[2023-03-17 11:25:37,447] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:25:37,461] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:25:37,461] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf53f53e-a34f-4e4c-88b6-499ed9884fc3/dqc_reference
[2023-03-17 11:25:38,557] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:25:38,557] [INFO] Task started: Prodigal
[2023-03-17 11:25:38,557] [INFO] Running command: cat /var/lib/cwl/stg58446c1f-36b6-4a02-8be9-d7203c08040f/OceanDNA-b13446.fa | prodigal -d OceanDNA-b13446/cds.fna -a OceanDNA-b13446/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:25:45,474] [INFO] Task succeeded: Prodigal
[2023-03-17 11:25:45,474] [INFO] Task started: HMMsearch
[2023-03-17 11:25:45,474] [INFO] Running command: hmmsearch --tblout OceanDNA-b13446/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf53f53e-a34f-4e4c-88b6-499ed9884fc3/dqc_reference/reference_markers.hmm OceanDNA-b13446/protein.faa > /dev/null
[2023-03-17 11:25:45,658] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:25:45,658] [INFO] Found 6/6 markers.
[2023-03-17 11:25:45,795] [INFO] Query marker FASTA was written to OceanDNA-b13446/markers.fasta
[2023-03-17 11:25:45,797] [INFO] Task started: Blastn
[2023-03-17 11:25:45,797] [INFO] Running command: blastn -query OceanDNA-b13446/markers.fasta -db /var/lib/cwl/stgdf53f53e-a34f-4e4c-88b6-499ed9884fc3/dqc_reference/reference_markers.fasta -out OceanDNA-b13446/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:25:46,355] [INFO] Task succeeded: Blastn
[2023-03-17 11:25:46,409] [INFO] Selected 15 target genomes.
[2023-03-17 11:25:46,409] [INFO] Target genome list was writen to OceanDNA-b13446/target_genomes.txt
[2023-03-17 11:25:46,418] [INFO] Task started: fastANI
[2023-03-17 11:25:46,418] [INFO] Running command: fastANI --query /var/lib/cwl/stg58446c1f-36b6-4a02-8be9-d7203c08040f/OceanDNA-b13446.fa --refList OceanDNA-b13446/target_genomes.txt --output OceanDNA-b13446/fastani_result.tsv --threads 1
[2023-03-17 11:25:53,363] [INFO] Task succeeded: fastANI
[2023-03-17 11:25:53,363] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf53f53e-a34f-4e4c-88b6-499ed9884fc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:25:53,364] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf53f53e-a34f-4e4c-88b6-499ed9884fc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:25:53,372] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:25:53,373] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 11:25:53,373] [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
Poseidonibacter lekithochrous	strain=DSM 100870	GCA_013283835.1	1904463	1904463	type	True	80.7498	323	471	95	below_threshold
Poseidonibacter lekithochrous	strain=LFT 1.7	GCA_001878855.1	1904463	1904463	type	True	80.6628	322	471	95	below_threshold
Arcobacter acticola	strain=KCTC 52212	GCA_013177675.1	1849015	1849015	type	True	80.2117	338	471	95	below_threshold
Arcobacter suis	strain=CECT7833	GCA_004023465.1	1278212	1278212	type	True	80.0067	286	471	95	below_threshold
Arcobacter venerupis	strain=LMG 26156	GCA_013201665.1	1054033	1054033	type	True	79.9637	290	471	95	below_threshold
Arcobacter suis	strain=CECT 7833	GCA_003544815.1	1278212	1278212	type	True	79.9442	293	471	95	below_threshold
Arcobacter venerupis	strain=CECT7836	GCA_004023405.1	1054033	1054033	type	True	79.9249	281	471	95	below_threshold
Malaciobacter pacificus	strain=CGMCC 1.11011	GCA_014636355.1	1080223	1080223	type	True	79.8225	290	471	95	below_threshold
Arcobacter defluvii	strain=CECT 7697	GCA_004115775.1	873191	873191	type	True	79.8061	286	471	95	below_threshold
Arcobacter cloacae	strain=CECT 7834	GCA_004115805.1	1054034	1054034	type	True	79.7796	278	471	95	below_threshold
Arcobacter aquimarinus	strain=CECT 8442	GCA_004115795.1	1315211	1315211	type	True	79.7688	291	471	95	below_threshold
