[2023-03-15 15:55:17,956] [INFO] DFAST_QC pipeline started.
[2023-03-15 15:55:17,956] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 15:55:17,956] [INFO] DQC Reference Directory: /var/lib/cwl/stg48f7310a-feae-4504-95c7-7d96d5f636a1/dqc_reference
[2023-03-15 15:55:19,021] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 15:55:19,021] [INFO] Task started: Prodigal
[2023-03-15 15:55:19,022] [INFO] Running command: cat /var/lib/cwl/stg506b5fe1-1cd8-413a-8c36-93eb110dcc28/OceanDNA-b10103.fa | prodigal -d OceanDNA-b10103/cds.fna -a OceanDNA-b10103/protein.faa -g 11 -q > /dev/null
[2023-03-15 15:55:31,597] [INFO] Task succeeded: Prodigal
[2023-03-15 15:55:31,597] [INFO] Task started: HMMsearch
[2023-03-15 15:55:31,597] [INFO] Running command: hmmsearch --tblout OceanDNA-b10103/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg48f7310a-feae-4504-95c7-7d96d5f636a1/dqc_reference/reference_markers.hmm OceanDNA-b10103/protein.faa > /dev/null
[2023-03-15 15:55:31,803] [INFO] Task succeeded: HMMsearch
[2023-03-15 15:55:31,803] [INFO] Found 6/6 markers.
[2023-03-15 15:55:31,818] [INFO] Query marker FASTA was written to OceanDNA-b10103/markers.fasta
[2023-03-15 15:55:31,819] [INFO] Task started: Blastn
[2023-03-15 15:55:31,819] [INFO] Running command: blastn -query OceanDNA-b10103/markers.fasta -db /var/lib/cwl/stg48f7310a-feae-4504-95c7-7d96d5f636a1/dqc_reference/reference_markers.fasta -out OceanDNA-b10103/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:55:32,448] [INFO] Task succeeded: Blastn
[2023-03-15 15:55:32,449] [INFO] Selected 27 target genomes.
[2023-03-15 15:55:32,449] [INFO] Target genome list was writen to OceanDNA-b10103/target_genomes.txt
[2023-03-15 15:55:32,464] [INFO] Task started: fastANI
[2023-03-15 15:55:32,464] [INFO] Running command: fastANI --query /var/lib/cwl/stg506b5fe1-1cd8-413a-8c36-93eb110dcc28/OceanDNA-b10103.fa --refList OceanDNA-b10103/target_genomes.txt --output OceanDNA-b10103/fastani_result.tsv --threads 1
[2023-03-15 15:55:48,081] [INFO] Task succeeded: fastANI
[2023-03-15 15:55:48,081] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg48f7310a-feae-4504-95c7-7d96d5f636a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 15:55:48,081] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg48f7310a-feae-4504-95c7-7d96d5f636a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 15:55:48,096] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 15:55:48,096] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 15:55:48,096] [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 pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	78.0274	317	669	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	77.9186	289	669	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	77.8596	264	669	95	below_threshold
Polaribacter reichenbachii	strain=LMG 26443	GCA_020532845.1	996801	996801	type	True	77.7726	298	669	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	77.7607	306	669	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	77.7511	275	669	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	77.7473	279	669	95	below_threshold
Polaribacter atrinae	strain=KACC 17473	GCA_001640115.1	1333662	1333662	type	True	77.7417	272	669	95	below_threshold
Polaribacter reichenbachii	strain=6Alg 8T	GCA_001975665.1	996801	996801	type	True	77.739	299	669	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_900106865.1	326329	326329	type	True	77.7128	276	669	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_001280865.1	326329	326329	type	True	77.7109	277	669	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_001680875.1	996801	996801	type	True	77.7098	301	669	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	77.7079	302	669	95	below_threshold
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	77.6795	283	669	95	below_threshold
Polaribacter aquimarinus	strain=ZY113	GCA_003129485.1	2100726	2100726	type	True	77.6729	299	669	95	below_threshold
Polaribacter glomeratus	strain=ATCC 43844	GCA_002954665.1	102	102	type	True	77.6453	298	669	95	below_threshold
Polaribacter glomeratus	strain=ACAM 171	GCA_007997115.1	102	102	type	True	77.6368	296	669	95	below_threshold
Polaribacter filamentus	strain=ATCC 700397	GCA_002943715.1	53483	53483	type	True	77.5764	270	669	95	below_threshold
Polaribacter porphyrae	strain=LMG 26671	GCA_020532745.1	1137780	1137780	type	True	77.4629	301	669	95	below_threshold
Polaribacter litorisediminis	strain=OITF-11	GCA_019968605.1	1908341	1908341	type	True	77.4	285	669	95	below_threshold
Polaribacter porphyrae	strain=NBRC 108759	GCA_002954685.1	1137780	1137780	type	True	77.3955	307	669	95	below_threshold
Tenacibaculum finnmarkense	strain=TNO006	GCA_900239185.1	2781243	2781243	type	True	77.3175	165	669	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	77.2607	262	669	95	below_threshold
Tenacibaculum mesophilum	strain=DSM 13764	GCA_009362255.1	104268	104268	type	True	77.1263	211	669	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	76.1402	65	669	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	76.107	76	669	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.0976	89	669	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 15:55:48,096] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10103/tc_result.tsv
