[2023-03-18 04:04:53,906] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:04:53,906] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:04:53,906] [INFO] DQC Reference Directory: /var/lib/cwl/stg860f8b97-7c85-4d2d-9248-901ef8dd8f7e/dqc_reference
[2023-03-18 04:04:55,032] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:04:55,032] [INFO] Task started: Prodigal
[2023-03-18 04:04:55,032] [INFO] Running command: cat /var/lib/cwl/stg39819b6b-e310-466b-8ef5-6a4cf2c73af7/OceanDNA-b9877.fa | prodigal -d OceanDNA-b9877/cds.fna -a OceanDNA-b9877/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:05:07,266] [INFO] Task succeeded: Prodigal
[2023-03-18 04:05:07,266] [INFO] Task started: HMMsearch
[2023-03-18 04:05:07,266] [INFO] Running command: hmmsearch --tblout OceanDNA-b9877/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg860f8b97-7c85-4d2d-9248-901ef8dd8f7e/dqc_reference/reference_markers.hmm OceanDNA-b9877/protein.faa > /dev/null
[2023-03-18 04:05:07,467] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:05:07,467] [INFO] Found 6/6 markers.
[2023-03-18 04:05:07,483] [INFO] Query marker FASTA was written to OceanDNA-b9877/markers.fasta
[2023-03-18 04:05:07,484] [INFO] Task started: Blastn
[2023-03-18 04:05:07,484] [INFO] Running command: blastn -query OceanDNA-b9877/markers.fasta -db /var/lib/cwl/stg860f8b97-7c85-4d2d-9248-901ef8dd8f7e/dqc_reference/reference_markers.fasta -out OceanDNA-b9877/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:05:08,052] [INFO] Task succeeded: Blastn
[2023-03-18 04:05:08,053] [INFO] Selected 18 target genomes.
[2023-03-18 04:05:08,053] [INFO] Target genome list was writen to OceanDNA-b9877/target_genomes.txt
[2023-03-18 04:05:08,077] [INFO] Task started: fastANI
[2023-03-18 04:05:08,077] [INFO] Running command: fastANI --query /var/lib/cwl/stg39819b6b-e310-466b-8ef5-6a4cf2c73af7/OceanDNA-b9877.fa --refList OceanDNA-b9877/target_genomes.txt --output OceanDNA-b9877/fastani_result.tsv --threads 1
[2023-03-18 04:05:19,390] [INFO] Task succeeded: fastANI
[2023-03-18 04:05:19,390] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg860f8b97-7c85-4d2d-9248-901ef8dd8f7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:05:19,390] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg860f8b97-7c85-4d2d-9248-901ef8dd8f7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:05:19,401] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 04:05:19,401] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 04:05:19,401] [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 butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	79.8337	417	627	95	below_threshold
Polaribacter atrinae	strain=KACC 17473	GCA_001640115.1	1333662	1333662	type	True	79.7299	388	627	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	79.6727	402	627	95	below_threshold
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	79.5972	406	627	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	79.4467	392	627	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	79.1385	369	627	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	79.0665	363	627	95	below_threshold
Polaribacter aquimarinus	strain=ZY113	GCA_003129485.1	2100726	2100726	type	True	79.0507	375	627	95	below_threshold
Polaribacter glomeratus	strain=ACAM 171	GCA_007997115.1	102	102	type	True	79.0341	334	627	95	below_threshold
Polaribacter glomeratus	strain=ATCC 43844	GCA_002954665.1	102	102	type	True	79.0261	334	627	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	78.9072	360	627	95	below_threshold
Polaribacter filamentus	strain=ATCC 700397	GCA_002943715.1	53483	53483	type	True	78.8608	357	627	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	78.8281	337	627	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	78.6472	342	627	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_900106865.1	326329	326329	type	True	78.5118	320	627	95	below_threshold
Polaribacter litorisediminis	strain=OITF-11	GCA_019968605.1	1908341	1908341	type	True	78.509	338	627	95	below_threshold
Polaribacter porphyrae	strain=LMG 26671	GCA_020532745.1	1137780	1137780	type	True	78.4219	325	627	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	78.1397	270	627	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 04:05:19,401] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9877/tc_result.tsv
