[2023-03-15 11:22:20,123] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:22:20,123] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:22:20,123] [INFO] DQC Reference Directory: /var/lib/cwl/stg3d1e0e5e-f7d8-4188-a886-566dede4af7b/dqc_reference
[2023-03-15 11:22:21,236] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:22:21,236] [INFO] Task started: Prodigal
[2023-03-15 11:22:21,237] [INFO] Running command: cat /var/lib/cwl/stg174191a8-f3c7-4dd9-8c9d-9898c7d3b094/OceanDNA-b20906.fa | prodigal -d OceanDNA-b20906/cds.fna -a OceanDNA-b20906/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:22:39,556] [INFO] Task succeeded: Prodigal
[2023-03-15 11:22:39,556] [INFO] Task started: HMMsearch
[2023-03-15 11:22:39,556] [INFO] Running command: hmmsearch --tblout OceanDNA-b20906/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3d1e0e5e-f7d8-4188-a886-566dede4af7b/dqc_reference/reference_markers.hmm OceanDNA-b20906/protein.faa > /dev/null
[2023-03-15 11:22:39,771] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:22:39,772] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg174191a8-f3c7-4dd9-8c9d-9898c7d3b094/OceanDNA-b20906.fa]
[2023-03-15 11:22:39,815] [INFO] Query marker FASTA was written to OceanDNA-b20906/markers.fasta
[2023-03-15 11:22:39,817] [INFO] Task started: Blastn
[2023-03-15 11:22:39,817] [INFO] Running command: blastn -query OceanDNA-b20906/markers.fasta -db /var/lib/cwl/stg3d1e0e5e-f7d8-4188-a886-566dede4af7b/dqc_reference/reference_markers.fasta -out OceanDNA-b20906/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:22:40,351] [INFO] Task succeeded: Blastn
[2023-03-15 11:22:40,357] [INFO] Selected 15 target genomes.
[2023-03-15 11:22:40,357] [INFO] Target genome list was writen to OceanDNA-b20906/target_genomes.txt
[2023-03-15 11:22:40,366] [INFO] Task started: fastANI
[2023-03-15 11:22:40,366] [INFO] Running command: fastANI --query /var/lib/cwl/stg174191a8-f3c7-4dd9-8c9d-9898c7d3b094/OceanDNA-b20906.fa --refList OceanDNA-b20906/target_genomes.txt --output OceanDNA-b20906/fastani_result.tsv --threads 1
[2023-03-15 11:22:52,376] [INFO] Task succeeded: fastANI
[2023-03-15 11:22:52,376] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3d1e0e5e-f7d8-4188-a886-566dede4af7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:22:52,376] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3d1e0e5e-f7d8-4188-a886-566dede4af7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:22:52,381] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:22:52,381] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 11:22:52,381] [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
Plesiocystis pacifica	strain=SIR-1	GCA_000170895.1	191768	191768	type	True	76.3682	166	852	95	below_threshold
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	75.4222	137	852	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	75.4097	136	852	95	below_threshold
Haliangium ochraceum	strain=DSM 14365	GCA_000024805.1	80816	80816	type	True	75.1722	69	852	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:22:52,383] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20906/tc_result.tsv
[2023-03-15 11:22:52,386] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:22:52,386] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:22:52,386] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3d1e0e5e-f7d8-4188-a886-566dede4af7b/dqc_reference/checkm_data
[2023-03-15 11:22:52,386] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:22:52,396] [INFO] Task started: CheckM
[2023-03-15 11:22:52,396] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20906/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20906/checkm_input OceanDNA-b20906/checkm_result
[2023-03-15 11:23:39,334] [INFO] Task succeeded: CheckM
[2023-03-15 11:23:39,335] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.95%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:23:39,372] [INFO] ===== Completeness check finished =====
[2023-03-15 11:23:39,373] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:23:39,373] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20906/markers.fasta)
[2023-03-15 11:23:39,374] [INFO] Task started: Blastn
[2023-03-15 11:23:39,374] [INFO] Running command: blastn -query OceanDNA-b20906/markers.fasta -db /var/lib/cwl/stg3d1e0e5e-f7d8-4188-a886-566dede4af7b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20906/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:23:40,113] [INFO] Task succeeded: Blastn
[2023-03-15 11:23:40,123] [INFO] Selected 23 target genomes.
[2023-03-15 11:23:40,123] [INFO] Target genome list was writen to OceanDNA-b20906/target_genomes_gtdb.txt
[2023-03-15 11:23:40,145] [INFO] Task started: fastANI
[2023-03-15 11:23:40,145] [INFO] Running command: fastANI --query /var/lib/cwl/stg174191a8-f3c7-4dd9-8c9d-9898c7d3b094/OceanDNA-b20906.fa --refList OceanDNA-b20906/target_genomes_gtdb.txt --output OceanDNA-b20906/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:23:58,896] [INFO] Task succeeded: fastANI
[2023-03-15 11:23:58,901] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:23:58,901] [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
GCF_000170895.1	s__Plesiocystis pacifica	76.3571	167	852	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Plesiocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002994615.1	s__Enhygromyxa salina_A	76.2485	150	852	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Enhygromyxa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002994635.1	s__Enhygromyxa salina_B	75.6845	143	852	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Enhygromyxa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709225.1	s__Ga0077550 sp016709225	75.6239	96	852	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Ga0077550	95.0	99.66	99.17	0.98	0.94	4	-
GCA_001464385.1	s__Ga0077550 sp001464385	75.6214	137	852	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Ga0077550	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002343915.1	s__Nannocystis exedens	75.4363	135	852	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	99.98	99.98	1.00	1.00	2	-
GCA_003696955.1	s__J032 sp003696955	75.2988	51	852	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__J032	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:23:58,903] [INFO] GTDB search result was written to OceanDNA-b20906/result_gtdb.tsv
[2023-03-15 11:23:58,904] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:23:58,908] [INFO] DFAST_QC result json was written to OceanDNA-b20906/dqc_result.json
[2023-03-15 11:23:58,908] [INFO] DFAST_QC completed!
[2023-03-15 11:23:58,908] [INFO] Total running time: 0h1m39s