[2023-03-18 09:26:42,703] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:26:42,703] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:26:42,703] [INFO] DQC Reference Directory: /var/lib/cwl/stgd455d8e8-8e60-471b-b7e0-c2fd4bca9193/dqc_reference
[2023-03-18 09:26:43,798] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:26:43,799] [INFO] Task started: Prodigal
[2023-03-18 09:26:43,799] [INFO] Running command: cat /var/lib/cwl/stg121cc199-c1d8-4ef9-bbe8-d64675c1afdd/OceanDNA-b34924.fa | prodigal -d OceanDNA-b34924/cds.fna -a OceanDNA-b34924/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:27:12,262] [INFO] Task succeeded: Prodigal
[2023-03-18 09:27:12,263] [INFO] Task started: HMMsearch
[2023-03-18 09:27:12,263] [INFO] Running command: hmmsearch --tblout OceanDNA-b34924/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd455d8e8-8e60-471b-b7e0-c2fd4bca9193/dqc_reference/reference_markers.hmm OceanDNA-b34924/protein.faa > /dev/null
[2023-03-18 09:27:12,497] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:27:12,498] [INFO] Found 6/6 markers.
[2023-03-18 09:27:12,525] [INFO] Query marker FASTA was written to OceanDNA-b34924/markers.fasta
[2023-03-18 09:27:12,526] [INFO] Task started: Blastn
[2023-03-18 09:27:12,526] [INFO] Running command: blastn -query OceanDNA-b34924/markers.fasta -db /var/lib/cwl/stgd455d8e8-8e60-471b-b7e0-c2fd4bca9193/dqc_reference/reference_markers.fasta -out OceanDNA-b34924/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:27:13,176] [INFO] Task succeeded: Blastn
[2023-03-18 09:27:13,176] [INFO] Selected 22 target genomes.
[2023-03-18 09:27:13,177] [INFO] Target genome list was writen to OceanDNA-b34924/target_genomes.txt
[2023-03-18 09:27:13,187] [INFO] Task started: fastANI
[2023-03-18 09:27:13,187] [INFO] Running command: fastANI --query /var/lib/cwl/stg121cc199-c1d8-4ef9-bbe8-d64675c1afdd/OceanDNA-b34924.fa --refList OceanDNA-b34924/target_genomes.txt --output OceanDNA-b34924/fastani_result.tsv --threads 1
[2023-03-18 09:27:28,771] [INFO] Task succeeded: fastANI
[2023-03-18 09:27:28,771] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd455d8e8-8e60-471b-b7e0-c2fd4bca9193/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:27:28,771] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd455d8e8-8e60-471b-b7e0-c2fd4bca9193/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:27:28,780] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 09:27:28,780] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 09:27:28,780] [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 mesophila	strain=KMM 241	GCA_000315015.1	197222	197222	type	True	98.7018	1476	1669	95	conclusive
Paraglaciecola polaris	strain=LMG 21857	GCA_000315055.1	222814	222814	type	True	80.5397	698	1669	95	below_threshold
Paraglaciecola aquimarina	strain=GGW-M5	GCA_021532655.1	1235557	1235557	type	True	78.0252	137	1669	95	below_threshold
Paraglaciecola hydrolytica	strain=S66	GCA_001565895.1	1799789	1799789	type	True	77.9859	172	1669	95	below_threshold
Alteromonas lipotrueae	strain=MD_652	GCA_019249215.1	2803814	2803814	type	True	77.64	116	1669	95	below_threshold
Alteromonas hispanica	strain=LMG 22958	GCA_010500915.1	315421	315421	type	True	77.5645	74	1669	95	below_threshold
Paraglaciecola marina	strain=D3211	GCA_004360155.1	2500157	2500157	type	True	77.5618	140	1669	95	below_threshold
Paraglaciecola arctica	strain=BSs20135	GCA_000314995.1	1128911	1128911	type	True	77.3958	168	1669	95	below_threshold
Aliiglaciecola lipolytica	strain=E3	GCA_000314975.1	477689	477689	type	True	77.3594	104	1669	95	below_threshold
Glaciecola pallidula	strain=DSM 14239	GCA_000428905.1	56807	56807	type	True	77.2307	66	1669	95	below_threshold
Glaciecola pallidula	strain=ACAM 615	GCA_000315035.1	56807	56807	type	True	77.1984	65	1669	95	below_threshold
Alteromonas naphthalenivorans	strain=SN2	GCA_000213655.1	715451	715451	type	True	77.1661	116	1669	95	below_threshold
