[2023-03-18 01:14:00,934] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:14:00,934] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:14:00,934] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e8a8b48-4189-4c7b-828b-54d4ad541719/dqc_reference
[2023-03-18 01:14:02,014] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:14:02,015] [INFO] Task started: Prodigal
[2023-03-18 01:14:02,015] [INFO] Running command: cat /var/lib/cwl/stg423e3f63-ab52-472a-9ee7-d03853c69b1a/OceanDNA-b13454.fa | prodigal -d OceanDNA-b13454/cds.fna -a OceanDNA-b13454/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:14:09,214] [INFO] Task succeeded: Prodigal
[2023-03-18 01:14:09,214] [INFO] Task started: HMMsearch
[2023-03-18 01:14:09,214] [INFO] Running command: hmmsearch --tblout OceanDNA-b13454/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e8a8b48-4189-4c7b-828b-54d4ad541719/dqc_reference/reference_markers.hmm OceanDNA-b13454/protein.faa > /dev/null
[2023-03-18 01:14:09,375] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:14:09,375] [INFO] Found 6/6 markers.
[2023-03-18 01:14:09,387] [INFO] Query marker FASTA was written to OceanDNA-b13454/markers.fasta
[2023-03-18 01:14:09,388] [INFO] Task started: Blastn
[2023-03-18 01:14:09,388] [INFO] Running command: blastn -query OceanDNA-b13454/markers.fasta -db /var/lib/cwl/stg5e8a8b48-4189-4c7b-828b-54d4ad541719/dqc_reference/reference_markers.fasta -out OceanDNA-b13454/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:14:09,905] [INFO] Task succeeded: Blastn
[2023-03-18 01:14:09,906] [INFO] Selected 15 target genomes.
[2023-03-18 01:14:09,906] [INFO] Target genome list was writen to OceanDNA-b13454/target_genomes.txt
[2023-03-18 01:14:09,916] [INFO] Task started: fastANI
[2023-03-18 01:14:09,916] [INFO] Running command: fastANI --query /var/lib/cwl/stg423e3f63-ab52-472a-9ee7-d03853c69b1a/OceanDNA-b13454.fa --refList OceanDNA-b13454/target_genomes.txt --output OceanDNA-b13454/fastani_result.tsv --threads 1
[2023-03-18 01:14:14,967] [INFO] Task succeeded: fastANI
[2023-03-18 01:14:14,967] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e8a8b48-4189-4c7b-828b-54d4ad541719/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:14:14,967] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e8a8b48-4189-4c7b-828b-54d4ad541719/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:14:14,975] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:14:14,975] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 01:14:14,975] [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
Sulfurimonas gotlandica	strain=GD 1	GCA_000156095.1	1176482	1176482	type	True	78.2952	142	452	95	below_threshold
Sulfurimonas gotlandica	strain=GD1	GCA_000242915.2	1176482	1176482	type	True	78.2634	145	452	95	below_threshold
Candidatus Sulfurimonas marisnigri	strain=SoZ1	GCA_015265475.1	2740405	2740405	type	True	78.1613	149	452	95	below_threshold
Candidatus Sulfurimonas baltica	strain=GD2	GCA_015265455.1	2740404	2740404	type	True	77.8913	131	452	95	below_threshold
Sulfurimonas indica	strain=NW8N	GCA_009192995.1	2508707	2508707	type	True	77.6165	94	452	95	below_threshold
Sulfurimonas paralvinellae	strain=GO25	GCA_014905135.1	317658	317658	type	True	77.5966	72	452	95	below_threshold
Sulfurimonas xiamenensis	strain=1-1N	GCA_009258045.1	2590021	2590021	type	True	77.5724	93	452	95	below_threshold
Sulfurimonas autotrophica	strain=DSM 16294	GCA_000147355.1	202747	202747	type	True	77.5369	120	452	95	below_threshold
Sulfurimonas denitrificans	strain=DSM 1251	GCA_000012965.1	39766	39766	type	True	77.3424	98	452	95	below_threshold
Sulfurimonas lithotrophica	strain=GYSZ_1	GCA_009258225.1	2590022	2590022	type	True	77.2918	99	452	95	below_threshold
Sulfurimonas hongkongensis	strain=AST-10	GCA_000445475.1	1172190	1172190	type	True	76.9608	116	452	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 01:14:14,975] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13454/tc_result.tsv
[2023-03-18 01:14:14,975] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:14:14,976] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:14:14,976] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e8a8b48-4189-4c7b-828b-54d4ad541719/dqc_reference/checkm_data
