[2023-03-16 22:05:57,070] [INFO] DFAST_QC pipeline started.
[2023-03-16 22:05:57,070] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 22:05:57,070] [INFO] DQC Reference Directory: /var/lib/cwl/stga257798c-517d-4652-aa9b-ee8e5cd98557/dqc_reference
[2023-03-16 22:05:58,247] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 22:05:58,248] [INFO] Task started: Prodigal
[2023-03-16 22:05:58,248] [INFO] Running command: cat /var/lib/cwl/stg51f1013f-d1b2-47c9-a00f-9ec58383f97e/OceanDNA-b10043.fa | prodigal -d OceanDNA-b10043/cds.fna -a OceanDNA-b10043/protein.faa -g 11 -q > /dev/null
[2023-03-16 22:06:06,407] [INFO] Task succeeded: Prodigal
[2023-03-16 22:06:06,407] [INFO] Task started: HMMsearch
[2023-03-16 22:06:06,407] [INFO] Running command: hmmsearch --tblout OceanDNA-b10043/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga257798c-517d-4652-aa9b-ee8e5cd98557/dqc_reference/reference_markers.hmm OceanDNA-b10043/protein.faa > /dev/null
[2023-03-16 22:06:06,572] [INFO] Task succeeded: HMMsearch
[2023-03-16 22:06:06,573] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg51f1013f-d1b2-47c9-a00f-9ec58383f97e/OceanDNA-b10043.fa]
[2023-03-16 22:06:06,586] [INFO] Query marker FASTA was written to OceanDNA-b10043/markers.fasta
[2023-03-16 22:06:06,587] [INFO] Task started: Blastn
[2023-03-16 22:06:06,587] [INFO] Running command: blastn -query OceanDNA-b10043/markers.fasta -db /var/lib/cwl/stga257798c-517d-4652-aa9b-ee8e5cd98557/dqc_reference/reference_markers.fasta -out OceanDNA-b10043/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 22:06:07,091] [INFO] Task succeeded: Blastn
[2023-03-16 22:06:07,091] [INFO] Selected 11 target genomes.
[2023-03-16 22:06:07,091] [INFO] Target genome list was writen to OceanDNA-b10043/target_genomes.txt
[2023-03-16 22:06:07,099] [INFO] Task started: fastANI
[2023-03-16 22:06:07,099] [INFO] Running command: fastANI --query /var/lib/cwl/stg51f1013f-d1b2-47c9-a00f-9ec58383f97e/OceanDNA-b10043.fa --refList OceanDNA-b10043/target_genomes.txt --output OceanDNA-b10043/fastani_result.tsv --threads 1
[2023-03-16 22:06:13,031] [INFO] Task succeeded: fastANI
[2023-03-16 22:06:13,031] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga257798c-517d-4652-aa9b-ee8e5cd98557/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 22:06:13,031] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga257798c-517d-4652-aa9b-ee8e5cd98557/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 22:06:13,038] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2023-03-16 22:06:13,039] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 22:06:13,039] [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 dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	98.6112	396	399	95	conclusive
Polaribacter dokdonensis	strain=DSW-5	GCA_900106865.1	326329	326329	type	True	98.6105	397	399	95	conclusive
Polaribacter dokdonensis	strain=DSW-5	GCA_001280865.1	326329	326329	type	True	98.6104	397	399	95	conclusive
Polaribacter reichenbachii	strain=KCTC 23969	GCA_001680875.1	996801	996801	type	True	80.8086	285	399	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	80.7995	286	399	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	80.3236	287	399	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001680885.1	1774273	1774273	type	True	80.2932	286	399	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	79.3927	246	399	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	79.118	217	399	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	78.5323	217	399	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	78.2911	199	399	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 22:06:13,039] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10043/tc_result.tsv
[2023-03-16 22:06:13,039] [INFO] ===== Taxonomy check completed =====
[2023-03-16 22:06:13,039] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 22:06:13,039] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga257798c-517d-4652-aa9b-ee8e5cd98557/dqc_reference/checkm_data
[2023-03-16 22:06:13,040] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 22:06:13,043] [INFO] Task started: CheckM
[2023-03-16 22:06:13,043] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10043/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10043/checkm_input OceanDNA-b10043/checkm_result
[2023-03-16 22:06:38,549] [INFO] Task succeeded: CheckM
[2023-03-16 22:06:38,550] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 22:06:38,552] [INFO] ===== Completeness check finished =====
[2023-03-16 22:06:38,552] [INFO] ===== Start GTDB Search =====
[2023-03-16 22:06:38,552] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10043/markers.fasta)
[2023-03-16 22:06:38,552] [INFO] Task started: Blastn
[2023-03-16 22:06:38,552] [INFO] Running command: blastn -query OceanDNA-b10043/markers.fasta -db /var/lib/cwl/stga257798c-517d-4652-aa9b-ee8e5cd98557/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10043/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 22:06:39,252] [INFO] Task succeeded: Blastn
[2023-03-16 22:06:39,253] [INFO] Selected 9 target genomes.
[2023-03-16 22:06:39,253] [INFO] Target genome list was writen to OceanDNA-b10043/target_genomes_gtdb.txt
[2023-03-16 22:06:39,345] [INFO] Task started: fastANI
[2023-03-16 22:06:39,345] [INFO] Running command: fastANI --query /var/lib/cwl/stg51f1013f-d1b2-47c9-a00f-9ec58383f97e/OceanDNA-b10043.fa --refList OceanDNA-b10043/target_genomes_gtdb.txt --output OceanDNA-b10043/fastani_result_gtdb.tsv --threads 1
[2023-03-16 22:06:45,616] [INFO] Task succeeded: fastANI
[2023-03-16 22:06:45,622] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 22:06:45,622] [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_001280865.1	s__Polaribacter dokdonensis	98.6104	397	399	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000152945.2	s__Polaribacter sp000152945	86.0162	379	399	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975665.1	s__Polaribacter reichenbachii	80.7971	284	399	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.98	99.97	1.00	1.00	3	-
GCF_018861005.1	s__Polaribacter vadi_A	80.7096	286	399	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001761365.1	s__Polaribacter vadi	80.3236	287	399	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000687935.1	s__Polaribacter sp000687935	80.0401	293	399	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105145.1	s__Polaribacter sp900105145	79.466	250	399	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	79.2459	268	399	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003129485.1	s__Polaribacter sp003129485	78.8787	221	399	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 22:06:45,622] [INFO] GTDB search result was written to OceanDNA-b10043/result_gtdb.tsv
[2023-03-16 22:06:45,622] [INFO] ===== GTDB Search completed =====
[2023-03-16 22:06:45,624] [INFO] DFAST_QC result json was written to OceanDNA-b10043/dqc_result.json
[2023-03-16 22:06:45,624] [INFO] DFAST_QC completed!
[2023-03-16 22:06:45,624] [INFO] Total running time: 0h0m49s