[2023-03-15 20:34:26,719] [INFO] DFAST_QC pipeline started.
[2023-03-15 20:34:26,719] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 20:34:26,719] [INFO] DQC Reference Directory: /var/lib/cwl/stgeb23ab74-9318-4e13-a550-9424193c8a1d/dqc_reference
[2023-03-15 20:34:28,460] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 20:34:28,460] [INFO] Task started: Prodigal
[2023-03-15 20:34:28,461] [INFO] Running command: cat /var/lib/cwl/stg4a242da7-70c9-412a-8f66-ee601726d19b/OceanDNA-b38508.fa | prodigal -d OceanDNA-b38508/cds.fna -a OceanDNA-b38508/protein.faa -g 11 -q > /dev/null
[2023-03-15 20:34:39,261] [INFO] Task succeeded: Prodigal
[2023-03-15 20:34:39,261] [INFO] Task started: HMMsearch
[2023-03-15 20:34:39,261] [INFO] Running command: hmmsearch --tblout OceanDNA-b38508/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeb23ab74-9318-4e13-a550-9424193c8a1d/dqc_reference/reference_markers.hmm OceanDNA-b38508/protein.faa > /dev/null
[2023-03-15 20:34:39,428] [INFO] Task succeeded: HMMsearch
[2023-03-15 20:34:39,428] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4a242da7-70c9-412a-8f66-ee601726d19b/OceanDNA-b38508.fa]
[2023-03-15 20:34:39,447] [INFO] Query marker FASTA was written to OceanDNA-b38508/markers.fasta
[2023-03-15 20:34:39,447] [INFO] Task started: Blastn
[2023-03-15 20:34:39,447] [INFO] Running command: blastn -query OceanDNA-b38508/markers.fasta -db /var/lib/cwl/stgeb23ab74-9318-4e13-a550-9424193c8a1d/dqc_reference/reference_markers.fasta -out OceanDNA-b38508/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 20:34:39,941] [INFO] Task succeeded: Blastn
[2023-03-15 20:34:39,942] [INFO] Selected 17 target genomes.
[2023-03-15 20:34:39,942] [INFO] Target genome list was writen to OceanDNA-b38508/target_genomes.txt
[2023-03-15 20:34:39,953] [INFO] Task started: fastANI
[2023-03-15 20:34:39,953] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a242da7-70c9-412a-8f66-ee601726d19b/OceanDNA-b38508.fa --refList OceanDNA-b38508/target_genomes.txt --output OceanDNA-b38508/fastani_result.tsv --threads 1
[2023-03-15 20:34:50,328] [INFO] Task succeeded: fastANI
[2023-03-15 20:34:50,328] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeb23ab74-9318-4e13-a550-9424193c8a1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 20:34:50,328] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeb23ab74-9318-4e13-a550-9424193c8a1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 20:34:50,334] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2023-03-15 20:34:50,334] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 20:34:50,334] [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
Marinomonas communis	strain=DSM 5604	GCA_004363305.1	28254	28254	type	True	97.6215	583	603	95	conclusive
Marinomonas aquimarina	strain=11SM4	GCA_001639695.1	295068	295068	type	True	81.6868	307	603	95	below_threshold
Marinomonas aquimarina	strain=CECT 5080	GCA_900089755.1	295068	295068	type	True	81.6313	310	603	95	below_threshold
Marinomonas fungiae	strain=JCM 18476	GCA_001517305.1	1137284	1137284	type	True	81.6238	305	603	95	below_threshold
Marinomonas fungiae	strain=JCM 18476	GCA_001418205.1	1137284	1137284	type	True	81.6238	305	603	95	below_threshold
Marinomonas ostreistagni	strain=UST010306-043	GCA_016888445.1	359209	359209	type	True	80.6436	210	603	95	below_threshold
Marinomonas atlantica	strain=Cmf 18.22	GCA_001639725.1	1806668	1806668	type	True	80.1749	262	603	95	below_threshold
Marinomonas gallaica	strain=Cmf 17.2	GCA_001639745.1	1806667	1806667	type	True	79.9884	286	603	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 20:34:50,335] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38508/tc_result.tsv
[2023-03-15 20:34:50,335] [INFO] ===== Taxonomy check completed =====
[2023-03-15 20:34:50,335] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 20:34:50,335] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeb23ab74-9318-4e13-a550-9424193c8a1d/dqc_reference/checkm_data
[2023-03-15 20:34:50,336] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 20:34:50,340] [INFO] Task started: CheckM
[2023-03-15 20:34:50,340] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38508/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38508/checkm_input OceanDNA-b38508/checkm_result
[2023-03-15 20:35:21,914] [INFO] Task succeeded: CheckM
[2023-03-15 20:35:21,915] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.81%
Contamintation: 5.56%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-15 20:35:21,998] [INFO] ===== Completeness check finished =====
[2023-03-15 20:35:21,998] [INFO] ===== Start GTDB Search =====
[2023-03-15 20:35:21,998] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38508/markers.fasta)
[2023-03-15 20:35:21,998] [INFO] Task started: Blastn
[2023-03-15 20:35:21,999] [INFO] Running command: blastn -query OceanDNA-b38508/markers.fasta -db /var/lib/cwl/stgeb23ab74-9318-4e13-a550-9424193c8a1d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38508/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 20:35:22,664] [INFO] Task succeeded: Blastn
[2023-03-15 20:35:22,665] [INFO] Selected 13 target genomes.
[2023-03-15 20:35:22,665] [INFO] Target genome list was writen to OceanDNA-b38508/target_genomes_gtdb.txt
[2023-03-15 20:35:22,675] [INFO] Task started: fastANI
[2023-03-15 20:35:22,676] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a242da7-70c9-412a-8f66-ee601726d19b/OceanDNA-b38508.fa --refList OceanDNA-b38508/target_genomes_gtdb.txt --output OceanDNA-b38508/fastani_result_gtdb.tsv --threads 1
[2023-03-15 20:35:30,880] [INFO] Task succeeded: fastANI
[2023-03-15 20:35:30,886] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 20:35:30,886] [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_004363305.1	s__Marinomonas communis	97.6215	583	603	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	97.16	97.04	0.89	0.87	3	conclusive
GCF_016461785.1	s__Marinomonas ostreistagni_A	88.9059	519	603	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418205.1	s__Marinomonas fungiae	81.6238	305	603	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900089755.1	s__Marinomonas aquimarina	81.6082	311	603	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016888445.1	s__Marinomonas ostreistagni	80.6436	210	603	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001639725.1	s__Marinomonas atlantica	80.1749	262	603	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001639745.1	s__Marinomonas gallaica	79.9884	286	603	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	96.95	96.94	0.89	0.89	3	-
GCF_016463975.1	s__Marinomonas sp016463975	77.861	84	603	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 20:35:30,886] [INFO] GTDB search result was written to OceanDNA-b38508/result_gtdb.tsv
[2023-03-15 20:35:30,886] [INFO] ===== GTDB Search completed =====
[2023-03-15 20:35:30,887] [INFO] DFAST_QC result json was written to OceanDNA-b38508/dqc_result.json
[2023-03-15 20:35:30,887] [INFO] DFAST_QC completed!
[2023-03-15 20:35:30,887] [INFO] Total running time: 0h1m4s