[2023-03-18 22:44:57,939] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:44:57,942] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:44:57,942] [INFO] DQC Reference Directory: /var/lib/cwl/stg702be18d-c57a-4fbf-8658-c9363c4ca809/dqc_reference
[2023-03-18 22:44:59,066] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:44:59,067] [INFO] Task started: Prodigal
[2023-03-18 22:44:59,067] [INFO] Running command: cat /var/lib/cwl/stg93052a8c-6cfa-4271-b7d3-d151c7490670/OceanDNA-b1836.fa | prodigal -d OceanDNA-b1836/cds.fna -a OceanDNA-b1836/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:45:22,668] [INFO] Task succeeded: Prodigal
[2023-03-18 22:45:22,668] [INFO] Task started: HMMsearch
[2023-03-18 22:45:22,668] [INFO] Running command: hmmsearch --tblout OceanDNA-b1836/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg702be18d-c57a-4fbf-8658-c9363c4ca809/dqc_reference/reference_markers.hmm OceanDNA-b1836/protein.faa > /dev/null
[2023-03-18 22:45:22,879] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:45:22,880] [INFO] Found 6/6 markers.
[2023-03-18 22:45:22,906] [INFO] Query marker FASTA was written to OceanDNA-b1836/markers.fasta
[2023-03-18 22:45:22,907] [INFO] Task started: Blastn
[2023-03-18 22:45:22,907] [INFO] Running command: blastn -query OceanDNA-b1836/markers.fasta -db /var/lib/cwl/stg702be18d-c57a-4fbf-8658-c9363c4ca809/dqc_reference/reference_markers.fasta -out OceanDNA-b1836/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:45:23,742] [INFO] Task succeeded: Blastn
[2023-03-18 22:45:23,745] [INFO] Selected 15 target genomes.
[2023-03-18 22:45:23,745] [INFO] Target genome list was writen to OceanDNA-b1836/target_genomes.txt
[2023-03-18 22:45:23,755] [INFO] Task started: fastANI
[2023-03-18 22:45:23,755] [INFO] Running command: fastANI --query /var/lib/cwl/stg93052a8c-6cfa-4271-b7d3-d151c7490670/OceanDNA-b1836.fa --refList OceanDNA-b1836/target_genomes.txt --output OceanDNA-b1836/fastani_result.tsv --threads 1
[2023-03-18 22:45:37,569] [INFO] Task succeeded: fastANI
[2023-03-18 22:45:37,569] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg702be18d-c57a-4fbf-8658-c9363c4ca809/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:45:37,569] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg702be18d-c57a-4fbf-8658-c9363c4ca809/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:45:37,579] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:45:37,579] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 22:45:37,579] [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
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	78.3992	483	1268	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	77.5787	435	1268	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	77.0681	285	1268	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	76.3745	401	1268	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	76.3586	319	1268	95	below_threshold
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	76.3279	199	1268	95	below_threshold
Nocardioides cavernae	strain=KCTC 39551	GCA_014779675.1	1921566	1921566	type	True	75.6446	267	1268	95	below_threshold
Nocardioides cavernae	strain=DSM 29950	GCA_016907475.1	1921566	1921566	type	True	75.6185	267	1268	95	below_threshold
Nocardioides perillae	strain=DSM 24552	GCA_013409425.1	1119534	1119534	type	True	75.5973	310	1268	95	below_threshold
Streptomyces fradiae	strain=NRRL B-1195	GCA_002154445.1	1906	1906	suspected-type	True	75.4918	204	1268	95	below_threshold
Tessaracoccus oleiagri	strain=CGMCC 1.9159	GCA_900103275.1	686624	686624	type	True	75.4295	162	1268	95	below_threshold
Streptomyces lavendofoliae	strain=JCM 4391	GCA_014649735.1	67314	67314	type	True	75.4012	270	1268	95	below_threshold
Catellatospora sichuanensis	strain=H14505	GCA_007483665.1	1969805	1969805	type	True	75.1881	317	1268	95	below_threshold
Bradyrhizobium guangxiense	strain=CCBAU 53363	GCA_004114915.1	1325115	1325115	type	True	74.8423	131	1268	95	below_threshold
Bradyrhizobium sacchari	strain=p9-20	GCA_002068095.1	1399419	1399419	type	True	74.7428	123	1268	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 22:45:37,581] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1836/tc_result.tsv
[2023-03-18 22:45:37,582] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:45:37,582] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:45:37,582] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg702be18d-c57a-4fbf-8658-c9363c4ca809/dqc_reference/checkm_data
[2023-03-18 22:45:37,583] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:45:37,625] [INFO] Task started: CheckM
[2023-03-18 22:45:37,625] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1836/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1836/checkm_input OceanDNA-b1836/checkm_result
[2023-03-18 22:46:59,708] [INFO] Task succeeded: CheckM
[2023-03-18 22:46:59,709] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 22:46:59,713] [INFO] ===== Completeness check finished =====
[2023-03-18 22:46:59,713] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:46:59,714] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1836/markers.fasta)
[2023-03-18 22:46:59,714] [INFO] Task started: Blastn
[2023-03-18 22:46:59,714] [INFO] Running command: blastn -query OceanDNA-b1836/markers.fasta -db /var/lib/cwl/stg702be18d-c57a-4fbf-8658-c9363c4ca809/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1836/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:47:01,051] [INFO] Task succeeded: Blastn
[2023-03-18 22:47:01,055] [INFO] Selected 23 target genomes.
