[2023-03-16 09:43:37,173] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:43:37,173] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:43:37,173] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c73045b-3eb3-4ea0-b388-62541575b725/dqc_reference
[2023-03-16 09:43:39,239] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:43:39,239] [INFO] Task started: Prodigal
[2023-03-16 09:43:39,239] [INFO] Running command: cat /var/lib/cwl/stgcb8269eb-c607-40cc-af9f-81a1afd1d1f1/OceanDNA-b7519.fa | prodigal -d OceanDNA-b7519/cds.fna -a OceanDNA-b7519/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:44:08,223] [INFO] Task succeeded: Prodigal
[2023-03-16 09:44:08,223] [INFO] Task started: HMMsearch
[2023-03-16 09:44:08,223] [INFO] Running command: hmmsearch --tblout OceanDNA-b7519/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c73045b-3eb3-4ea0-b388-62541575b725/dqc_reference/reference_markers.hmm OceanDNA-b7519/protein.faa > /dev/null
[2023-03-16 09:44:08,437] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:44:08,437] [INFO] Found 6/6 markers.
[2023-03-16 09:44:08,463] [INFO] Query marker FASTA was written to OceanDNA-b7519/markers.fasta
[2023-03-16 09:44:08,463] [INFO] Task started: Blastn
[2023-03-16 09:44:08,463] [INFO] Running command: blastn -query OceanDNA-b7519/markers.fasta -db /var/lib/cwl/stg5c73045b-3eb3-4ea0-b388-62541575b725/dqc_reference/reference_markers.fasta -out OceanDNA-b7519/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:44:09,069] [INFO] Task succeeded: Blastn
[2023-03-16 09:44:09,070] [INFO] Selected 11 target genomes.
[2023-03-16 09:44:09,070] [INFO] Target genome list was writen to OceanDNA-b7519/target_genomes.txt
[2023-03-16 09:44:09,082] [INFO] Task started: fastANI
[2023-03-16 09:44:09,083] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb8269eb-c607-40cc-af9f-81a1afd1d1f1/OceanDNA-b7519.fa --refList OceanDNA-b7519/target_genomes.txt --output OceanDNA-b7519/fastani_result.tsv --threads 1
[2023-03-16 09:44:17,839] [INFO] Task succeeded: fastANI
[2023-03-16 09:44:17,839] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c73045b-3eb3-4ea0-b388-62541575b725/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:44:17,839] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c73045b-3eb3-4ea0-b388-62541575b725/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:44:17,847] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2023-03-16 09:44:17,847] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 09:44:17,847] [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
Leeuwenhoekiella marinoflava	strain=DSM 3653	GCA_900129005.1	988	988	type	True	98.5457	1312	1492	95	conclusive
Leeuwenhoekiella marinoflava	strain=LMG 1345	GCA_004104035.1	988	988	type	True	98.5341	1307	1492	95	conclusive
Leeuwenhoekiella aestuarii	strain=R-48165	GCA_004104055.1	2249426	2249426	type	True	86.1804	1062	1492	95	below_threshold
Leeuwenhoekiella blandensis	strain=MED217	GCA_000152985.1	360293	360293	type	True	80.1472	729	1492	95	below_threshold
Leeuwenhoekiella palythoae	strain=DSM 19859	GCA_900130045.1	573501	573501	type	True	79.669	708	1492	95	below_threshold
Leeuwenhoekiella palythoae	strain=LMG 24856	GCA_004104045.1	573501	573501	type	True	79.5953	704	1492	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	77.0211	64	1492	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.3386	81	1492	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	75.982	58	1492	95	below_threshold
Abyssalbus ytuae	strain=MT3330	GCA_022807975.1	2926907	2926907	type	True	75.7035	59	1492	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	75.5027	81	1492	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 09:44:17,847] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7519/tc_result.tsv
[2023-03-16 09:44:17,847] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:44:17,848] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:44:17,848] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c73045b-3eb3-4ea0-b388-62541575b725/dqc_reference/checkm_data
[2023-03-16 09:44:17,848] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:44:17,854] [INFO] Task started: CheckM
[2023-03-16 09:44:17,854] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7519/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7519/checkm_input OceanDNA-b7519/checkm_result
[2023-03-16 09:45:28,483] [INFO] Task succeeded: CheckM
[2023-03-16 09:45:28,483] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.73%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 09:45:28,685] [INFO] ===== Completeness check finished =====
[2023-03-16 09:45:28,686] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:45:28,686] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7519/markers.fasta)
[2023-03-16 09:45:28,687] [INFO] Task started: Blastn
[2023-03-16 09:45:28,687] [INFO] Running command: blastn -query OceanDNA-b7519/markers.fasta -db /var/lib/cwl/stg5c73045b-3eb3-4ea0-b388-62541575b725/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7519/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:45:29,593] [INFO] Task succeeded: Blastn
[2023-03-16 09:45:29,605] [INFO] Selected 6 target genomes.
[2023-03-16 09:45:29,605] [INFO] Target genome list was writen to OceanDNA-b7519/target_genomes_gtdb.txt
[2023-03-16 09:45:29,607] [INFO] Task started: fastANI
[2023-03-16 09:45:29,607] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb8269eb-c607-40cc-af9f-81a1afd1d1f1/OceanDNA-b7519.fa --refList OceanDNA-b7519/target_genomes_gtdb.txt --output OceanDNA-b7519/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:45:35,618] [INFO] Task succeeded: fastANI
[2023-03-16 09:45:35,623] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 09:45:35,623] [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_900129005.1	s__Leeuwenhoekiella marinoflava	98.5457	1312	1492	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_004104075.1	s__Leeuwenhoekiella polynyae	86.8854	1094	1492	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004104055.1	s__Leeuwenhoekiella aestuarii	86.1852	1061	1492	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.75	99.75	0.97	0.97	2	-
GCF_000152985.1	s__Leeuwenhoekiella blandensis	80.151	728	1492	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	97.86	97.58	0.89	0.73	11	-
GCF_900130045.1	s__Leeuwenhoekiella palythoae	79.6863	706	1492	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	96.69	96.09	0.92	0.86	9	-
GCF_000687915.1	s__Leeuwenhoekiella sp000687915	79.1103	582	1492	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 09:45:35,626] [INFO] GTDB search result was written to OceanDNA-b7519/result_gtdb.tsv
[2023-03-16 09:45:35,631] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:45:35,637] [INFO] DFAST_QC result json was written to OceanDNA-b7519/dqc_result.json
[2023-03-16 09:45:35,637] [INFO] DFAST_QC completed!
[2023-03-16 09:45:35,637] [INFO] Total running time: 0h1m58s