[2023-03-17 09:41:39,968] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:41:39,969] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:41:39,969] [INFO] DQC Reference Directory: /var/lib/cwl/stg8a9e927c-2fe8-4e19-8c26-6f2aa49745ce/dqc_reference
[2023-03-17 09:41:41,757] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:41:41,757] [INFO] Task started: Prodigal
[2023-03-17 09:41:41,757] [INFO] Running command: cat /var/lib/cwl/stg86926983-243b-4d0a-99e2-5b587928cb88/OceanDNA-b3972.fa | prodigal -d OceanDNA-b3972/cds.fna -a OceanDNA-b3972/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:41:54,312] [INFO] Task succeeded: Prodigal
[2023-03-17 09:41:54,312] [INFO] Task started: HMMsearch
[2023-03-17 09:41:54,312] [INFO] Running command: hmmsearch --tblout OceanDNA-b3972/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8a9e927c-2fe8-4e19-8c26-6f2aa49745ce/dqc_reference/reference_markers.hmm OceanDNA-b3972/protein.faa > /dev/null
[2023-03-17 09:41:54,491] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:41:54,492] [INFO] Found 6/6 markers.
[2023-03-17 09:41:54,511] [INFO] Query marker FASTA was written to OceanDNA-b3972/markers.fasta
[2023-03-17 09:41:54,512] [INFO] Task started: Blastn
[2023-03-17 09:41:54,512] [INFO] Running command: blastn -query OceanDNA-b3972/markers.fasta -db /var/lib/cwl/stg8a9e927c-2fe8-4e19-8c26-6f2aa49745ce/dqc_reference/reference_markers.fasta -out OceanDNA-b3972/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:41:55,046] [INFO] Task succeeded: Blastn
[2023-03-17 09:41:55,051] [INFO] Selected 27 target genomes.
[2023-03-17 09:41:55,051] [INFO] Target genome list was writen to OceanDNA-b3972/target_genomes.txt
[2023-03-17 09:41:55,149] [INFO] Task started: fastANI
[2023-03-17 09:41:55,149] [INFO] Running command: fastANI --query /var/lib/cwl/stg86926983-243b-4d0a-99e2-5b587928cb88/OceanDNA-b3972.fa --refList OceanDNA-b3972/target_genomes.txt --output OceanDNA-b3972/fastani_result.tsv --threads 1
[2023-03-17 09:42:14,494] [INFO] Task succeeded: fastANI
[2023-03-17 09:42:14,495] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8a9e927c-2fe8-4e19-8c26-6f2aa49745ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:42:14,495] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8a9e927c-2fe8-4e19-8c26-6f2aa49745ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:42:14,500] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 09:42:14,500] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 09:42:14,500] [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
Algoriphagus sanaruensis	strain=M8-2	GCA_001593605.1	1727163	1727163	type	True	77.2247	71	384	95	below_threshold
Algoriphagus boritolerans	strain=DSM 17298	GCA_900108085.1	308111	308111	type	True	77.0046	59	384	95	below_threshold
Algoriphagus terrigena	strain=DSM 22685	GCA_000429445.1	344884	344884	type	True	76.7934	53	384	95	below_threshold
Algoriphagus alkaliphilus	strain=DSM 22703	GCA_900103735.1	279824	279824	type	True	76.6989	59	384	95	below_threshold
Algoriphagus aquaeductus	strain=T4	GCA_003253485.1	475299	475299	type	True	76.5538	97	384	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 09:42:14,502] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3972/tc_result.tsv
[2023-03-17 09:42:14,507] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:42:14,508] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:42:14,508] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8a9e927c-2fe8-4e19-8c26-6f2aa49745ce/dqc_reference/checkm_data
[2023-03-17 09:42:14,509] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:42:14,554] [INFO] Task started: CheckM
[2023-03-17 09:42:14,555] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3972/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3972/checkm_input OceanDNA-b3972/checkm_result
[2023-03-17 09:42:50,367] [INFO] Task succeeded: CheckM
[2023-03-17 09:42:50,368] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.71%
Contamintation: 0.84%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-17 09:42:50,437] [INFO] ===== Completeness check finished =====
[2023-03-17 09:42:50,437] [INFO] ===== Start GTDB Search =====
[2023-03-17 09:42:50,437] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3972/markers.fasta)
[2023-03-17 09:42:50,439] [INFO] Task started: Blastn
[2023-03-17 09:42:50,439] [INFO] Running command: blastn -query OceanDNA-b3972/markers.fasta -db /var/lib/cwl/stg8a9e927c-2fe8-4e19-8c26-6f2aa49745ce/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3972/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:42:51,166] [INFO] Task succeeded: Blastn
[2023-03-17 09:42:51,167] [INFO] Selected 23 target genomes.
[2023-03-17 09:42:51,167] [INFO] Target genome list was writen to OceanDNA-b3972/target_genomes_gtdb.txt
[2023-03-17 09:42:51,373] [INFO] Task started: fastANI
[2023-03-17 09:42:51,373] [INFO] Running command: fastANI --query /var/lib/cwl/stg86926983-243b-4d0a-99e2-5b587928cb88/OceanDNA-b3972.fa --refList OceanDNA-b3972/target_genomes_gtdb.txt --output OceanDNA-b3972/fastani_result_gtdb.tsv --threads 1
[2023-03-17 09:43:06,304] [INFO] Task succeeded: fastANI
[2023-03-17 09:43:06,310] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 09:43:06,310] [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_903952135.1	s__Algoriphagus sp903952135	82.7605	304	384	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.47	99.47	0.91	0.91	2	-
GCA_005788235.1	s__Algoriphagus sp005788235	80.4796	220	384	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016866385.1	s__Algoriphagus sp016866385	78.8123	161	384	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108085.1	s__Algoriphagus boritolerans	77.0046	59	384	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.80	99.80	0.99	0.99	2	-
GCA_018336015.1	s__Algoriphagus sp018336015	76.9942	88	384	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103735.1	s__Algoriphagus alkaliphilus	76.6989	59	384	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.41	99.41	0.93	0.93	2	-
GCF_014324365.1	s__Algoriphagus sp014324365	76.6796	88	384	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003253485.1	s__Algoriphagus aquaeductus	76.5333	98	384	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 09:43:06,312] [INFO] GTDB search result was written to OceanDNA-b3972/result_gtdb.tsv
[2023-03-17 09:43:06,313] [INFO] ===== GTDB Search completed =====
[2023-03-17 09:43:06,315] [INFO] DFAST_QC result json was written to OceanDNA-b3972/dqc_result.json
[2023-03-17 09:43:06,315] [INFO] DFAST_QC completed!
[2023-03-17 09:43:06,315] [INFO] Total running time: 0h1m26s