[2023-03-15 15:55:48,096] [INFO] ===== Taxonomy check completed =====
[2023-03-15 15:55:48,097] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 15:55:48,097] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg48f7310a-feae-4504-95c7-7d96d5f636a1/dqc_reference/checkm_data
[2023-03-15 15:55:48,097] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 15:55:48,101] [INFO] Task started: CheckM
[2023-03-15 15:55:48,101] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10103/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10103/checkm_input OceanDNA-b10103/checkm_result
[2023-03-15 15:56:23,372] [INFO] Task succeeded: CheckM
[2023-03-15 15:56:23,373] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.59%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 15:56:23,375] [INFO] ===== Completeness check finished =====
[2023-03-15 15:56:23,375] [INFO] ===== Start GTDB Search =====
[2023-03-15 15:56:23,375] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10103/markers.fasta)
[2023-03-15 15:56:23,376] [INFO] Task started: Blastn
[2023-03-15 15:56:23,377] [INFO] Running command: blastn -query OceanDNA-b10103/markers.fasta -db /var/lib/cwl/stg48f7310a-feae-4504-95c7-7d96d5f636a1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10103/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:56:24,332] [INFO] Task succeeded: Blastn
[2023-03-15 15:56:24,333] [INFO] Selected 20 target genomes.
[2023-03-15 15:56:24,333] [INFO] Target genome list was writen to OceanDNA-b10103/target_genomes_gtdb.txt
[2023-03-15 15:56:24,345] [INFO] Task started: fastANI
[2023-03-15 15:56:24,346] [INFO] Running command: fastANI --query /var/lib/cwl/stg506b5fe1-1cd8-413a-8c36-93eb110dcc28/OceanDNA-b10103.fa --refList OceanDNA-b10103/target_genomes_gtdb.txt --output OceanDNA-b10103/fastani_result_gtdb.tsv --threads 1
[2023-03-15 15:56:35,648] [INFO] Task succeeded: fastANI
[2023-03-15 15:56:35,660] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 15:56:35,660] [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_000383355.1	s__SCGC-AAA160-P02 sp000383355	80.1187	396	669	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SCGC-AAA160-P02	95.0	96.64	95.28	0.86	0.84	6	-
GCA_905479435.1	s__SCGC-AAA160-P02 sp905479435	78.6993	232	669	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SCGC-AAA160-P02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015665265.1	s__SCGC-AAA160-P02 sp015665265	78.5255	336	669	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SCGC-AAA160-P02	95.0	96.43	96.43	0.88	0.88	2	-
GCA_018608485.1	s__SCGC-AAA160-P02 sp018608485	78.3777	273	669	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SCGC-AAA160-P02	95.0	99.40	99.40	0.78	0.78	2	-
GCF_000766795.1	s__Polaribacter sp000766795	78.301	318	669	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016763215.1	s__SCGC-AAA160-P02 sp016763215	78.1317	203	669	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SCGC-AAA160-P02	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163835.1	s__Polaribacter sp002163835	78.1196	327	669	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827455.1	s__VISM01 sp007827455	77.9464	299	669	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__VISM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105145.1	s__Polaribacter sp900105145	77.9439	304	669	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	77.873	263	669	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480405.1	s__Polaribacter sp905480405	77.7294	277	669	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	77.7109	277	669	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009796785.1	s__Polaribacter sp009796785	77.6665	279	669	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	77.5663	271	669	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004762155.1	s__Tenacibaculum sp004762155	77.4259	245	669	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954685.1	s__Polaribacter porphyrae	77.3857	308	669	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	77.3119	260	669	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000430545.1	s__Tenacibaculum ovolyticum	77.2817	234	669	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.63	97.63	0.88	0.88	2	-
GCF_002836595.1	s__Tenacibaculum sp002836595	77.1346	244	669	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105985.1	s__Tenacibaculum sp900105985	76.9342	229	669	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	98.69	98.69	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-03-15 15:56:35,660] [INFO] GTDB search result was written to OceanDNA-b10103/result_gtdb.tsv
[2023-03-15 15:56:35,661] [INFO] ===== GTDB Search completed =====
[2023-03-15 15:56:35,663] [INFO] DFAST_QC result json was written to OceanDNA-b10103/dqc_result.json
[2023-03-15 15:56:35,663] [INFO] DFAST_QC completed!
[2023-03-15 15:56:35,663] [INFO] Total running time: 0h1m18s