[2023-03-18 21:18:16,436] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:18:16,436] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:18:16,436] [INFO] DQC Reference Directory: /var/lib/cwl/stgb4d2b403-1c99-4a42-b684-d5259e4c65ae/dqc_reference
[2023-03-18 21:18:17,514] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:18:17,515] [INFO] Task started: Prodigal
[2023-03-18 21:18:17,515] [INFO] Running command: cat /var/lib/cwl/stg6ee35fc2-6170-4d5a-b888-9ce7652ddf65/OceanDNA-b1358.fa | prodigal -d OceanDNA-b1358/cds.fna -a OceanDNA-b1358/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:18:34,332] [INFO] Task succeeded: Prodigal
[2023-03-18 21:18:34,332] [INFO] Task started: HMMsearch
[2023-03-18 21:18:34,332] [INFO] Running command: hmmsearch --tblout OceanDNA-b1358/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb4d2b403-1c99-4a42-b684-d5259e4c65ae/dqc_reference/reference_markers.hmm OceanDNA-b1358/protein.faa > /dev/null
[2023-03-18 21:18:34,549] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:18:34,550] [INFO] Found 6/6 markers.
[2023-03-18 21:18:34,573] [INFO] Query marker FASTA was written to OceanDNA-b1358/markers.fasta
[2023-03-18 21:18:34,575] [INFO] Task started: Blastn
[2023-03-18 21:18:34,575] [INFO] Running command: blastn -query OceanDNA-b1358/markers.fasta -db /var/lib/cwl/stgb4d2b403-1c99-4a42-b684-d5259e4c65ae/dqc_reference/reference_markers.fasta -out OceanDNA-b1358/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:18:35,135] [INFO] Task succeeded: Blastn
[2023-03-18 21:18:35,136] [INFO] Selected 26 target genomes.
[2023-03-18 21:18:35,136] [INFO] Target genome list was writen to OceanDNA-b1358/target_genomes.txt
[2023-03-18 21:18:35,152] [INFO] Task started: fastANI
[2023-03-18 21:18:35,152] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ee35fc2-6170-4d5a-b888-9ce7652ddf65/OceanDNA-b1358.fa --refList OceanDNA-b1358/target_genomes.txt --output OceanDNA-b1358/fastani_result.tsv --threads 1
[2023-03-18 21:18:50,410] [INFO] Task succeeded: fastANI
[2023-03-18 21:18:50,411] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb4d2b403-1c99-4a42-b684-d5259e4c65ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:18:50,411] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb4d2b403-1c99-4a42-b684-d5259e4c65ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:18:50,416] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:18:50,416] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 21:18:50,416] [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
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.1631	75	814	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	75.7193	50	814	95	below_threshold
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	75.6757	64	814	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	75.6573	79	814	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	75.6206	71	814	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	75.5998	87	814	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 21:18:50,417] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1358/tc_result.tsv
[2023-03-18 21:18:50,417] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:18:50,417] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:18:50,417] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb4d2b403-1c99-4a42-b684-d5259e4c65ae/dqc_reference/checkm_data
[2023-03-18 21:18:50,418] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:18:50,423] [INFO] Task started: CheckM
[2023-03-18 21:18:50,423] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1358/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1358/checkm_input OceanDNA-b1358/checkm_result
[2023-03-18 21:19:35,037] [INFO] Task succeeded: CheckM
[2023-03-18 21:19:35,038] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:19:35,041] [INFO] ===== Completeness check finished =====
[2023-03-18 21:19:35,041] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:19:35,041] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1358/markers.fasta)
[2023-03-18 21:19:35,042] [INFO] Task started: Blastn
[2023-03-18 21:19:35,042] [INFO] Running command: blastn -query OceanDNA-b1358/markers.fasta -db /var/lib/cwl/stgb4d2b403-1c99-4a42-b684-d5259e4c65ae/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1358/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:19:35,849] [INFO] Task succeeded: Blastn
[2023-03-18 21:19:35,850] [INFO] Selected 32 target genomes.
[2023-03-18 21:19:35,850] [INFO] Target genome list was writen to OceanDNA-b1358/target_genomes_gtdb.txt
[2023-03-18 21:19:35,875] [INFO] Task started: fastANI
[2023-03-18 21:19:35,875] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ee35fc2-6170-4d5a-b888-9ce7652ddf65/OceanDNA-b1358.fa --refList OceanDNA-b1358/target_genomes_gtdb.txt --output OceanDNA-b1358/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:19:52,794] [INFO] Task succeeded: fastANI
[2023-03-18 21:19:52,801] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 21:19:52,801] [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_013151655.1	s__JAADHX01 sp013151655	76.8969	111	814	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__JAADHX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014238065.1	s__JABABU01 sp014238065	76.6931	92	814	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__JABABU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009843525.1	s__WTFX01 sp009843525	76.1041	68	814	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__WTFX01	95.0	98.04	97.52	0.89	0.86	18	-
GCA_009699605.1	s__WLNW01 sp009699605	75.9179	52	814	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__WLNW01;g__WLNW01	95.0	99.58	99.52	0.88	0.87	4	-
GCA_011051915.1	s__DRKF01 sp011051915	75.8203	60	814	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__DRKF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004366205.1	s__SIRW01 sp004366205	75.7501	57	814	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SIRW01;g__SIRW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002694825.1	s__UBA11606 sp002694825	75.6718	53	814	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	97.28	96.77	0.84	0.81	7	-
GCF_009650215.1	s__Actinomarinicola tropica	75.6206	71	814	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__Actinomarinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012730075.1	s__JAAYBP01 sp012730075	75.579	58	814	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JAAYBP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007121465.1	s__SKKL01 sp007121465	75.5406	65	814	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__SKKL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377505.1	s__WHTX01 sp009377505	75.4544	59	814	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__CAIXPF01;g__WHTX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 21:19:52,802] [INFO] GTDB search result was written to OceanDNA-b1358/result_gtdb.tsv
[2023-03-18 21:19:52,802] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:19:52,804] [INFO] DFAST_QC result json was written to OceanDNA-b1358/dqc_result.json
[2023-03-18 21:19:52,804] [INFO] DFAST_QC completed!
[2023-03-18 21:19:52,804] [INFO] Total running time: 0h1m36s