[2023-03-18 04:05:19,402] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:05:19,402] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:05:19,402] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg860f8b97-7c85-4d2d-9248-901ef8dd8f7e/dqc_reference/checkm_data
[2023-03-18 04:05:19,402] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:05:19,406] [INFO] Task started: CheckM
[2023-03-18 04:05:19,406] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9877/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9877/checkm_input OceanDNA-b9877/checkm_result
[2023-03-18 04:05:53,443] [INFO] Task succeeded: CheckM
[2023-03-18 04:05:53,443] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.28%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 04:05:53,474] [INFO] ===== Completeness check finished =====
[2023-03-18 04:05:53,475] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:05:53,475] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9877/markers.fasta)
[2023-03-18 04:05:53,475] [INFO] Task started: Blastn
[2023-03-18 04:05:53,475] [INFO] Running command: blastn -query OceanDNA-b9877/markers.fasta -db /var/lib/cwl/stg860f8b97-7c85-4d2d-9248-901ef8dd8f7e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9877/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:05:54,316] [INFO] Task succeeded: Blastn
[2023-03-18 04:05:54,317] [INFO] Selected 19 target genomes.
[2023-03-18 04:05:54,317] [INFO] Target genome list was writen to OceanDNA-b9877/target_genomes_gtdb.txt
[2023-03-18 04:05:54,657] [INFO] Task started: fastANI
[2023-03-18 04:05:54,657] [INFO] Running command: fastANI --query /var/lib/cwl/stg39819b6b-e310-466b-8ef5-6a4cf2c73af7/OceanDNA-b9877.fa --refList OceanDNA-b9877/target_genomes_gtdb.txt --output OceanDNA-b9877/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:06:06,445] [INFO] Task succeeded: fastANI
[2023-03-18 04:06:06,456] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 04:06:06,456] [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_018608545.1	s__Polaribacter sp018608545	81.5055	414	627	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	97.39	97.39	0.93	0.93	2	-
GCF_000766795.1	s__Polaribacter sp000766795	80.9363	452	627	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163675.1	s__Polaribacter sp002163675	80.4797	442	627	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163835.1	s__Polaribacter sp002163835	80.0829	394	627	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106075.1	s__Polaribacter sp900106075	80.0596	395	627	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	98.66	98.45	0.96	0.92	5	-
GCF_009796785.1	s__Polaribacter sp009796785	79.9952	416	627	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954605.1	s__Polaribacter butkevichii	79.8417	416	627	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019263805.1	s__Polaribacter sp011379025	79.8206	403	627	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	98.52	98.52	0.95	0.95	2	-
GCF_016858305.2	s__Polaribacter sp016858305	79.7576	400	627	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001640115.1	s__Polaribacter atrinae	79.7382	387	627	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000981625.1	s__Polaribacter sp000981625	79.5257	319	627	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	79.4521	370	627	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	79.1385	369	627	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007997075.1	s__Polaribacter sp007997075	79.1307	352	627	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	79.0704	373	627	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002943715.1	s__Polaribacter filamentus	78.8607	357	627	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017569185.1	s__Polaribacter sp017569185	78.8022	339	627	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002005425.1	s__Polaribacter sp002005425	78.7513	360	627	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	96.81	96.81	0.92	0.92	2	-
GCF_007827455.1	s__VISM01 sp007827455	78.2306	295	627	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__VISM01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 04:06:06,458] [INFO] GTDB search result was written to OceanDNA-b9877/result_gtdb.tsv
[2023-03-18 04:06:06,459] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:06:06,462] [INFO] DFAST_QC result json was written to OceanDNA-b9877/dqc_result.json
[2023-03-18 04:06:06,462] [INFO] DFAST_QC completed!
[2023-03-18 04:06:06,462] [INFO] Total running time: 0h1m13s