[2023-03-17 05:16:57,860] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:16:57,860] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:16:57,860] [INFO] DQC Reference Directory: /var/lib/cwl/stgee0c52f4-2e6c-48f6-aad7-422e60454355/dqc_reference
[2023-03-17 05:16:59,366] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:16:59,367] [INFO] Task started: Prodigal
[2023-03-17 05:16:59,367] [INFO] Running command: cat /var/lib/cwl/stga997e76d-cb90-46eb-b332-73242c40bb33/OceanDNA-b10018.fa | prodigal -d OceanDNA-b10018/cds.fna -a OceanDNA-b10018/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:17:22,177] [INFO] Task succeeded: Prodigal
[2023-03-17 05:17:22,177] [INFO] Task started: HMMsearch
[2023-03-17 05:17:22,177] [INFO] Running command: hmmsearch --tblout OceanDNA-b10018/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgee0c52f4-2e6c-48f6-aad7-422e60454355/dqc_reference/reference_markers.hmm OceanDNA-b10018/protein.faa > /dev/null
[2023-03-17 05:17:22,388] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:17:22,389] [INFO] Found 6/6 markers.
[2023-03-17 05:17:22,410] [INFO] Query marker FASTA was written to OceanDNA-b10018/markers.fasta
[2023-03-17 05:17:22,412] [INFO] Task started: Blastn
[2023-03-17 05:17:22,412] [INFO] Running command: blastn -query OceanDNA-b10018/markers.fasta -db /var/lib/cwl/stgee0c52f4-2e6c-48f6-aad7-422e60454355/dqc_reference/reference_markers.fasta -out OceanDNA-b10018/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:17:23,000] [INFO] Task succeeded: Blastn
[2023-03-17 05:17:23,001] [INFO] Selected 10 target genomes.
[2023-03-17 05:17:23,001] [INFO] Target genome list was writen to OceanDNA-b10018/target_genomes.txt
[2023-03-17 05:17:23,046] [INFO] Task started: fastANI
[2023-03-17 05:17:23,046] [INFO] Running command: fastANI --query /var/lib/cwl/stga997e76d-cb90-46eb-b332-73242c40bb33/OceanDNA-b10018.fa --refList OceanDNA-b10018/target_genomes.txt --output OceanDNA-b10018/fastani_result.tsv --threads 1
[2023-03-17 05:17:30,418] [INFO] Task succeeded: fastANI
[2023-03-17 05:17:30,419] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgee0c52f4-2e6c-48f6-aad7-422e60454355/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:17:30,419] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgee0c52f4-2e6c-48f6-aad7-422e60454355/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:17:30,426] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:17:30,426] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 05:17:30,426] [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 reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	81.824	709	1219	95	below_threshold
Polaribacter reichenbachii	strain=6Alg 8T	GCA_001975665.1	996801	996801	type	True	81.7606	709	1219	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_001680875.1	996801	996801	type	True	81.7597	707	1219	95	below_threshold
Polaribacter reichenbachii	strain=LMG 26443	GCA_020532845.1	996801	996801	type	True	81.7574	697	1219	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	81.6408	672	1219	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001680885.1	1774273	1774273	type	True	81.5252	683	1219	95	below_threshold
Polaribacter litorisediminis	strain=OITF-11	GCA_019968605.1	1908341	1908341	type	True	80.8526	668	1219	95	below_threshold
Polaribacter porphyrae	strain=LMG 26671	GCA_020532745.1	1137780	1137780	type	True	80.7699	663	1219	95	below_threshold
Polaribacter porphyrae	strain=NBRC 108759	GCA_002954685.1	1137780	1137780	type	True	80.6883	670	1219	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	80.3952	599	1219	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 05:17:30,426] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10018/tc_result.tsv
[2023-03-17 05:17:30,427] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:17:30,427] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:17:30,427] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgee0c52f4-2e6c-48f6-aad7-422e60454355/dqc_reference/checkm_data
[2023-03-17 05:17:30,427] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:17:30,482] [INFO] Task started: CheckM
[2023-03-17 05:17:30,482] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10018/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10018/checkm_input OceanDNA-b10018/checkm_result
[2023-03-17 05:18:27,183] [INFO] Task succeeded: CheckM
[2023-03-17 05:18:27,184] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:18:27,196] [INFO] ===== Completeness check finished =====
[2023-03-17 05:18:27,196] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:18:27,196] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10018/markers.fasta)
[2023-03-17 05:18:27,197] [INFO] Task started: Blastn
[2023-03-17 05:18:27,197] [INFO] Running command: blastn -query OceanDNA-b10018/markers.fasta -db /var/lib/cwl/stgee0c52f4-2e6c-48f6-aad7-422e60454355/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10018/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:18:28,077] [INFO] Task succeeded: Blastn
[2023-03-17 05:18:28,083] [INFO] Selected 11 target genomes.
[2023-03-17 05:18:28,083] [INFO] Target genome list was writen to OceanDNA-b10018/target_genomes_gtdb.txt
[2023-03-17 05:18:28,368] [INFO] Task started: fastANI
[2023-03-17 05:18:28,369] [INFO] Running command: fastANI --query /var/lib/cwl/stga997e76d-cb90-46eb-b332-73242c40bb33/OceanDNA-b10018.fa --refList OceanDNA-b10018/target_genomes_gtdb.txt --output OceanDNA-b10018/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:18:37,009] [INFO] Task succeeded: fastANI
[2023-03-17 05:18:37,016] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 05:18:37,016] [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_001975665.1	s__Polaribacter reichenbachii	81.743	711	1219	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	81.6534	723	1219	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	81.6347	672	1219	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	81.1713	727	1219	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280865.1	s__Polaribacter dokdonensis	80.7433	597	1219	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002954685.1	s__Polaribacter porphyrae	80.6923	670	1219	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014784055.1	s__Polaribacter haliotis	80.5984	592	1219	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000766795.1	s__Polaribacter sp000766795	80.574	586	1219	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009832745.1	s__Polaribacter sp009832745	80.3819	600	1219	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152945.2	s__Polaribacter sp000152945	80.2364	557	1219	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997085.1	s__Polaribacter sp007997085	80.1333	617	1219	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.89	99.89	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-03-17 05:18:37,017] [INFO] GTDB search result was written to OceanDNA-b10018/result_gtdb.tsv
[2023-03-17 05:18:37,017] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:18:37,019] [INFO] DFAST_QC result json was written to OceanDNA-b10018/dqc_result.json
[2023-03-17 05:18:37,019] [INFO] DFAST_QC completed!
[2023-03-17 05:18:37,019] [INFO] Total running time: 0h1m39s