[2023-03-18 01:14:14,976] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:14:14,989] [INFO] Task started: CheckM
[2023-03-18 01:14:14,989] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13454/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13454/checkm_input OceanDNA-b13454/checkm_result
[2023-03-18 01:14:38,860] [INFO] Task succeeded: CheckM
[2023-03-18 01:14:38,861] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.72%
Contamintation: 6.99%
Strain heterogeneity: 12.50%
--------------------------------------------------------------------------------
[2023-03-18 01:14:38,863] [INFO] ===== Completeness check finished =====
[2023-03-18 01:14:38,863] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:14:38,863] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13454/markers.fasta)
[2023-03-18 01:14:38,864] [INFO] Task started: Blastn
[2023-03-18 01:14:38,864] [INFO] Running command: blastn -query OceanDNA-b13454/markers.fasta -db /var/lib/cwl/stg5e8a8b48-4189-4c7b-828b-54d4ad541719/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13454/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:14:39,605] [INFO] Task succeeded: Blastn
[2023-03-18 01:14:39,606] [INFO] Selected 17 target genomes.
[2023-03-18 01:14:39,606] [INFO] Target genome list was writen to OceanDNA-b13454/target_genomes_gtdb.txt
[2023-03-18 01:14:39,623] [INFO] Task started: fastANI
[2023-03-18 01:14:39,623] [INFO] Running command: fastANI --query /var/lib/cwl/stg423e3f63-ab52-472a-9ee7-d03853c69b1a/OceanDNA-b13454.fa --refList OceanDNA-b13454/target_genomes_gtdb.txt --output OceanDNA-b13454/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:14:45,935] [INFO] Task succeeded: fastANI
[2023-03-18 01:14:45,945] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 01:14:45,945] [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_014381585.1	s__Sulfurimonas ponti	85.7907	337	452	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.38	99.38	0.90	0.90	2	-
GCA_016744115.1	s__Sulfurimonas sp016744115	79.0151	195	452	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016764205.1	s__Sulfurimonas sp016764205	78.8364	121	452	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002335055.1	s__Sulfurimonas sp002335055	78.7857	132	452	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.96	99.95	0.96	0.95	3	-
GCA_002732645.1	s__Sulfurimonas sp002732645	78.6305	86	452	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733945.2	s__Sulfurimonas sp002733945	78.5362	130	452	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017357825.1	s__Sulfurimonas sp017357825	78.4548	131	452	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015487435.1	s__Sulfurimonas sp015487435	78.3806	112	452	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000242915.1	s__Sulfurimonas gotlandica	78.2634	145	452	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.99	99.99	1.00	1.00	2	-
GCA_016744025.1	s__Sulfurimonas sp016744025	78.2081	141	452	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015265475.1	s__Sulfurimonas marisnigri	78.1675	148	452	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018698455.1	s__Sulfurimonas sp018698455	78.1461	146	452	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013153755.1	s__Sulfurimonas sp013153755	77.9479	97	452	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015487265.1	s__Sulfurimonas sp015487265	77.4099	110	452	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001829715.1	s__Sulfurimonas sp001829715	77.1094	75	452	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	98.65	98.65	0.90	0.90	2	-
GCA_903892995.1	s__CAITKP01 sp903892995	76.9512	65	452	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__CAITKP01	95.0	99.47	98.97	0.95	0.95	3	-
GCA_903903705.1	s__Sulfurimonas sp903903705	76.9484	56	452	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 01:14:45,946] [INFO] GTDB search result was written to OceanDNA-b13454/result_gtdb.tsv
[2023-03-18 01:14:45,946] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:14:45,947] [INFO] DFAST_QC result json was written to OceanDNA-b13454/dqc_result.json
[2023-03-18 01:14:45,947] [INFO] DFAST_QC completed!
[2023-03-18 01:14:45,948] [INFO] Total running time: 0h0m45s