[2023-03-15 04:14:00,547] [INFO] DFAST_QC pipeline started.
[2023-03-15 04:14:00,547] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 04:14:00,547] [INFO] DQC Reference Directory: /var/lib/cwl/stg140e96d1-0653-4fa4-a825-672454795add/dqc_reference
[2023-03-15 04:14:01,681] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 04:14:01,682] [INFO] Task started: Prodigal
[2023-03-15 04:14:01,682] [INFO] Running command: cat /var/lib/cwl/stgb90f2f12-7afe-4808-88ae-b828318174a6/OceanDNA-b7318.fa | prodigal -d OceanDNA-b7318/cds.fna -a OceanDNA-b7318/protein.faa -g 11 -q > /dev/null
[2023-03-15 04:14:11,949] [INFO] Task succeeded: Prodigal
[2023-03-15 04:14:11,950] [INFO] Task started: HMMsearch
[2023-03-15 04:14:11,950] [INFO] Running command: hmmsearch --tblout OceanDNA-b7318/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg140e96d1-0653-4fa4-a825-672454795add/dqc_reference/reference_markers.hmm OceanDNA-b7318/protein.faa > /dev/null
[2023-03-15 04:14:12,112] [INFO] Task succeeded: HMMsearch
[2023-03-15 04:14:12,113] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb90f2f12-7afe-4808-88ae-b828318174a6/OceanDNA-b7318.fa]
[2023-03-15 04:14:12,157] [INFO] Query marker FASTA was written to OceanDNA-b7318/markers.fasta
[2023-03-15 04:14:12,159] [INFO] Task started: Blastn
[2023-03-15 04:14:12,159] [INFO] Running command: blastn -query OceanDNA-b7318/markers.fasta -db /var/lib/cwl/stg140e96d1-0653-4fa4-a825-672454795add/dqc_reference/reference_markers.fasta -out OceanDNA-b7318/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:14:12,786] [INFO] Task succeeded: Blastn
[2023-03-15 04:14:12,796] [INFO] Selected 26 target genomes.
[2023-03-15 04:14:12,797] [INFO] Target genome list was writen to OceanDNA-b7318/target_genomes.txt
[2023-03-15 04:14:12,816] [INFO] Task started: fastANI
[2023-03-15 04:14:12,816] [INFO] Running command: fastANI --query /var/lib/cwl/stgb90f2f12-7afe-4808-88ae-b828318174a6/OceanDNA-b7318.fa --refList OceanDNA-b7318/target_genomes.txt --output OceanDNA-b7318/fastani_result.tsv --threads 1
[2023-03-15 04:14:27,950] [INFO] Task succeeded: fastANI
[2023-03-15 04:14:27,950] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg140e96d1-0653-4fa4-a825-672454795add/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 04:14:27,950] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg140e96d1-0653-4fa4-a825-672454795add/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 04:14:27,970] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 04:14:27,970] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 04:14:27,970] [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
Psychroserpens jangbogonensis	strain=PAMC 27130	GCA_000797465.1	1484460	1484460	type	True	76.4094	54	469	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	76.2879	70	469	95	below_threshold
Olleya marilimosa	strain=CAM030	GCA_000518485.1	272164	272164	type	True	76.2054	59	469	95	below_threshold
Formosa sediminum	strain=PS13	GCA_007197735.1	2594004	2594004	type	True	76.1971	53	469	95	below_threshold
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	76.0424	62	469	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	76.0424	62	469	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	76.0042	59	469	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	75.9226	69	469	95	below_threshold
Winogradskyella undariae	strain=CCUG 63832	GCA_013285155.1	1285465	1285465	type	True	75.9061	62	469	95	below_threshold
Olleya aquimaris	strain=DSM 24464	GCA_003259525.1	639310	639310	type	True	75.8918	57	469	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	75.8857	57	469	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	75.7907	55	469	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	75.7606	51	469	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	75.6941	58	469	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	75.6193	61	469	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 04:14:27,970] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7318/tc_result.tsv
[2023-03-15 04:14:27,971] [INFO] ===== Taxonomy check completed =====
[2023-03-15 04:14:27,971] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 04:14:27,971] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg140e96d1-0653-4fa4-a825-672454795add/dqc_reference/checkm_data
[2023-03-15 04:14:27,972] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 04:14:27,976] [INFO] Task started: CheckM
[2023-03-15 04:14:27,976] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7318/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7318/checkm_input OceanDNA-b7318/checkm_result
[2023-03-15 04:15:00,632] [INFO] Task succeeded: CheckM
[2023-03-15 04:15:00,632] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.09%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 04:15:00,634] [INFO] ===== Completeness check finished =====
[2023-03-15 04:15:00,635] [INFO] ===== Start GTDB Search =====
[2023-03-15 04:15:00,635] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7318/markers.fasta)
[2023-03-15 04:15:00,636] [INFO] Task started: Blastn
[2023-03-15 04:15:00,636] [INFO] Running command: blastn -query OceanDNA-b7318/markers.fasta -db /var/lib/cwl/stg140e96d1-0653-4fa4-a825-672454795add/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7318/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:15:01,674] [INFO] Task succeeded: Blastn
[2023-03-15 04:15:01,676] [INFO] Selected 9 target genomes.
[2023-03-15 04:15:01,676] [INFO] Target genome list was writen to OceanDNA-b7318/target_genomes_gtdb.txt
[2023-03-15 04:15:01,708] [INFO] Task started: fastANI
[2023-03-15 04:15:01,708] [INFO] Running command: fastANI --query /var/lib/cwl/stgb90f2f12-7afe-4808-88ae-b828318174a6/OceanDNA-b7318.fa --refList OceanDNA-b7318/target_genomes_gtdb.txt --output OceanDNA-b7318/fastani_result_gtdb.tsv --threads 1
[2023-03-15 04:15:05,677] [INFO] Task succeeded: fastANI
[2023-03-15 04:15:05,684] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 04:15:05,684] [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_018608725.1	s__Hel1-33-131 sp018608725	91.8065	348	469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608765.1	s__Hel1-33-131 sp018608765	84.0078	353	469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001735745.1	s__Hel1-33-131 sp001735745	83.0087	354	469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018673215.1	s__Hel1-33-131 sp018673215	82.1513	332	469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608735.1	s__Hel1-33-131 sp018608735	80.0555	247	469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479095.1	s__Hel1-33-131 sp905479095	79.3911	254	469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181825.1	s__Hel1-33-131 sp905181825	77.9645	164	469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	99.01	99.01	0.77	0.77	2	-
GCA_018608625.1	s__Hel1-33-131 sp018608625	77.6492	175	469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	98.93	97.98	0.88	0.82	3	-
GCF_003387355.1	s__Winogradskyella sediminis	75.767	56	469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.63	98.63	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-03-15 04:15:05,684] [INFO] GTDB search result was written to OceanDNA-b7318/result_gtdb.tsv
[2023-03-15 04:15:05,685] [INFO] ===== GTDB Search completed =====
[2023-03-15 04:15:05,686] [INFO] DFAST_QC result json was written to OceanDNA-b7318/dqc_result.json
[2023-03-15 04:15:05,686] [INFO] DFAST_QC completed!
[2023-03-15 04:15:05,686] [INFO] Total running time: 0h1m5s