[2023-03-16 04:39:48,543] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:39:48,543] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:39:48,543] [INFO] DQC Reference Directory: /var/lib/cwl/stg35425291-8ebc-44b2-9a98-30185f35a7f6/dqc_reference
[2023-03-16 04:39:49,655] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:39:49,655] [INFO] Task started: Prodigal
[2023-03-16 04:39:49,655] [INFO] Running command: cat /var/lib/cwl/stgdd545948-32e3-4b06-9c18-45b772d2a32a/OceanDNA-b6183.fa | prodigal -d OceanDNA-b6183/cds.fna -a OceanDNA-b6183/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:40:05,144] [INFO] Task succeeded: Prodigal
[2023-03-16 04:40:05,144] [INFO] Task started: HMMsearch
[2023-03-16 04:40:05,144] [INFO] Running command: hmmsearch --tblout OceanDNA-b6183/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg35425291-8ebc-44b2-9a98-30185f35a7f6/dqc_reference/reference_markers.hmm OceanDNA-b6183/protein.faa > /dev/null
[2023-03-16 04:40:05,330] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:40:05,330] [INFO] Found 6/6 markers.
[2023-03-16 04:40:05,347] [INFO] Query marker FASTA was written to OceanDNA-b6183/markers.fasta
[2023-03-16 04:40:05,347] [INFO] Task started: Blastn
[2023-03-16 04:40:05,347] [INFO] Running command: blastn -query OceanDNA-b6183/markers.fasta -db /var/lib/cwl/stg35425291-8ebc-44b2-9a98-30185f35a7f6/dqc_reference/reference_markers.fasta -out OceanDNA-b6183/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:40:05,900] [INFO] Task succeeded: Blastn
[2023-03-16 04:40:05,900] [INFO] Selected 31 target genomes.
[2023-03-16 04:40:05,901] [INFO] Target genome list was writen to OceanDNA-b6183/target_genomes.txt
[2023-03-16 04:40:05,916] [INFO] Task started: fastANI
[2023-03-16 04:40:05,916] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd545948-32e3-4b06-9c18-45b772d2a32a/OceanDNA-b6183.fa --refList OceanDNA-b6183/target_genomes.txt --output OceanDNA-b6183/fastani_result.tsv --threads 1
[2023-03-16 04:40:21,047] [INFO] Task succeeded: fastANI
[2023-03-16 04:40:21,048] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg35425291-8ebc-44b2-9a98-30185f35a7f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:40:21,048] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg35425291-8ebc-44b2-9a98-30185f35a7f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:40:21,054] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:40:21,054] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:40:21,054] [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
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	76.2697	61	818	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	76.2375	61	818	95	below_threshold
Wenyingzhuangia heitensis	strain=DSM 101599	GCA_011762155.1	1487859	1487859	type	True	76.1877	58	818	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	76.1594	59	818	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_001680875.1	996801	996801	type	True	76.075	60	818	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	76.0294	65	818	95	below_threshold
Polaribacter porphyrae	strain=NBRC 108759	GCA_002954685.1	1137780	1137780	type	True	75.6744	62	818	95	below_threshold
Polaribacter porphyrae	strain=LMG 26671	GCA_020532745.1	1137780	1137780	type	True	75.657	61	818	95	below_threshold
Tenacibaculum holothuriorum	strain=S2-2	GCA_002120225.1	1635173	1635173	type	True	75.5586	50	818	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:40:21,054] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6183/tc_result.tsv
[2023-03-16 04:40:21,054] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:40:21,055] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:40:21,055] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg35425291-8ebc-44b2-9a98-30185f35a7f6/dqc_reference/checkm_data
[2023-03-16 04:40:21,055] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:40:21,059] [INFO] Task started: CheckM
[2023-03-16 04:40:21,059] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6183/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6183/checkm_input OceanDNA-b6183/checkm_result
[2023-03-16 04:41:01,673] [INFO] Task succeeded: CheckM
[2023-03-16 04:41:01,674] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:41:01,676] [INFO] ===== Completeness check finished =====
[2023-03-16 04:41:01,677] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:41:01,677] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6183/markers.fasta)
[2023-03-16 04:41:01,677] [INFO] Task started: Blastn
[2023-03-16 04:41:01,677] [INFO] Running command: blastn -query OceanDNA-b6183/markers.fasta -db /var/lib/cwl/stg35425291-8ebc-44b2-9a98-30185f35a7f6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6183/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:41:02,469] [INFO] Task succeeded: Blastn
[2023-03-16 04:41:02,484] [INFO] Selected 30 target genomes.
[2023-03-16 04:41:02,484] [INFO] Target genome list was writen to OceanDNA-b6183/target_genomes_gtdb.txt
[2023-03-16 04:41:02,530] [INFO] Task started: fastANI
[2023-03-16 04:41:02,530] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd545948-32e3-4b06-9c18-45b772d2a32a/OceanDNA-b6183.fa --refList OceanDNA-b6183/target_genomes_gtdb.txt --output OceanDNA-b6183/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:41:18,715] [INFO] Task succeeded: fastANI
[2023-03-16 04:41:18,719] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 04:41:18,719] [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
GCA_013215105.1	s__DT-33 sp013215105	99.7766	771	818	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__DT-33	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000766795.1	s__Polaribacter sp000766795	76.3307	57	818	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002814075.1	s__Polaribacter sejongensis	76.2989	60	818	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	97.48	97.48	0.89	0.89	2	-
GCF_002954605.1	s__Polaribacter butkevichii	76.0923	61	818	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016858305.2	s__Polaribacter sp016858305	76.0922	61	818	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954685.1	s__Polaribacter porphyrae	75.657	61	818	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:41:18,719] [INFO] GTDB search result was written to OceanDNA-b6183/result_gtdb.tsv
[2023-03-16 04:41:18,720] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:41:18,721] [INFO] DFAST_QC result json was written to OceanDNA-b6183/dqc_result.json
[2023-03-16 04:41:18,721] [INFO] DFAST_QC completed!
[2023-03-16 04:41:18,721] [INFO] Total running time: 0h1m30s