[2023-03-18 22:47:01,055] [INFO] Target genome list was writen to OceanDNA-b1836/target_genomes_gtdb.txt
[2023-03-18 22:47:01,122] [INFO] Task started: fastANI
[2023-03-18 22:47:01,122] [INFO] Running command: fastANI --query /var/lib/cwl/stg93052a8c-6cfa-4271-b7d3-d151c7490670/OceanDNA-b1836.fa --refList OceanDNA-b1836/target_genomes_gtdb.txt --output OceanDNA-b1836/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:47:17,868] [INFO] Task succeeded: fastANI
[2023-03-18 22:47:17,881] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 22:47:17,881] [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
GCF_009650215.1	s__Actinomarinicola tropica	78.3992	481	1268	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__Actinomarinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882935.1	s__JADGOP01 sp017882935	77.8233	261	1268	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JADGOP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019048865.1	s__Aquihabitans sp019048865	77.7551	502	1268	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__Aquihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013694495.1	s__JACDCH01 sp013694495	77.746	373	1268	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__JACDCH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017577565.1	s__ZC4RG19 sp017577565	77.7295	448	1268	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__ZC4RG19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012513855.1	s__JAAZBK01 sp012513855	77.7007	290	1268	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JAAZBK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016649895.1	s__Actinomarinicola sp016649895	77.5266	361	1268	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__Actinomarinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004366205.1	s__SIRW01 sp004366205	77.5021	416	1268	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SIRW01;g__SIRW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018969405.1	s__F1-20-MAGs160 sp018969405	77.4255	232	1268	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__F1-20-MAGs160	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012730075.1	s__JAAYBP01 sp012730075	77.303	340	1268	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JAAYBP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002346745.1	s__S20-B6 sp002346745	77.174	237	1268	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	97.72	96.97	0.85	0.81	8	-
GCA_902805555.1	s__CADCSY01 sp902805555	77.1076	350	1268	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__CADCSY01;g__CADCSY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016845305.1	s__UBA9410 sp016845305	76.9021	297	1268	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903868545.1	s__CAIPVR01 sp903868545	76.8643	317	1268	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__CAIPVR01	95.0	99.51	99.50	0.87	0.86	3	-
GCA_014381945.1	s__S20-B6 sp014381945	76.8011	190	1268	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009705225.1	s__F1-20-MAGs160 sp009705225	76.6231	97	1268	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__F1-20-MAGs160	95.0	99.41	99.41	0.86	0.86	2	-
GCA_016870595.1	s__CAIUKV01 sp016870595	76.3614	244	1268	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__IMCC26256;f__PALSA-555;g__CAIUKV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882925.1	s__Chersky-534 sp017882925	76.0856	244	1268	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__IMCC26256;f__Chersky-534;g__Chersky-534	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427795.1	s__Nocardioides sp001427795	75.4713	225	1268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014649735.1	s__Streptomyces lavendofoliae	75.3812	270	1268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105395.1	s__Kitasatospora sp900105395	75.3063	367	1268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003391135.1	s__Streptomyces olivoreticuli	75.2987	282	1268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018614585.1	s__Streptomyces sp018614585	75.1764	202	1268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 22:47:17,885] [INFO] GTDB search result was written to OceanDNA-b1836/result_gtdb.tsv
[2023-03-18 22:47:17,887] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:47:17,891] [INFO] DFAST_QC result json was written to OceanDNA-b1836/dqc_result.json
[2023-03-18 22:47:17,892] [INFO] DFAST_QC completed!
[2023-03-18 22:47:17,892] [INFO] Total running time: 0h2m20s