[2023-03-15 07:03:38,777] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:03:38,782] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:03:38,782] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e1b61f8-5bc1-4039-bf4d-98d5d6e0021e/dqc_reference
[2023-03-15 07:03:39,978] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:03:39,978] [INFO] Task started: Prodigal
[2023-03-15 07:03:39,978] [INFO] Running command: cat /var/lib/cwl/stg6a337d98-7c6b-4165-9ea0-8c113b4dc153/OceanDNA-b26755.fa | prodigal -d OceanDNA-b26755/cds.fna -a OceanDNA-b26755/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:03:53,211] [INFO] Task succeeded: Prodigal
[2023-03-15 07:03:53,211] [INFO] Task started: HMMsearch
[2023-03-15 07:03:53,211] [INFO] Running command: hmmsearch --tblout OceanDNA-b26755/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e1b61f8-5bc1-4039-bf4d-98d5d6e0021e/dqc_reference/reference_markers.hmm OceanDNA-b26755/protein.faa > /dev/null
[2023-03-15 07:03:53,386] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:03:53,387] [INFO] Found 6/6 markers.
[2023-03-15 07:03:53,415] [INFO] Query marker FASTA was written to OceanDNA-b26755/markers.fasta
[2023-03-15 07:03:53,416] [INFO] Task started: Blastn
[2023-03-15 07:03:53,416] [INFO] Running command: blastn -query OceanDNA-b26755/markers.fasta -db /var/lib/cwl/stg5e1b61f8-5bc1-4039-bf4d-98d5d6e0021e/dqc_reference/reference_markers.fasta -out OceanDNA-b26755/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:03:54,289] [INFO] Task succeeded: Blastn
[2023-03-15 07:03:54,306] [INFO] Selected 15 target genomes.
[2023-03-15 07:03:54,307] [INFO] Target genome list was writen to OceanDNA-b26755/target_genomes.txt
[2023-03-15 07:03:54,315] [INFO] Task started: fastANI
[2023-03-15 07:03:54,315] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a337d98-7c6b-4165-9ea0-8c113b4dc153/OceanDNA-b26755.fa --refList OceanDNA-b26755/target_genomes.txt --output OceanDNA-b26755/fastani_result.tsv --threads 1
[2023-03-15 07:04:04,922] [INFO] Task succeeded: fastANI
[2023-03-15 07:04:04,923] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e1b61f8-5bc1-4039-bf4d-98d5d6e0021e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:04:04,923] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e1b61f8-5bc1-4039-bf4d-98d5d6e0021e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:04:04,932] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:04:04,932] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 07:04:04,932] [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
Methyloceanibacter methanicus	strain=R-67174	GCA_001723285.1	1774968	1774968	type	True	92.7038	668	716	95	below_threshold
Methyloceanibacter stevinii	strain=R-67176	GCA_001723355.1	1774970	1774970	type	True	83.6372	591	716	95	below_threshold
Methyloceanibacter caenitepidi	strain=Gela4	GCA_000828475.1	1384459	1384459	type	True	83.185	555	716	95	below_threshold
Methyloceanibacter superfactus	strain=R-67175	GCA_001723305.1	1774969	1774969	type	True	79.3765	397	716	95	below_threshold
Methyloceanibacter marginalis	strain=R-67177	GCA_001723295.1	1774971	1774971	type	True	79.3335	313	716	95	below_threshold
Methyloligella halotolerans	strain=VKM B-2706	GCA_001708935.1	1177755	1177755	type	True	77.4071	212	716	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	76.7871	103	716	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	76.6784	123	716	95	below_threshold
Hyphomicrobium album	strain=XQ2	GCA_009708035.1	2665159	2665159	type	True	76.6345	120	716	95	below_threshold
Methylobacterium isbiliense	strain=DSM 17168	GCA_022179325.1	315478	315478	type	True	76.4188	124	716	95	below_threshold
Candidatus Rhodoblastus alkanivorans		GCA_022760755.1	2954117	2954117	type	True	76.3322	77	716	95	below_threshold
Methylobacterium hispanicum	strain=DSM 16372	GCA_022179285.1	270350	270350	type	True	76.1417	114	716	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	75.7682	50	716	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	75.5672	84	716	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 07:04:04,936] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26755/tc_result.tsv
[2023-03-15 07:04:04,940] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:04:04,940] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:04:04,940] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e1b61f8-5bc1-4039-bf4d-98d5d6e0021e/dqc_reference/checkm_data
[2023-03-15 07:04:04,941] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:04:04,953] [INFO] Task started: CheckM
[2023-03-15 07:04:04,954] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26755/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26755/checkm_input OceanDNA-b26755/checkm_result
[2023-03-15 07:04:40,534] [INFO] Task succeeded: CheckM
[2023-03-15 07:04:40,535] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 07:04:40,554] [INFO] ===== Completeness check finished =====
[2023-03-15 07:04:40,554] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:04:40,554] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26755/markers.fasta)
[2023-03-15 07:04:40,555] [INFO] Task started: Blastn
[2023-03-15 07:04:40,555] [INFO] Running command: blastn -query OceanDNA-b26755/markers.fasta -db /var/lib/cwl/stg5e1b61f8-5bc1-4039-bf4d-98d5d6e0021e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26755/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:04:42,265] [INFO] Task succeeded: Blastn
[2023-03-15 07:04:42,269] [INFO] Selected 8 target genomes.
[2023-03-15 07:04:42,269] [INFO] Target genome list was writen to OceanDNA-b26755/target_genomes_gtdb.txt
[2023-03-15 07:04:42,348] [INFO] Task started: fastANI
[2023-03-15 07:04:42,348] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a337d98-7c6b-4165-9ea0-8c113b4dc153/OceanDNA-b26755.fa --refList OceanDNA-b26755/target_genomes_gtdb.txt --output OceanDNA-b26755/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:04:47,950] [INFO] Task succeeded: fastANI
[2023-03-15 07:04:47,956] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 07:04:47,956] [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_001723285.1	s__Methyloceanibacter methanicus	92.7038	668	716	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloceanibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001723355.1	s__Methyloceanibacter stevinii	83.6372	591	716	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloceanibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003071365.1	s__Methyloceanibacter sp003071365	83.5245	591	716	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloceanibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000828475.1	s__Methyloceanibacter caenitepidi	83.2007	554	716	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloceanibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002482645.1	s__Methyloceanibacter sp002482645	82.0062	529	716	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloceanibacter	95.0	98.85	98.85	0.80	0.80	2	-
GCA_016124795.1	s__Pseudolabrys sp016124795	76.3862	87	716	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823365.1	s__Parvibaculum sp013823365	76.1636	56	716	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008000895.1	s__Methylobacterium sp008000895	76.1358	104	716	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.09	98.22	0.92	0.85	3	-
--------------------------------------------------------------------------------
[2023-03-15 07:04:47,960] [INFO] GTDB search result was written to OceanDNA-b26755/result_gtdb.tsv
[2023-03-15 07:04:47,965] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:04:47,970] [INFO] DFAST_QC result json was written to OceanDNA-b26755/dqc_result.json
[2023-03-15 07:04:47,970] [INFO] DFAST_QC completed!
[2023-03-15 07:04:47,970] [INFO] Total running time: 0h1m9s