[2023-03-16 11:01:17,014] [INFO] DFAST_QC pipeline started.
[2023-03-16 11:01:17,014] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 11:01:17,014] [INFO] DQC Reference Directory: /var/lib/cwl/stg75f4563e-29d7-4a16-ba5b-178bcc52f09b/dqc_reference
[2023-03-16 11:01:18,260] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 11:01:18,261] [INFO] Task started: Prodigal
[2023-03-16 11:01:18,261] [INFO] Running command: cat /var/lib/cwl/stg8e4b1fe6-f27f-4188-ae0d-60217cf96633/OceanDNA-b10181.fa | prodigal -d OceanDNA-b10181/cds.fna -a OceanDNA-b10181/protein.faa -g 11 -q > /dev/null
[2023-03-16 11:01:30,252] [INFO] Task succeeded: Prodigal
[2023-03-16 11:01:30,253] [INFO] Task started: HMMsearch
[2023-03-16 11:01:30,253] [INFO] Running command: hmmsearch --tblout OceanDNA-b10181/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg75f4563e-29d7-4a16-ba5b-178bcc52f09b/dqc_reference/reference_markers.hmm OceanDNA-b10181/protein.faa > /dev/null
[2023-03-16 11:01:30,439] [INFO] Task succeeded: HMMsearch
[2023-03-16 11:01:30,439] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8e4b1fe6-f27f-4188-ae0d-60217cf96633/OceanDNA-b10181.fa]
[2023-03-16 11:01:30,453] [INFO] Query marker FASTA was written to OceanDNA-b10181/markers.fasta
[2023-03-16 11:01:30,454] [INFO] Task started: Blastn
[2023-03-16 11:01:30,454] [INFO] Running command: blastn -query OceanDNA-b10181/markers.fasta -db /var/lib/cwl/stg75f4563e-29d7-4a16-ba5b-178bcc52f09b/dqc_reference/reference_markers.fasta -out OceanDNA-b10181/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:01:31,015] [INFO] Task succeeded: Blastn
[2023-03-16 11:01:31,017] [INFO] Selected 22 target genomes.
[2023-03-16 11:01:31,017] [INFO] Target genome list was writen to OceanDNA-b10181/target_genomes.txt
[2023-03-16 11:01:31,033] [INFO] Task started: fastANI
[2023-03-16 11:01:31,034] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e4b1fe6-f27f-4188-ae0d-60217cf96633/OceanDNA-b10181.fa --refList OceanDNA-b10181/target_genomes.txt --output OceanDNA-b10181/fastani_result.tsv --threads 1
[2023-03-16 11:01:51,971] [INFO] Task succeeded: fastANI
[2023-03-16 11:01:51,971] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg75f4563e-29d7-4a16-ba5b-178bcc52f09b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 11:01:51,971] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg75f4563e-29d7-4a16-ba5b-178bcc52f09b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 11:01:51,984] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 11:01:51,984] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 11:01:51,984] [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 aquimarinus	strain=ZY113	GCA_003129485.1	2100726	2100726	type	True	77.3585	162	485	95	below_threshold
Polaribacter porphyrae	strain=LMG 26671	GCA_020532745.1	1137780	1137780	type	True	77.0771	154	485	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	77.072	136	485	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_900106865.1	326329	326329	type	True	77.0624	136	485	95	below_threshold
Polaribacter porphyrae	strain=NBRC 108759	GCA_002954685.1	1137780	1137780	type	True	77.0598	156	485	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_001280865.1	326329	326329	type	True	77.0419	136	485	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	76.7908	145	485	95	below_threshold
Polaribacter glomeratus	strain=ACAM 171	GCA_007997115.1	102	102	type	True	76.7605	135	485	95	below_threshold
Polaribacter glomeratus	strain=ATCC 43844	GCA_002954665.1	102	102	type	True	76.7325	138	485	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	76.7081	122	485	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	76.6776	145	485	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	76.6619	146	485	95	below_threshold
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	76.6244	134	485	95	below_threshold
Polaribacter tangerinus	strain=WS2-14	GCA_002201235.1	1920034	1920034	type	True	76.607	108	485	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	76.601	134	485	95	below_threshold
Polaribacter reichenbachii	strain=LMG 26443	GCA_020532845.1	996801	996801	type	True	76.5816	149	485	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	76.5791	148	485	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_001680875.1	996801	996801	type	True	76.5784	148	485	95	below_threshold