Arcobacter cloacae	strain=LMG 26153	GCA_013201935.1	1054034	1054034	type	True	79.7294	289	471	95	below_threshold
Malaciobacter pacificus	strain=LMG 26638	GCA_004214795.1	1080223	1080223	type	True	79.7213	298	471	95	below_threshold
Arcobacter defluvii	strain=LMG 25694	GCA_013201725.1	873191	873191	type	True	79.6954	288	471	95	below_threshold
Malaciobacter molluscorum	strain=CECT 7696	GCA_003544935.1	1032072	1032072	type	True	78.6074	250	471	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 11:25:53,384] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13446/tc_result.tsv
[2023-03-17 11:25:53,416] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:25:53,416] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:25:53,416] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf53f53e-a34f-4e4c-88b6-499ed9884fc3/dqc_reference/checkm_data
[2023-03-17 11:25:53,417] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:25:53,423] [INFO] Task started: CheckM
[2023-03-17 11:25:53,423] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13446/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13446/checkm_input OceanDNA-b13446/checkm_result
[2023-03-17 11:26:16,185] [INFO] Task succeeded: CheckM
[2023-03-17 11:26:16,185] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:26:16,564] [INFO] ===== Completeness check finished =====
[2023-03-17 11:26:16,564] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:26:16,565] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13446/markers.fasta)
[2023-03-17 11:26:16,565] [INFO] Task started: Blastn
[2023-03-17 11:26:16,565] [INFO] Running command: blastn -query OceanDNA-b13446/markers.fasta -db /var/lib/cwl/stgdf53f53e-a34f-4e4c-88b6-499ed9884fc3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13446/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:26:17,316] [INFO] Task succeeded: Blastn
[2023-03-17 11:26:17,362] [INFO] Selected 8 target genomes.
[2023-03-17 11:26:17,362] [INFO] Target genome list was writen to OceanDNA-b13446/target_genomes_gtdb.txt
[2023-03-17 11:26:17,370] [INFO] Task started: fastANI
[2023-03-17 11:26:17,370] [INFO] Running command: fastANI --query /var/lib/cwl/stg58446c1f-36b6-4a02-8be9-d7203c08040f/OceanDNA-b13446.fa --refList OceanDNA-b13446/target_genomes_gtdb.txt --output OceanDNA-b13446/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:26:21,663] [INFO] Task succeeded: fastANI
[2023-03-17 11:26:21,668] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 11:26:21,668] [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_905479135.1	s__Poseidonibacter sp905479135	96.2334	355	471	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009208075.1	s__Poseidonibacter sp009208075	87.454	423	471	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	99.63	99.63	0.93	0.93	3	-
GCF_018861145.1	s__Poseidonibacter lekithochrous_A	86.0208	403	471	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002685075.1	s__Poseidonibacter sp002685075	84.9481	360	471	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001956695.1	s__Poseidonibacter parvus	83.8803	390	471	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	98.33	98.33	0.91	0.91	2	-
GCF_003667345.1	s__Poseidonibacter antarcticus	83.2887	370	471	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013283835.1	s__Poseidonibacter lekithochrous	80.7289	325	471	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	99.16	98.33	0.97	0.93	3	-
GCA_001895145.1	s__Halarcobacter sp001895145	79.737	279	471	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 11:26:21,671] [INFO] GTDB search result was written to OceanDNA-b13446/result_gtdb.tsv
[2023-03-17 11:26:21,674] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:26:21,680] [INFO] DFAST_QC result json was written to OceanDNA-b13446/dqc_result.json
[2023-03-17 11:26:21,680] [INFO] DFAST_QC completed!
[2023-03-17 11:26:21,680] [INFO] Total running time: 0h0m44s