[2023-03-16 05:32:42,932] [INFO] DFAST_QC pipeline started.
[2023-03-16 05:32:42,932] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 05:32:42,932] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a9f54e1-587a-4d2c-bb45-0796ae258573/dqc_reference
[2023-03-16 05:32:44,041] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 05:32:44,042] [INFO] Task started: Prodigal
[2023-03-16 05:32:44,042] [INFO] Running command: cat /var/lib/cwl/stg5395e7d3-d934-4546-8c9a-cfea9ffd68fb/OceanDNA-b6561.fa | prodigal -d OceanDNA-b6561/cds.fna -a OceanDNA-b6561/protein.faa -g 11 -q > /dev/null
[2023-03-16 05:33:23,717] [INFO] Task succeeded: Prodigal
[2023-03-16 05:33:23,717] [INFO] Task started: HMMsearch
[2023-03-16 05:33:23,717] [INFO] Running command: hmmsearch --tblout OceanDNA-b6561/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a9f54e1-587a-4d2c-bb45-0796ae258573/dqc_reference/reference_markers.hmm OceanDNA-b6561/protein.faa > /dev/null
[2023-03-16 05:33:23,955] [INFO] Task succeeded: HMMsearch
[2023-03-16 05:33:23,956] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5395e7d3-d934-4546-8c9a-cfea9ffd68fb/OceanDNA-b6561.fa]
[2023-03-16 05:33:23,988] [INFO] Query marker FASTA was written to OceanDNA-b6561/markers.fasta
[2023-03-16 05:33:23,989] [INFO] Task started: Blastn
[2023-03-16 05:33:23,989] [INFO] Running command: blastn -query OceanDNA-b6561/markers.fasta -db /var/lib/cwl/stg4a9f54e1-587a-4d2c-bb45-0796ae258573/dqc_reference/reference_markers.fasta -out OceanDNA-b6561/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:33:24,525] [INFO] Task succeeded: Blastn
[2023-03-16 05:33:24,525] [INFO] Selected 11 target genomes.
[2023-03-16 05:33:24,526] [INFO] Target genome list was writen to OceanDNA-b6561/target_genomes.txt
[2023-03-16 05:33:24,533] [INFO] Task started: fastANI
[2023-03-16 05:33:24,533] [INFO] Running command: fastANI --query /var/lib/cwl/stg5395e7d3-d934-4546-8c9a-cfea9ffd68fb/OceanDNA-b6561.fa --refList OceanDNA-b6561/target_genomes.txt --output OceanDNA-b6561/fastani_result.tsv --threads 1
[2023-03-16 05:33:35,056] [INFO] Task succeeded: fastANI
[2023-03-16 05:33:35,056] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a9f54e1-587a-4d2c-bb45-0796ae258573/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 05:33:35,056] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a9f54e1-587a-4d2c-bb45-0796ae258573/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 05:33:35,063] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2023-03-16 05:33:35,063] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 05:33:35,063] [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
Arenibacter troitsensis	strain=DSM 19835	GCA_900177645.1	188872	188872	type	True	99.3485	1529	1730	95	conclusive
Arenibacter palladensis	strain=DSM 17539	GCA_900129275.1	237373	237373	type	True	93.1838	1324	1730	95	below_threshold
Arenibacter echinorum	strain=DSM 23522	GCA_003259375.1	440515	440515	type	True	87.1203	1223	1730	95	below_threshold
Arenibacter algicola	strain=TG409	GCA_000733925.1	616991	616991	type	True	86.9721	1216	1730	95	below_threshold
Arenibacter arenosicollis	strain=BSSL-BM3	GCA_014397245.1	2762274	2762274	type	True	82.451	1039	1730	95	below_threshold
Cellulophaga tyrosinoxydans	strain=DSM 21164	GCA_900176415.1	504486	504486	type	True	76.18	137	1730	95	below_threshold
Zobellia barbeyronii	strain=KMM 6746	GCA_018603515.1	2748009	2748009	type	True	75.8166	111	1730	95	below_threshold
Muricauda onchidii	strain=XY-359	GCA_004804315.1	2562684	2562684	type	True	75.7768	107	1730	95	below_threshold
Muricauda amoyensis	strain=GCL-11	GCA_003058265.1	2169401	2169401	type	True	75.7355	102	1730	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 05:33:35,063] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6561/tc_result.tsv
[2023-03-16 05:33:35,063] [INFO] ===== Taxonomy check completed =====
[2023-03-16 05:33:35,063] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 05:33:35,064] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a9f54e1-587a-4d2c-bb45-0796ae258573/dqc_reference/checkm_data
[2023-03-16 05:33:35,064] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 05:33:35,236] [INFO] Task started: CheckM
[2023-03-16 05:33:35,236] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6561/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6561/checkm_input OceanDNA-b6561/checkm_result
[2023-03-16 05:35:07,599] [INFO] Task succeeded: CheckM
[2023-03-16 05:35:07,600] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.74%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 05:35:07,613] [INFO] ===== Completeness check finished =====
[2023-03-16 05:35:07,613] [INFO] ===== Start GTDB Search =====
[2023-03-16 05:35:07,613] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6561/markers.fasta)
[2023-03-16 05:35:07,615] [INFO] Task started: Blastn
[2023-03-16 05:35:07,615] [INFO] Running command: blastn -query OceanDNA-b6561/markers.fasta -db /var/lib/cwl/stg4a9f54e1-587a-4d2c-bb45-0796ae258573/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6561/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:35:08,517] [INFO] Task succeeded: Blastn
[2023-03-16 05:35:08,518] [INFO] Selected 6 target genomes.
[2023-03-16 05:35:08,519] [INFO] Target genome list was writen to OceanDNA-b6561/target_genomes_gtdb.txt
[2023-03-16 05:35:08,586] [INFO] Task started: fastANI
[2023-03-16 05:35:08,587] [INFO] Running command: fastANI --query /var/lib/cwl/stg5395e7d3-d934-4546-8c9a-cfea9ffd68fb/OceanDNA-b6561.fa --refList OceanDNA-b6561/target_genomes_gtdb.txt --output OceanDNA-b6561/fastani_result_gtdb.tsv --threads 1
[2023-03-16 05:35:16,663] [INFO] Task succeeded: fastANI
[2023-03-16 05:35:16,668] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 05:35:16,668] [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_900177645.1	s__Arenibacter troitsensis	99.3485	1529	1730	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900129275.1	s__Arenibacter palladensis	93.1977	1323	1730	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	97.38	97.38	0.84	0.84	2	-
GCF_018860365.1	s__Arenibacter algicola_B	88.0787	1268	1730	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259375.1	s__Arenibacter echinorum	87.1379	1221	1730	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000733925.1	s__Arenibacter algicola	86.9391	1219	1730	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	98.04	97.34	0.85	0.81	5	-
GCF_003426735.1	s__Arenibacter sp003426735	84.0738	1094	1730	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 05:35:16,669] [INFO] GTDB search result was written to OceanDNA-b6561/result_gtdb.tsv
[2023-03-16 05:35:16,670] [INFO] ===== GTDB Search completed =====
[2023-03-16 05:35:16,671] [INFO] DFAST_QC result json was written to OceanDNA-b6561/dqc_result.json
[2023-03-16 05:35:16,671] [INFO] DFAST_QC completed!
[2023-03-16 05:35:16,671] [INFO] Total running time: 0h2m34s