Alteromonas genovensis	strain=LMG 24078	GCA_010500895.1	471225	471225	type	True	77.129	101	1669	95	below_threshold
Alteromonas confluentis	strain=KCTC 42603	GCA_001757105.1	1656094	1656094	type	True	77.035	66	1669	95	below_threshold
Alteromonas oceanisediminis	strain=SM 2104	GCA_018474025.1	2836180	2836180	type	True	76.7936	51	1669	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 09:27:28,781] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34924/tc_result.tsv
[2023-03-18 09:27:28,781] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:27:28,781] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:27:28,781] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd455d8e8-8e60-471b-b7e0-c2fd4bca9193/dqc_reference/checkm_data
[2023-03-18 09:27:28,782] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:27:28,896] [INFO] Task started: CheckM
[2023-03-18 09:27:28,896] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34924/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34924/checkm_input OceanDNA-b34924/checkm_result
[2023-03-18 09:28:37,723] [INFO] Task succeeded: CheckM
[2023-03-18 09:28:37,724] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 09:28:37,727] [INFO] ===== Completeness check finished =====
[2023-03-18 09:28:37,727] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:28:37,727] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34924/markers.fasta)
[2023-03-18 09:28:37,727] [INFO] Task started: Blastn
[2023-03-18 09:28:37,727] [INFO] Running command: blastn -query OceanDNA-b34924/markers.fasta -db /var/lib/cwl/stgd455d8e8-8e60-471b-b7e0-c2fd4bca9193/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34924/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:28:38,751] [INFO] Task succeeded: Blastn
[2023-03-18 09:28:38,752] [INFO] Selected 9 target genomes.
[2023-03-18 09:28:38,752] [INFO] Target genome list was writen to OceanDNA-b34924/target_genomes_gtdb.txt
[2023-03-18 09:28:38,760] [INFO] Task started: fastANI
[2023-03-18 09:28:38,760] [INFO] Running command: fastANI --query /var/lib/cwl/stg121cc199-c1d8-4ef9-bbe8-d64675c1afdd/OceanDNA-b34924.fa --refList OceanDNA-b34924/target_genomes_gtdb.txt --output OceanDNA-b34924/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:28:47,561] [INFO] Task succeeded: fastANI
[2023-03-18 09:28:47,567] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 09:28:47,567] [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_000315015.1	s__Paraglaciecola mesophila	98.7018	1476	1669	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	98.29	98.05	0.87	0.80	4	conclusive
GCF_000014225.1	s__Paraglaciecola atlantica_A	91.0243	1437	1669	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000314955.1	s__Paraglaciecola chathamensis	83.2934	1074	1669	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	98.24	97.58	0.90	0.88	8	-
GCF_009906955.1	s__Paraglaciecola mesophila_A	82.1281	988	1669	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000315055.1	s__Paraglaciecola polaris	80.5395	698	1669	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011378905.1	s__Paraglaciecola sp011378905	80.4019	724	1669	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500915.1	s__Alteromonas hispanica	77.5645	74	1669	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.81	97.72	0.82	0.79	5	-
GCF_000314975.1	s__Aliiglaciecola lipolytica	77.3743	105	1669	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliiglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007197995.1	s__Aliiglaciecola sp007197995	77.2024	94	1669	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliiglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 09:28:47,568] [INFO] GTDB search result was written to OceanDNA-b34924/result_gtdb.tsv
[2023-03-18 09:28:47,568] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:28:47,569] [INFO] DFAST_QC result json was written to OceanDNA-b34924/dqc_result.json
[2023-03-18 09:28:47,569] [INFO] DFAST_QC completed!
[2023-03-18 09:28:47,569] [INFO] Total running time: 0h2m5s