[2023-03-15 12:33:51,708] [INFO] DFAST_QC pipeline started.
[2023-03-15 12:33:51,708] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 12:33:51,708] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4e91c11-804f-463b-a485-253ec222dd60/dqc_reference
[2023-03-15 12:33:52,869] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 12:33:52,870] [INFO] Task started: Prodigal
[2023-03-15 12:33:52,870] [INFO] Running command: cat /var/lib/cwl/stg45c0bb84-a1fe-4007-a0a9-26df23216f28/OceanDNA-b9732.fa | prodigal -d OceanDNA-b9732/cds.fna -a OceanDNA-b9732/protein.faa -g 11 -q > /dev/null
[2023-03-15 12:34:07,126] [INFO] Task succeeded: Prodigal
[2023-03-15 12:34:07,126] [INFO] Task started: HMMsearch
[2023-03-15 12:34:07,126] [INFO] Running command: hmmsearch --tblout OceanDNA-b9732/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4e91c11-804f-463b-a485-253ec222dd60/dqc_reference/reference_markers.hmm OceanDNA-b9732/protein.faa > /dev/null
[2023-03-15 12:34:07,313] [INFO] Task succeeded: HMMsearch
[2023-03-15 12:34:07,314] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg45c0bb84-a1fe-4007-a0a9-26df23216f28/OceanDNA-b9732.fa]
[2023-03-15 12:34:07,336] [INFO] Query marker FASTA was written to OceanDNA-b9732/markers.fasta
[2023-03-15 12:34:07,336] [INFO] Task started: Blastn
[2023-03-15 12:34:07,336] [INFO] Running command: blastn -query OceanDNA-b9732/markers.fasta -db /var/lib/cwl/stgf4e91c11-804f-463b-a485-253ec222dd60/dqc_reference/reference_markers.fasta -out OceanDNA-b9732/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:34:07,895] [INFO] Task succeeded: Blastn
[2023-03-15 12:34:07,897] [INFO] Selected 14 target genomes.
[2023-03-15 12:34:07,897] [INFO] Target genome list was writen to OceanDNA-b9732/target_genomes.txt
[2023-03-15 12:34:07,906] [INFO] Task started: fastANI
[2023-03-15 12:34:07,906] [INFO] Running command: fastANI --query /var/lib/cwl/stg45c0bb84-a1fe-4007-a0a9-26df23216f28/OceanDNA-b9732.fa --refList OceanDNA-b9732/target_genomes.txt --output OceanDNA-b9732/fastani_result.tsv --threads 1
[2023-03-15 12:34:15,983] [INFO] Task succeeded: fastANI
[2023-03-15 12:34:15,984] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4e91c11-804f-463b-a485-253ec222dd60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 12:34:15,984] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4e91c11-804f-463b-a485-253ec222dd60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 12:34:15,991] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2023-03-15 12:34:15,991] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 12:34:15,992] [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
Mesonia mobilis	strain=DSM 19841	GCA_000423405.1	369791	369791	type	True	95.3126	554	676	95	conclusive
Mesonia mobilis	strain=KCTC 12708	GCA_014651475.1	369791	369791	type	True	95.2062	551	676	95	conclusive
Mesonia oceanica	strain=ISS653	GCA_902499555.1	2687242	2687242	type	True	81.1384	435	676	95	below_threshold
Mesonia phycicola	strain=DSM 21425	GCA_900141885.1	579105	579105	type	True	80.5765	386	676	95	below_threshold
Mesonia algae	strain=DSM 15361	GCA_003253545.1	213248	213248	type	True	77.6244	185	676	95	below_threshold
Salegentibacter lacus	strain=LM13S	GCA_020164555.1	2873599	2873599	type	True	76.5316	88	676	95	below_threshold
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	76.3259	60	676	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	76.1614	52	676	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	75.9798	57	676	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	75.7277	70	676	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	75.6584	54	676	95	below_threshold
Cellulophaga tyrosinoxydans	strain=DSM 21164	GCA_900176415.1	504486	504486	type	True	75.6282	52	676	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 12:34:15,993] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9732/tc_result.tsv
[2023-03-15 12:34:15,993] [INFO] ===== Taxonomy check completed =====
[2023-03-15 12:34:15,993] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 12:34:15,993] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4e91c11-804f-463b-a485-253ec222dd60/dqc_reference/checkm_data
[2023-03-15 12:34:15,994] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 12:34:16,000] [INFO] Task started: CheckM
[2023-03-15 12:34:16,000] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9732/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9732/checkm_input OceanDNA-b9732/checkm_result
[2023-03-15 12:34:55,197] [INFO] Task succeeded: CheckM
[2023-03-15 12:34:55,198] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 12:34:55,213] [INFO] ===== Completeness check finished =====
[2023-03-15 12:34:55,213] [INFO] ===== Start GTDB Search =====
[2023-03-15 12:34:55,214] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9732/markers.fasta)
[2023-03-15 12:34:55,215] [INFO] Task started: Blastn
[2023-03-15 12:34:55,215] [INFO] Running command: blastn -query OceanDNA-b9732/markers.fasta -db /var/lib/cwl/stgf4e91c11-804f-463b-a485-253ec222dd60/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9732/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:34:55,990] [INFO] Task succeeded: Blastn
[2023-03-15 12:34:55,993] [INFO] Selected 7 target genomes.
[2023-03-15 12:34:55,993] [INFO] Target genome list was writen to OceanDNA-b9732/target_genomes_gtdb.txt
[2023-03-15 12:34:56,088] [INFO] Task started: fastANI
[2023-03-15 12:34:56,088] [INFO] Running command: fastANI --query /var/lib/cwl/stg45c0bb84-a1fe-4007-a0a9-26df23216f28/OceanDNA-b9732.fa --refList OceanDNA-b9732/target_genomes_gtdb.txt --output OceanDNA-b9732/fastani_result_gtdb.tsv --threads 1
[2023-03-15 12:35:00,724] [INFO] Task succeeded: fastANI
[2023-03-15 12:35:00,729] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 12:35:00,730] [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_000423405.1	s__Mesonia mobilis	95.3126	554	676	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	99.98	99.98	0.99	0.99	2	conclusive
GCA_012964435.1	s__Mesonia sp012964435	91.5634	510	676	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	99.98	99.98	0.99	0.99	2	-
GCF_008692195.1	s__Mesonia sp008692195	84.3048	466	676	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902499555.1	s__Mesonia oceanica	81.1384	435	676	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	99.91	99.87	0.96	0.92	8	-
GCF_900141885.1	s__Mesonia phycicola	80.5765	386	676	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003253545.1	s__Mesonia algae	77.6244	185	676	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	95.16	95.16	0.83	0.83	2	-
GCF_001889045.1	s__Tenacibaculum_A todarodis	76.1614	52	676	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 12:35:00,732] [INFO] GTDB search result was written to OceanDNA-b9732/result_gtdb.tsv
[2023-03-15 12:35:00,736] [INFO] ===== GTDB Search completed =====
[2023-03-15 12:35:00,739] [INFO] DFAST_QC result json was written to OceanDNA-b9732/dqc_result.json
[2023-03-15 12:35:00,740] [INFO] DFAST_QC completed!
[2023-03-15 12:35:00,740] [INFO] Total running time: 0h1m9s