gtdb.txt --output OceanDNA-b12230/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:14:59,497] [INFO] Task succeeded: fastANI
[2023-03-18 20:14:59,502] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 20:14:59,502] [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_002716065.1	s__GCA-2716065 sp002716065	99.8267	693	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__GCA-2716065	95.0	97.60	97.60	0.88	0.88	2	conclusive
GCA_002723085.1	s__GCA-2723085 sp002723085	76.3917	120	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__GCA-2723085	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686655.1	s__MED-G20 sp002686655	76.2489	77	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	96.65	96.65	0.87	0.87	2	-
GCA_002721285.1	s__SP287 sp002721285	76.1513	55	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__SP287	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016780365.1	s__MED-G20 sp016780365	76.0979	67	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	98.18	97.06	0.79	0.71	6	-
GCA_905182525.1	s__MED-G20 sp905182525	76.0901	81	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	96.07	96.07	0.86	0.86	2	-
GCA_002691605.1	s__MED-G20 sp002691605	76.0448	73	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	96.19	95.12	0.79	0.76	3	-
GCA_002727735.1	s__GCA-002727735 sp002727735	75.9459	61	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__GCA-002727735	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 20:14:59,503] [INFO] GTDB search result was written to OceanDNA-b12230/result_gtdb.tsv
[2023-03-18 20:14:59,503] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:14:59,504] [INFO] DFAST_QC result json was written to OceanDNA-b12230/dqc_result.json
[2023-03-18 20:14:59,504] [INFO] DFAST_QC completed!
[2023-03-18 20:14:59,504] [INFO] Total running time: 0h1m27s