[2023-03-19 04:29:38,147] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:29:38,147] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:29:38,147] [INFO] DQC Reference Directory: /var/lib/cwl/stga551e8f8-f3db-44f4-8fda-d2014bfdb73d/dqc_reference
[2023-03-19 04:29:39,836] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:29:39,836] [INFO] Task started: Prodigal
[2023-03-19 04:29:39,837] [INFO] Running command: cat /var/lib/cwl/stg9791c958-2657-429c-b50e-29597018313a/OceanDNA-b13459.fa | prodigal -d OceanDNA-b13459/cds.fna -a OceanDNA-b13459/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:29:49,121] [INFO] Task succeeded: Prodigal
[2023-03-19 04:29:49,122] [INFO] Task started: HMMsearch
[2023-03-19 04:29:49,122] [INFO] Running command: hmmsearch --tblout OceanDNA-b13459/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga551e8f8-f3db-44f4-8fda-d2014bfdb73d/dqc_reference/reference_markers.hmm OceanDNA-b13459/protein.faa > /dev/null
[2023-03-19 04:29:49,300] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:29:49,300] [INFO] Found 6/6 markers.
[2023-03-19 04:29:49,316] [INFO] Query marker FASTA was written to OceanDNA-b13459/markers.fasta
[2023-03-19 04:29:49,316] [INFO] Task started: Blastn
[2023-03-19 04:29:49,316] [INFO] Running command: blastn -query OceanDNA-b13459/markers.fasta -db /var/lib/cwl/stga551e8f8-f3db-44f4-8fda-d2014bfdb73d/dqc_reference/reference_markers.fasta -out OceanDNA-b13459/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:29:49,841] [INFO] Task succeeded: Blastn
[2023-03-19 04:29:49,841] [INFO] Selected 15 target genomes.
[2023-03-19 04:29:49,842] [INFO] Target genome list was writen to OceanDNA-b13459/target_genomes.txt
[2023-03-19 04:29:49,848] [INFO] Task started: fastANI
[2023-03-19 04:29:49,848] [INFO] Running command: fastANI --query /var/lib/cwl/stg9791c958-2657-429c-b50e-29597018313a/OceanDNA-b13459.fa --refList OceanDNA-b13459/target_genomes.txt --output OceanDNA-b13459/fastani_result.tsv --threads 1
[2023-03-19 04:29:54,972] [INFO] Task succeeded: fastANI
[2023-03-19 04:29:54,972] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga551e8f8-f3db-44f4-8fda-d2014bfdb73d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:29:54,972] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga551e8f8-f3db-44f4-8fda-d2014bfdb73d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:29:54,979] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:29:54,980] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 04:29:54,980] [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
Candidatus Sulfurimonas baltica	strain=GD2	GCA_015265455.1	2740404	2740404	type	True	77.802	141	602	95	below_threshold
Sulfurimonas gotlandica	strain=GD 1	GCA_000156095.1	1176482	1176482	type	True	77.6277	176	602	95	below_threshold
Sulfurimonas gotlandica	strain=GD1	GCA_000242915.2	1176482	1176482	type	True	77.6225	180	602	95	below_threshold
Candidatus Sulfurimonas marisnigri	strain=SoZ1	GCA_015265475.1	2740405	2740405	type	True	77.5976	142	602	95	below_threshold
Sulfurimonas autotrophica	strain=DSM 16294	GCA_000147355.1	202747	202747	type	True	77.3639	145	602	95	below_threshold
Sulfurimonas indica	strain=NW8N	GCA_009192995.1	2508707	2508707	type	True	77.0253	134	602	95	below_threshold
Sulfurimonas paralvinellae	strain=GO25	GCA_014905135.1	317658	317658	type	True	76.8845	93	602	95	below_threshold
Sulfurimonas sediminis	strain=S2-6	GCA_014905115.1	2590020	2590020	type	True	76.8741	98	602	95	below_threshold
Sulfurimonas hydrogeniphila	strain=NW10	GCA_009068765.1	2509341	2509341	type	True	76.7483	105	602	95	below_threshold
Sulfurimonas hongkongensis	strain=AST-10	GCA_000445475.1	1172190	1172190	type	True	76.4728	125	602	95	below_threshold
Sulfurimonas crateris	strain=SN118	GCA_005217605.1	2574727	2574727	type	True	76.2423	55	602	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:29:54,980] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13459/tc_result.tsv
[2023-03-19 04:29:54,980] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:29:54,980] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:29:54,980] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga551e8f8-f3db-44f4-8fda-d2014bfdb73d/dqc_reference/checkm_data
