[2023-03-17 09:51:05,582] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:51:05,582] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:51:05,582] [INFO] DQC Reference Directory: /var/lib/cwl/stg8802374b-e502-46da-b324-74b2be9dc95c/dqc_reference
[2023-03-17 09:51:06,668] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:51:06,668] [INFO] Task started: Prodigal
[2023-03-17 09:51:06,669] [INFO] Running command: cat /var/lib/cwl/stga8ed310f-8a1c-4511-8bb0-ac3058519aff/OceanDNA-b13456.fa | prodigal -d OceanDNA-b13456/cds.fna -a OceanDNA-b13456/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:51:11,739] [INFO] Task succeeded: Prodigal
[2023-03-17 09:51:11,739] [INFO] Task started: HMMsearch
[2023-03-17 09:51:11,739] [INFO] Running command: hmmsearch --tblout OceanDNA-b13456/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8802374b-e502-46da-b324-74b2be9dc95c/dqc_reference/reference_markers.hmm OceanDNA-b13456/protein.faa > /dev/null
[2023-03-17 09:51:11,897] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:51:11,898] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga8ed310f-8a1c-4511-8bb0-ac3058519aff/OceanDNA-b13456.fa]
[2023-03-17 09:51:11,916] [INFO] Query marker FASTA was written to OceanDNA-b13456/markers.fasta
[2023-03-17 09:51:11,916] [INFO] Task started: Blastn
[2023-03-17 09:51:11,916] [INFO] Running command: blastn -query OceanDNA-b13456/markers.fasta -db /var/lib/cwl/stg8802374b-e502-46da-b324-74b2be9dc95c/dqc_reference/reference_markers.fasta -out OceanDNA-b13456/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:51:12,438] [INFO] Task succeeded: Blastn
[2023-03-17 09:51:12,441] [INFO] Selected 10 target genomes.
[2023-03-17 09:51:12,441] [INFO] Target genome list was writen to OceanDNA-b13456/target_genomes.txt
[2023-03-17 09:51:12,447] [INFO] Task started: fastANI
[2023-03-17 09:51:12,447] [INFO] Running command: fastANI --query /var/lib/cwl/stga8ed310f-8a1c-4511-8bb0-ac3058519aff/OceanDNA-b13456.fa --refList OceanDNA-b13456/target_genomes.txt --output OceanDNA-b13456/fastani_result.tsv --threads 1
[2023-03-17 09:51:16,013] [INFO] Task succeeded: fastANI
[2023-03-17 09:51:16,014] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8802374b-e502-46da-b324-74b2be9dc95c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:51:16,014] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8802374b-e502-46da-b324-74b2be9dc95c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:51:16,021] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 09:51:16,021] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 09:51:16,022] [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 marisnigri	strain=SoZ1	GCA_015265475.1	2740405	2740405	type	True	78.1179	124	330	95	below_threshold
Sulfurimonas gotlandica	strain=GD1	GCA_000242915.2	1176482	1176482	type	True	77.9542	139	330	95	below_threshold
Sulfurimonas gotlandica	strain=GD 1	GCA_000156095.1	1176482	1176482	type	True	77.9463	141	330	95	below_threshold
Candidatus Sulfurimonas baltica	strain=GD2	GCA_015265455.1	2740404	2740404	type	True	77.4859	105	330	95	below_threshold
Sulfurimonas paralvinellae	strain=GO25	GCA_014905135.1	317658	317658	type	True	76.9342	50	330	95	below_threshold
Sulfurimonas indica	strain=NW8N	GCA_009192995.1	2508707	2508707	type	True	76.8988	89	330	95	below_threshold
Sulfurimonas autotrophica	strain=DSM 16294	GCA_000147355.1	202747	202747	type	True	76.8974	98	330	95	below_threshold
Sulfurimonas xiamenensis	strain=1-1N	GCA_009258045.1	2590021	2590021	type	True	76.8008	76	330	95	below_threshold
Sulfurimonas hongkongensis	strain=AST-10	GCA_000445475.1	1172190	1172190	type	True	76.7819	89	330	95	below_threshold
Sulfurimonas denitrificans	strain=DSM 1251	GCA_000012965.1	39766	39766	type	True	76.5068	69	330	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 09:51:16,024] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13456/tc_result.tsv
[2023-03-17 09:51:16,026] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:51:16,026] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:51:16,026] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8802374b-e502-46da-b324-74b2be9dc95c/dqc_reference/checkm_data
[2023-03-17 09:51:16,027] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:51:16,029] [INFO] Task started: CheckM
[2023-03-17 09:51:16,029] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13456/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13456/checkm_input OceanDNA-b13456/checkm_result
[2023-03-17 09:51:34,183] [INFO] Task succeeded: CheckM
[2023-03-17 09:51:34,183] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 52.08%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 09:51:34,187] [INFO] ===== Completeness check finished =====
[2023-03-17 09:51:34,187] [INFO] ===== Start GTDB Search =====
[2023-03-17 09:51:34,187] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13456/markers.fasta)
[2023-03-17 09:51:34,188] [INFO] Task started: Blastn
[2023-03-17 09:51:34,188] [INFO] Running command: blastn -query OceanDNA-b13456/markers.fasta -db /var/lib/cwl/stg8802374b-e502-46da-b324-74b2be9dc95c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13456/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:51:34,935] [INFO] Task succeeded: Blastn
[2023-03-17 09:51:34,937] [INFO] Selected 13 target genomes.
[2023-03-17 09:51:34,938] [INFO] Target genome list was writen to OceanDNA-b13456/target_genomes_gtdb.txt
[2023-03-17 09:51:35,312] [INFO] Task started: fastANI
[2023-03-17 09:51:35,312] [INFO] Running command: fastANI --query /var/lib/cwl/stga8ed310f-8a1c-4511-8bb0-ac3058519aff/OceanDNA-b13456.fa --refList OceanDNA-b13456/target_genomes_gtdb.txt --output OceanDNA-b13456/fastani_result_gtdb.tsv --threads 1
[2023-03-17 09:51:39,929] [INFO] Task succeeded: fastANI
[2023-03-17 09:51:39,937] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 09:51:39,938] [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	80.2434	189	330	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.38	99.38	0.90	0.90	2	-
GCA_016764205.1	s__Sulfurimonas sp016764205	79.1661	90	330	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744115.1	s__Sulfurimonas sp016744115	78.7358	157	330	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	78.5758	109	330	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	78.3554	103	330	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	78.235	100	330	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	78.1179	124	330	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	78.1176	123	330	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	77.9689	137	330	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.99	99.99	1.00	1.00	2	-
GCA_013153755.1	s__Sulfurimonas sp013153755	77.6771	110	330	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	77.5567	92	330	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016938175.1	s__Sulfurimonas sp016938175	77.4841	87	330	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009192995.1	s__Sulfurimonas indica	76.8723	90	330	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 09:51:39,938] [INFO] GTDB search result was written to OceanDNA-b13456/result_gtdb.tsv
[2023-03-17 09:51:39,938] [INFO] ===== GTDB Search completed =====
[2023-03-17 09:51:39,940] [INFO] DFAST_QC result json was written to OceanDNA-b13456/dqc_result.json
[2023-03-17 09:51:39,940] [INFO] DFAST_QC completed!
[2023-03-17 09:51:39,940] [INFO] Total running time: 0h0m34s