[2023-03-14 12:33:23,793] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:33:23,793] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:33:23,793] [INFO] DQC Reference Directory: /var/lib/cwl/stg35aebf96-e7cd-4c0f-8c77-477320fee88d/dqc_reference
[2023-03-14 12:33:24,905] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:33:24,906] [INFO] Task started: Prodigal
[2023-03-14 12:33:24,906] [INFO] Running command: cat /var/lib/cwl/stgbdb029bd-ce40-4931-a374-cc1ee41b8082/OceanDNA-b38492.fa | prodigal -d OceanDNA-b38492/cds.fna -a OceanDNA-b38492/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:33:42,542] [INFO] Task succeeded: Prodigal
[2023-03-14 12:33:42,542] [INFO] Task started: HMMsearch
[2023-03-14 12:33:42,542] [INFO] Running command: hmmsearch --tblout OceanDNA-b38492/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg35aebf96-e7cd-4c0f-8c77-477320fee88d/dqc_reference/reference_markers.hmm OceanDNA-b38492/protein.faa > /dev/null
[2023-03-14 12:33:42,740] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:33:42,741] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgbdb029bd-ce40-4931-a374-cc1ee41b8082/OceanDNA-b38492.fa]
[2023-03-14 12:33:42,763] [INFO] Query marker FASTA was written to OceanDNA-b38492/markers.fasta
[2023-03-14 12:33:42,763] [INFO] Task started: Blastn
[2023-03-14 12:33:42,763] [INFO] Running command: blastn -query OceanDNA-b38492/markers.fasta -db /var/lib/cwl/stg35aebf96-e7cd-4c0f-8c77-477320fee88d/dqc_reference/reference_markers.fasta -out OceanDNA-b38492/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:33:43,324] [INFO] Task succeeded: Blastn
[2023-03-14 12:33:43,325] [INFO] Selected 13 target genomes.
[2023-03-14 12:33:43,325] [INFO] Target genome list was writen to OceanDNA-b38492/target_genomes.txt
[2023-03-14 12:33:43,334] [INFO] Task started: fastANI
[2023-03-14 12:33:43,334] [INFO] Running command: fastANI --query /var/lib/cwl/stgbdb029bd-ce40-4931-a374-cc1ee41b8082/OceanDNA-b38492.fa --refList OceanDNA-b38492/target_genomes.txt --output OceanDNA-b38492/fastani_result.tsv --threads 1
[2023-03-14 12:33:53,633] [INFO] Task succeeded: fastANI
[2023-03-14 12:33:53,634] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg35aebf96-e7cd-4c0f-8c77-477320fee88d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:33:53,634] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg35aebf96-e7cd-4c0f-8c77-477320fee88d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:33:53,641] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:33:53,641] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 12:33:53,641] [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 arctica	strain=328	GCA_003259225.1	383750	383750	type	True	92.6804	905	1035	95	below_threshold
Marinomonas arctica	strain=CGMCC 1.6498	GCA_014645175.1	383750	383750	type	True	92.5904	921	1035	95	below_threshold
Marinomonas shanghaiensis	strain=DSL-35	GCA_003259175.1	2202418	2202418	type	True	85.5152	861	1035	95	below_threshold
Marinomonas polaris	strain=DSM 16579	GCA_900129155.1	293552	293552	type	True	82.4715	784	1035	95	below_threshold
Marinomonas lutimaris	strain=E165	GCA_019426345.1	2846746	2846746	type	True	81.9923	755	1035	95	below_threshold
Marinomonas profundi	strain=M1K-6	GCA_012584435.1	2726122	2726122	type	True	81.0875	620	1035	95	below_threshold
Marinomonas alcarazii	strain=CECT 7730	GCA_003208215.1	491949	491949	type	True	80.8737	606	1035	95	below_threshold
Marinomonas rhizomae	strain=IVIA-Po-145	GCA_003721275.1	491948	491948	type	True	80.8214	625	1035	95	below_threshold
Marinomonas foliarum	strain=CECT 7731	GCA_003337275.1	491950	491950	type	True	80.8123	596	1035	95	below_threshold
Marinomonas primoryensis	strain=MPKMM3633	GCA_013372285.1	178399	178399	type	True	79.469	530	1035	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 12:33:53,737] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38492/tc_result.tsv
[2023-03-14 12:33:53,737] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:33:53,737] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:33:53,737] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg35aebf96-e7cd-4c0f-8c77-477320fee88d/dqc_reference/checkm_data
[2023-03-14 12:33:53,738] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:33:53,744] [INFO] Task started: CheckM
[2023-03-14 12:33:53,744] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38492/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38492/checkm_input OceanDNA-b38492/checkm_result
[2023-03-14 12:34:39,994] [INFO] Task succeeded: CheckM
[2023-03-14 12:34:39,994] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 12:34:39,997] [INFO] ===== Completeness check finished =====
[2023-03-14 12:34:39,997] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:34:39,997] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38492/markers.fasta)
[2023-03-14 12:34:39,998] [INFO] Task started: Blastn
[2023-03-14 12:34:39,999] [INFO] Running command: blastn -query OceanDNA-b38492/markers.fasta -db /var/lib/cwl/stg35aebf96-e7cd-4c0f-8c77-477320fee88d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38492/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:34:40,783] [INFO] Task succeeded: Blastn
[2023-03-14 12:34:40,784] [INFO] Selected 9 target genomes.
[2023-03-14 12:34:40,785] [INFO] Target genome list was writen to OceanDNA-b38492/target_genomes_gtdb.txt
[2023-03-14 12:34:40,789] [INFO] Task started: fastANI
[2023-03-14 12:34:40,790] [INFO] Running command: fastANI --query /var/lib/cwl/stgbdb029bd-ce40-4931-a374-cc1ee41b8082/OceanDNA-b38492.fa --refList OceanDNA-b38492/target_genomes_gtdb.txt --output OceanDNA-b38492/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:34:49,317] [INFO] Task succeeded: fastANI
[2023-03-14 12:34:49,323] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 12:34:49,323] [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_003259225.1	s__Marinomonas arctica	92.6804	905	1035	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	100.00	100.00	1.00	1.00	3	-
GCF_003259175.1	s__Marinomonas shanghaiensis	85.5152	861	1035	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129155.1	s__Marinomonas polaris	82.4786	783	1035	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	97.53	97.35	0.90	0.88	9	-
GCF_018336955.1	s__Marinomonas sp018336955	82.0723	744	1035	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000017285.1	s__Marinomonas sp000017285	81.7618	747	1035	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.39	98.39	0.88	0.88	2	-
GCF_012584435.1	s__Marinomonas sp012584435	81.0943	619	1035	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315485.1	s__Marinomonas rhizomae	80.8912	624	1035	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003208215.1	s__Marinomonas alcarazii	80.8884	604	1035	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.70	98.70	0.93	0.93	2	-
GCF_003337275.1	s__Marinomonas foliarum	80.8407	593	1035	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.18	98.18	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-03-14 12:34:49,323] [INFO] GTDB search result was written to OceanDNA-b38492/result_gtdb.tsv
[2023-03-14 12:34:49,323] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:34:49,325] [INFO] DFAST_QC result json was written to OceanDNA-b38492/dqc_result.json
[2023-03-14 12:34:49,325] [INFO] DFAST_QC completed!
[2023-03-14 12:34:49,325] [INFO] Total running time: 0h1m26s