[2023-03-19 04:29:54,981] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:29:54,984] [INFO] Task started: CheckM
[2023-03-19 04:29:54,984] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13459/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13459/checkm_input OceanDNA-b13459/checkm_result
[2023-03-19 04:30:22,820] [INFO] Task succeeded: CheckM
[2023-03-19 04:30:22,820] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.48%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:30:22,822] [INFO] ===== Completeness check finished =====
[2023-03-19 04:30:22,822] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:30:22,823] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13459/markers.fasta)
[2023-03-19 04:30:22,823] [INFO] Task started: Blastn
[2023-03-19 04:30:22,823] [INFO] Running command: blastn -query OceanDNA-b13459/markers.fasta -db /var/lib/cwl/stga551e8f8-f3db-44f4-8fda-d2014bfdb73d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13459/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:30:23,581] [INFO] Task succeeded: Blastn
[2023-03-19 04:30:23,582] [INFO] Selected 20 target genomes.
[2023-03-19 04:30:23,582] [INFO] Target genome list was writen to OceanDNA-b13459/target_genomes_gtdb.txt
[2023-03-19 04:30:23,665] [INFO] Task started: fastANI
[2023-03-19 04:30:23,665] [INFO] Running command: fastANI --query /var/lib/cwl/stg9791c958-2657-429c-b50e-29597018313a/OceanDNA-b13459.fa --refList OceanDNA-b13459/target_genomes_gtdb.txt --output OceanDNA-b13459/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:30:30,975] [INFO] Task succeeded: fastANI
[2023-03-19 04:30:30,986] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:30:30,986] [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_002335055.1	s__Sulfurimonas sp002335055	78.015	152	602	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.96	99.95	0.96	0.95	3	-
GCA_013153755.1	s__Sulfurimonas sp013153755	77.8859	126	602	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003978465.1	s__Sulfurimonas sp003978465	77.8249	135	602	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002732645.1	s__Sulfurimonas sp002732645	77.8175	103	602	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	77.778	167	602	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	77.7699	172	602	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015663215.1	s__Sulfurimonas sp015663215	77.7178	100	602	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	77.6975	200	602	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	77.6225	180	602	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_015265475.1	s__Sulfurimonas marisnigri	77.5976	142	602	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744025.1	s__Sulfurimonas sp016744025	77.4923	162	602	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	77.3765	137	602	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000147355.1	s__Sulfurimonas autotrophica	77.368	144	602	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733155.1	s__Sulfurimonas sp002733155	77.3359	123	602	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	77.0724	80	602	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014905095.1	s__Sulfurimonas sp014905095	77.0484	114	602	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014905135.1	s__Sulfurimonas paralvinellae	76.8845	93	602	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903892995.1	s__CAITKP01 sp903892995	76.7684	66	602	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__CAITKP01	95.0	99.47	98.97	0.95	0.95	3	-
GCF_000445475.1	s__Sulfurimonas hongkongensis	76.4728	125	602	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:30:30,986] [INFO] GTDB search result was written to OceanDNA-b13459/result_gtdb.tsv
[2023-03-19 04:30:30,986] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:30:30,988] [INFO] DFAST_QC result json was written to OceanDNA-b13459/dqc_result.json
[2023-03-19 04:30:30,988] [INFO] DFAST_QC completed!
[2023-03-19 04:30:30,988] [INFO] Total running time: 0h0m53s