[2023-03-16 18:10:15,293] [INFO] DFAST_QC pipeline started.
[2023-03-16 18:10:15,294] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 18:10:15,294] [INFO] DQC Reference Directory: /var/lib/cwl/stge4bf792b-b225-4e1e-9b0c-75080c243571/dqc_reference
[2023-03-16 18:10:17,878] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 18:10:17,881] [INFO] Task started: Prodigal
[2023-03-16 18:10:17,881] [INFO] Running command: cat /var/lib/cwl/stg40dc27cb-baec-485e-884e-a4aa1ddfd541/OceanDNA-b27609.fa | prodigal -d OceanDNA-b27609/cds.fna -a OceanDNA-b27609/protein.faa -g 11 -q > /dev/null
[2023-03-16 18:10:34,381] [INFO] Task succeeded: Prodigal
[2023-03-16 18:10:34,381] [INFO] Task started: HMMsearch
[2023-03-16 18:10:34,381] [INFO] Running command: hmmsearch --tblout OceanDNA-b27609/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge4bf792b-b225-4e1e-9b0c-75080c243571/dqc_reference/reference_markers.hmm OceanDNA-b27609/protein.faa > /dev/null
[2023-03-16 18:10:34,579] [INFO] Task succeeded: HMMsearch
[2023-03-16 18:10:34,580] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg40dc27cb-baec-485e-884e-a4aa1ddfd541/OceanDNA-b27609.fa]
[2023-03-16 18:10:34,603] [INFO] Query marker FASTA was written to OceanDNA-b27609/markers.fasta
[2023-03-16 18:10:34,604] [INFO] Task started: Blastn
[2023-03-16 18:10:34,604] [INFO] Running command: blastn -query OceanDNA-b27609/markers.fasta -db /var/lib/cwl/stge4bf792b-b225-4e1e-9b0c-75080c243571/dqc_reference/reference_markers.fasta -out OceanDNA-b27609/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:10:35,178] [INFO] Task succeeded: Blastn
[2023-03-16 18:10:35,179] [INFO] Selected 20 target genomes.
[2023-03-16 18:10:35,180] [INFO] Target genome list was writen to OceanDNA-b27609/target_genomes.txt
[2023-03-16 18:10:35,236] [INFO] Task started: fastANI
[2023-03-16 18:10:35,236] [INFO] Running command: fastANI --query /var/lib/cwl/stg40dc27cb-baec-485e-884e-a4aa1ddfd541/OceanDNA-b27609.fa --refList OceanDNA-b27609/target_genomes.txt --output OceanDNA-b27609/fastani_result.tsv --threads 1
[2023-03-16 18:10:54,175] [INFO] Task succeeded: fastANI
[2023-03-16 18:10:54,176] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge4bf792b-b225-4e1e-9b0c-75080c243571/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 18:10:54,176] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge4bf792b-b225-4e1e-9b0c-75080c243571/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 18:10:54,188] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 18:10:54,190] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 18:10:54,190] [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
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	78.9916	363	702	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	76.5127	103	702	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	76.4653	71	702	95	below_threshold
Ruegeria marina	strain=CGMCC 1.9108	GCA_900101475.1	639004	639004	type	True	76.449	101	702	95	below_threshold
Roseovarius litoreus	strain=DSM 28249	GCA_900142765.1	1155722	1155722	type	True	76.4201	85	702	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	76.3687	112	702	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	76.3685	112	702	95	below_threshold
Aliiroseovarius marinus	strain=A6024	GCA_004360145.1	2500159	2500159	type	True	76.3338	67	702	95	below_threshold
Puniceibacterium sediminis	strain=DSM 29052	GCA_900188035.1	1608407	1608407	type	True	76.278	75	702	95	below_threshold
Aliiroseovarius pelagivivens	strain=CECT 8811	GCA_900302485.1	1639690	1639690	type	True	76.2114	51	702	95	below_threshold
Sulfitobacter litoralis	strain=DSM 17584	GCA_900103185.1	335975	335975	type	True	76.1259	69	702	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.0687	73	702	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	76.0516	55	702	95	below_threshold
Actibacterium atlanticum	strain=22II-S11-z10	GCA_000671395.1	1461693	1461693	type	True	76.0388	62	702	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	75.9958	75	702	95	below_threshold
Profundibacter amoris	strain=BAR1	GCA_003544895.1	2171755	2171755	type	True	75.9539	62	702	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	75.6404	58	702	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 18:10:54,191] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27609/tc_result.tsv
[2023-03-16 18:10:54,191] [INFO] ===== Taxonomy check completed =====
