[2023-03-15 07:29:11,756] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:29:11,756] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:29:11,756] [INFO] DQC Reference Directory: /var/lib/cwl/stgf82e35f7-0c40-4c04-9e60-64d478a1738c/dqc_reference
[2023-03-15 07:29:13,589] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:29:13,589] [INFO] Task started: Prodigal
[2023-03-15 07:29:13,589] [INFO] Running command: cat /var/lib/cwl/stgb2141c13-8c7e-4204-a548-ba9f6542c639/OceanDNA-b34903.fa | prodigal -d OceanDNA-b34903/cds.fna -a OceanDNA-b34903/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:29:36,334] [INFO] Task succeeded: Prodigal
[2023-03-15 07:29:36,334] [INFO] Task started: HMMsearch
[2023-03-15 07:29:36,334] [INFO] Running command: hmmsearch --tblout OceanDNA-b34903/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf82e35f7-0c40-4c04-9e60-64d478a1738c/dqc_reference/reference_markers.hmm OceanDNA-b34903/protein.faa > /dev/null
[2023-03-15 07:29:36,605] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:29:36,605] [INFO] Found 6/6 markers.
[2023-03-15 07:29:36,630] [INFO] Query marker FASTA was written to OceanDNA-b34903/markers.fasta
[2023-03-15 07:29:36,632] [INFO] Task started: Blastn
[2023-03-15 07:29:36,632] [INFO] Running command: blastn -query OceanDNA-b34903/markers.fasta -db /var/lib/cwl/stgf82e35f7-0c40-4c04-9e60-64d478a1738c/dqc_reference/reference_markers.fasta -out OceanDNA-b34903/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:29:37,265] [INFO] Task succeeded: Blastn
[2023-03-15 07:29:37,266] [INFO] Selected 23 target genomes.
[2023-03-15 07:29:37,266] [INFO] Target genome list was writen to OceanDNA-b34903/target_genomes.txt
[2023-03-15 07:29:37,282] [INFO] Task started: fastANI
[2023-03-15 07:29:37,282] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2141c13-8c7e-4204-a548-ba9f6542c639/OceanDNA-b34903.fa --refList OceanDNA-b34903/target_genomes.txt --output OceanDNA-b34903/fastani_result.tsv --threads 1
[2023-03-15 07:29:53,471] [INFO] Task succeeded: fastANI
[2023-03-15 07:29:53,471] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf82e35f7-0c40-4c04-9e60-64d478a1738c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:29:53,472] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf82e35f7-0c40-4c04-9e60-64d478a1738c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:29:53,478] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:29:53,478] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 07:29:53,478] [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
Paraglaciecola arctica	strain=BSs20135	GCA_000314995.1	1128911	1128911	type	True	78.8934	459	1400	95	below_threshold
Paraglaciecola marina	strain=D3211	GCA_004360155.1	2500157	2500157	type	True	78.5191	219	1400	95	below_threshold
Paraglaciecola psychrophila	strain=170	GCA_000347635.1	326544	326544	type	True	78.2949	415	1400	95	below_threshold
Paraglaciecola psychrophila	strain=170	GCA_000315075.1	326544	326544	type	True	78.2429	417	1400	95	below_threshold
Paraglaciecola aquimarina	strain=GGW-M5	GCA_021532655.1	1235557	1235557	type	True	78.0942	257	1400	95	below_threshold
Paraglaciecola hydrolytica	strain=S66	GCA_001565895.1	1799789	1799789	type	True	77.4029	204	1400	95	below_threshold
Pseudoalteromonas neustonica	strain=PAMC 28425	GCA_001653135.1	1840331	1840331	type	True	76.0852	50	1400	95	below_threshold
Colwellia hornerae	strain=ACAM 607	GCA_007954355.1	89402	89402	type	True	75.9783	56	1400	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 07:29:53,478] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34903/tc_result.tsv
[2023-03-15 07:29:53,478] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:29:53,478] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:29:53,478] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf82e35f7-0c40-4c04-9e60-64d478a1738c/dqc_reference/checkm_data
[2023-03-15 07:29:53,479] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:29:53,485] [INFO] Task started: CheckM
[2023-03-15 07:29:53,485] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34903/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34903/checkm_input OceanDNA-b34903/checkm_result
[2023-03-15 07:30:50,251] [INFO] Task succeeded: CheckM
[2023-03-15 07:30:50,251] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.77%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 07:30:50,254] [INFO] ===== Completeness check finished =====
[2023-03-15 07:30:50,254] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:30:50,254] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34903/markers.fasta)
[2023-03-15 07:30:50,255] [INFO] Task started: Blastn
[2023-03-15 07:30:50,256] [INFO] Running command: blastn -query OceanDNA-b34903/markers.fasta -db /var/lib/cwl/stgf82e35f7-0c40-4c04-9e60-64d478a1738c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34903/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:30:51,273] [INFO] Task succeeded: Blastn
[2023-03-15 07:30:51,274] [INFO] Selected 18 target genomes.
[2023-03-15 07:30:51,274] [INFO] Target genome list was writen to OceanDNA-b34903/target_genomes_gtdb.txt
[2023-03-15 07:30:51,284] [INFO] Task started: fastANI
[2023-03-15 07:30:51,285] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2141c13-8c7e-4204-a548-ba9f6542c639/OceanDNA-b34903.fa --refList OceanDNA-b34903/target_genomes_gtdb.txt --output OceanDNA-b34903/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:31:05,332] [INFO] Task succeeded: fastANI
[2023-03-15 07:31:05,339] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 07:31:05,339] [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_003232445.1	s__Paraglaciecola arctica_A	78.9376	248	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000314995.1	s__Paraglaciecola arctica	78.9048	456	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002835935.1	s__Paraglaciecola sp002835935	78.6068	421	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004360155.1	s__Paraglaciecola sp004360155	78.5191	219	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018861065.1	s__Paraglaciecola arctica_B	78.4502	380	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000347635.1	s__Paraglaciecola psychrophila	78.3042	414	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	99.98	99.98	1.00	1.00	2	-
GCF_009796765.1	s__Paraglaciecola sp009796765	78.2558	246	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000315015.1	s__Paraglaciecola mesophila	77.9726	126	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	98.29	98.05	0.87	0.80	4	-
GCA_905479025.1	s__Paraglaciecola sp905479025	77.9064	201	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014225.1	s__Paraglaciecola atlantica_A	77.85	130	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860635.1	s__Aliiglaciecola lipolytica_A	77.7594	90	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliiglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373625.1	s__Alteromonas sp013373625	76.974	51	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 07:31:05,340] [INFO] GTDB search result was written to OceanDNA-b34903/result_gtdb.tsv
[2023-03-15 07:31:05,340] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:31:05,341] [INFO] DFAST_QC result json was written to OceanDNA-b34903/dqc_result.json
[2023-03-15 07:31:05,341] [INFO] DFAST_QC completed!
[2023-03-15 07:31:05,341] [INFO] Total running time: 0h1m54s