Tenacibaculum aiptasiae	strain=a4	GCA_008806755.1	426481	426481	type	True	76.5166	111	485	95	below_threshold
Polaribacter pacificus	strain=CGMCC 1.15763	GCA_014643655.1	1775173	1775173	type	True	76.3705	84	485	95	below_threshold
Tenacibaculum skagerrakense	strain=DSM 14836	GCA_004345825.1	186571	186571	type	True	76.2902	106	485	95	below_threshold
Wenyingzhuangia fucanilytica	strain=CZ1127	GCA_001697185.1	1790137	1790137	type	True	75.8653	66	485	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 11:01:51,985] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10181/tc_result.tsv
[2023-03-16 11:01:51,985] [INFO] ===== Taxonomy check completed =====
[2023-03-16 11:01:51,985] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 11:01:51,985] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg75f4563e-29d7-4a16-ba5b-178bcc52f09b/dqc_reference/checkm_data
[2023-03-16 11:01:51,986] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 11:01:51,989] [INFO] Task started: CheckM
[2023-03-16 11:01:51,989] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10181/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10181/checkm_input OceanDNA-b10181/checkm_result
[2023-03-16 11:02:19,477] [INFO] Task succeeded: CheckM
[2023-03-16 11:02:19,478] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.38%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 11:02:19,480] [INFO] ===== Completeness check finished =====
[2023-03-16 11:02:19,480] [INFO] ===== Start GTDB Search =====
[2023-03-16 11:02:19,481] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10181/markers.fasta)
[2023-03-16 11:02:19,482] [INFO] Task started: Blastn
[2023-03-16 11:02:19,482] [INFO] Running command: blastn -query OceanDNA-b10181/markers.fasta -db /var/lib/cwl/stg75f4563e-29d7-4a16-ba5b-178bcc52f09b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10181/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:02:20,552] [INFO] Task succeeded: Blastn
[2023-03-16 11:02:20,553] [INFO] Selected 11 target genomes.
[2023-03-16 11:02:20,553] [INFO] Target genome list was writen to OceanDNA-b10181/target_genomes_gtdb.txt
[2023-03-16 11:02:20,608] [INFO] Task started: fastANI
[2023-03-16 11:02:20,608] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e4b1fe6-f27f-4188-ae0d-60217cf96633/OceanDNA-b10181.fa --refList OceanDNA-b10181/target_genomes_gtdb.txt --output OceanDNA-b10181/fastani_result_gtdb.tsv --threads 1
[2023-03-16 11:02:26,333] [INFO] Task succeeded: fastANI
[2023-03-16 11:02:26,340] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 11:02:26,341] [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_905479435.1	s__SCGC-AAA160-P02 sp905479435	85.8337	350	485	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	82.2454	360	485	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	81.9256	305	485	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	-
GCA_000383355.1	s__SCGC-AAA160-P02 sp000383355	81.4019	358	485	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	-
GCF_001280865.1	s__Polaribacter dokdonensis	77.0417	136	485	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	76.9144	158	485	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373105.1	s__Polaribacter sp013373105	76.8622	135	485	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	76.6491	146	485	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	76.5961	136	485	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	97.48	97.48	0.89	0.89	2	-
GCF_008806755.1	s__Tenacibaculum aiptasiae	76.5166	111	485	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009796785.1	s__Polaribacter sp009796785	76.4113	144	485	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 11:02:26,341] [INFO] GTDB search result was written to OceanDNA-b10181/result_gtdb.tsv
[2023-03-16 11:02:26,341] [INFO] ===== GTDB Search completed =====
[2023-03-16 11:02:26,343] [INFO] DFAST_QC result json was written to OceanDNA-b10181/dqc_result.json
[2023-03-16 11:02:26,344] [INFO] DFAST_QC completed!
[2023-03-16 11:02:26,344] [INFO] Total running time: 0h1m9s