[2023-03-16 18:10:54,191] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 18:10:54,191] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge4bf792b-b225-4e1e-9b0c-75080c243571/dqc_reference/checkm_data
[2023-03-16 18:10:54,193] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 18:10:54,309] [INFO] Task started: CheckM
[2023-03-16 18:10:54,309] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27609/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27609/checkm_input OceanDNA-b27609/checkm_result
[2023-03-16 18:11:38,101] [INFO] Task succeeded: CheckM
[2023-03-16 18:11:38,101] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 33.05%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 18:11:38,106] [INFO] ===== Completeness check finished =====
[2023-03-16 18:11:38,106] [INFO] ===== Start GTDB Search =====
[2023-03-16 18:11:38,106] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27609/markers.fasta)
[2023-03-16 18:11:38,107] [INFO] Task started: Blastn
[2023-03-16 18:11:38,107] [INFO] Running command: blastn -query OceanDNA-b27609/markers.fasta -db /var/lib/cwl/stge4bf792b-b225-4e1e-9b0c-75080c243571/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27609/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:11:38,859] [INFO] Task succeeded: Blastn
[2023-03-16 18:11:38,860] [INFO] Selected 22 target genomes.
[2023-03-16 18:11:38,860] [INFO] Target genome list was writen to OceanDNA-b27609/target_genomes_gtdb.txt
[2023-03-16 18:11:39,124] [INFO] Task started: fastANI
[2023-03-16 18:11:39,125] [INFO] Running command: fastANI --query /var/lib/cwl/stg40dc27cb-baec-485e-884e-a4aa1ddfd541/OceanDNA-b27609.fa --refList OceanDNA-b27609/target_genomes_gtdb.txt --output OceanDNA-b27609/fastani_result_gtdb.tsv --threads 1
[2023-03-16 18:11:53,429] [INFO] Task succeeded: fastANI
[2023-03-16 18:11:53,440] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 18:11:53,440] [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_001262635.1	s__Aestuariivita boseongensis	78.9916	363	702	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507595.1	s__Ruegeria marisrubri	76.9694	97	702	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401465.1	s__Aestuariivita sp018401465	76.823	139	702	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	76.8204	107	702	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013032095.1	s__Ruegeria atlantica_E	76.7785	81	702	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017743935.1	s__Ruegeria_E sp017743935	76.7756	124	702	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019104745.1	s__CAU-1522 sp019104745	76.6433	87	702	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CAU-1522	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013035315.1	s__Ruegeria arenilitoris_D	76.6391	92	702	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	95.80	95.80	0.90	0.90	2	-
GCF_000152725.1	s__Pseudooceanicola batsensis	76.565	55	702	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938215.1	s__Ruegeria sediminis	76.5127	103	702	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015644665.1	s__Roseobacter sp015644665	76.4809	93	702	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016806125.1	s__AWRV01 sp000504185	76.4715	73	702	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__AWRV01	95.0	99.97	99.97	1.00	1.00	2	-
GCF_017743975.1	s__Ruegeria sp017743975	76.4338	109	702	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142765.1	s__Roseovarius litoreus	76.4201	85	702	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	95.85	95.85	0.86	0.86	2	-
GCF_003352045.1	s__JL08 sp003352045	76.3547	83	702	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JL08	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004360145.1	s__Aliiroseovarius marinus	76.3338	67	702	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013031405.1	s__Ruegeria sp013031405	76.294	108	702	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900302485.1	s__Aliiroseovarius pelagivivens	76.2114	51	702	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017311415.1	s__Salipiger abyssi_A	76.2026	71	702	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 18:11:53,441] [INFO] GTDB search result was written to OceanDNA-b27609/result_gtdb.tsv
[2023-03-16 18:11:53,442] [INFO] ===== GTDB Search completed =====
[2023-03-16 18:11:53,445] [INFO] DFAST_QC result json was written to OceanDNA-b27609/dqc_result.json
[2023-03-16 18:11:53,445] [INFO] DFAST_QC completed!
[2023-03-16 18:11:53,445] [INFO] Total running time: 0h1m38s