[2023-03-15 10:45:52,085] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:45:52,085] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:45:52,086] [INFO] DQC Reference Directory: /var/lib/cwl/stgbbdcc1af-8600-4aae-85a8-dad1744f8e73/dqc_reference
[2023-03-15 10:45:53,223] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:45:53,224] [INFO] Task started: Prodigal
[2023-03-15 10:45:53,224] [INFO] Running command: cat /var/lib/cwl/stgb37c2538-6f92-466f-937b-efc0f1ce8eb5/OceanDNA-b34223.fa | prodigal -d OceanDNA-b34223/cds.fna -a OceanDNA-b34223/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:46:04,471] [INFO] Task succeeded: Prodigal
[2023-03-15 10:46:04,471] [INFO] Task started: HMMsearch
[2023-03-15 10:46:04,471] [INFO] Running command: hmmsearch --tblout OceanDNA-b34223/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbbdcc1af-8600-4aae-85a8-dad1744f8e73/dqc_reference/reference_markers.hmm OceanDNA-b34223/protein.faa > /dev/null
[2023-03-15 10:46:04,647] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:46:04,648] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb37c2538-6f92-466f-937b-efc0f1ce8eb5/OceanDNA-b34223.fa]
[2023-03-15 10:46:04,662] [INFO] Query marker FASTA was written to OceanDNA-b34223/markers.fasta
[2023-03-15 10:46:04,664] [INFO] Task started: Blastn
[2023-03-15 10:46:04,664] [INFO] Running command: blastn -query OceanDNA-b34223/markers.fasta -db /var/lib/cwl/stgbbdcc1af-8600-4aae-85a8-dad1744f8e73/dqc_reference/reference_markers.fasta -out OceanDNA-b34223/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:46:05,289] [INFO] Task succeeded: Blastn
[2023-03-15 10:46:05,290] [INFO] Selected 28 target genomes.
[2023-03-15 10:46:05,291] [INFO] Target genome list was writen to OceanDNA-b34223/target_genomes.txt
[2023-03-15 10:46:05,403] [INFO] Task started: fastANI
[2023-03-15 10:46:05,404] [INFO] Running command: fastANI --query /var/lib/cwl/stgb37c2538-6f92-466f-937b-efc0f1ce8eb5/OceanDNA-b34223.fa --refList OceanDNA-b34223/target_genomes.txt --output OceanDNA-b34223/fastani_result.tsv --threads 1
[2023-03-15 10:46:23,330] [INFO] Task succeeded: fastANI
[2023-03-15 10:46:23,330] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbbdcc1af-8600-4aae-85a8-dad1744f8e73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:46:23,330] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbbdcc1af-8600-4aae-85a8-dad1744f8e73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:46:23,340] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:46:23,340] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 10:46:23,341] [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
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	77.1012	69	584	95	below_threshold
Ectothiorhodospira magna	strain=B7-7	GCA_900110965.1	867345	867345	type	True	76.7833	51	584	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	76.4206	54	584	95	below_threshold
Marichromatium bheemlicum	strain=DSM 18632	GCA_012276755.1	365339	365339	type	True	76.4011	54	584	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	76.2151	60	584	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.1911	52	584	95	below_threshold
Pseudomonas yangonensis	strain=MY50	GCA_009932725.1	2579922	2579922	type	True	76.1566	50	584	95	below_threshold
Ectothiorhodospira marina	strain=DSM 241	GCA_900109495.1	1396821	1396821	type	True	76.1382	61	584	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.0706	72	584	95	below_threshold
Thiocapsa rosea	strain=DSM 235	GCA_003634315.1	69360	69360	type	True	76.0313	56	584	95	below_threshold
Pseudomonas oryzae	strain=KCTC 32247	GCA_900104805.1	1392877	1392877	type	True	75.9538	57	584	95	below_threshold
Methylococcus geothermalis	strain=IM1	GCA_012769535.1	2681310	2681310	type	True	75.9423	50	584	95	below_threshold
Methyloterricola oryzae	strain=73a	GCA_000934725.1	1495050	1495050	type	True	75.7518	55	584	95	below_threshold
Aquisalimonas asiatica	strain=CGMCC 1.6291	GCA_900110585.1	406100	406100	type	True	75.7341	54	584	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	75.6093	53	584	95	below_threshold
Azotobacter chroococcum subsp. isscasi	strain=P205	GCA_004327895.1	2528971	353	type	True	75.5608	66	584	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 10:46:23,341] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34223/tc_result.tsv
[2023-03-15 10:46:23,341] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:46:23,341] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:46:23,341] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbbdcc1af-8600-4aae-85a8-dad1744f8e73/dqc_reference/checkm_data
[2023-03-15 10:46:23,342] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:46:23,345] [INFO] Task started: CheckM
[2023-03-15 10:46:23,345] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34223/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34223/checkm_input OceanDNA-b34223/checkm_result
[2023-03-15 10:46:55,338] [INFO] Task succeeded: CheckM
[2023-03-15 10:46:55,338] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.59%
Contamintation: 5.30%
Strain heterogeneity: 80.00%
--------------------------------------------------------------------------------
[2023-03-15 10:46:55,340] [INFO] ===== Completeness check finished =====
[2023-03-15 10:46:55,340] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:46:55,340] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34223/markers.fasta)
[2023-03-15 10:46:55,342] [INFO] Task started: Blastn
[2023-03-15 10:46:55,342] [INFO] Running command: blastn -query OceanDNA-b34223/markers.fasta -db /var/lib/cwl/stgbbdcc1af-8600-4aae-85a8-dad1744f8e73/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34223/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:46:56,351] [INFO] Task succeeded: Blastn
[2023-03-15 10:46:56,352] [INFO] Selected 29 target genomes.
[2023-03-15 10:46:56,352] [INFO] Target genome list was writen to OceanDNA-b34223/target_genomes_gtdb.txt
[2023-03-15 10:46:57,098] [INFO] Task started: fastANI
[2023-03-15 10:46:57,098] [INFO] Running command: fastANI --query /var/lib/cwl/stgb37c2538-6f92-466f-937b-efc0f1ce8eb5/OceanDNA-b34223.fa --refList OceanDNA-b34223/target_genomes_gtdb.txt --output OceanDNA-b34223/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:47:14,807] [INFO] Task succeeded: fastANI
[2023-03-15 10:47:14,816] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 10:47:14,816] [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_002356355.1	s__Thiohalobacter thiocyanaticus_A	77.0654	89	584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	98.53	98.53	0.93	0.93	2	-
GCF_000021985.1	s__Thioalkalivibrio_A sulfidiphilus	76.9565	95	584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390365.1	s__SLIM01 sp011390365	76.8803	71	584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__SLIM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699185.1	s__Thiohalobacter sp002699185	76.8126	72	584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019136395.1	s__M0108 sp019136395	76.7773	67	584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__M0108	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016584115.1	s__Ectothiorhodospira mobilis	76.622	75	584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Ectothiorhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051715.1	s__HyVt-443 sp011051715	76.5856	94	584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__HyVt-443	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009497875.2	s__JADGBD01 sp009497875	76.4976	83	584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__JADGBD01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341245.1	s__Plasticicumulans_A lactativorans	76.1965	62	584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000016565.1	s__Pseudomonas_E mendocina_A	76.097	55	584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.76	97.37	0.90	0.88	7	-
GCA_003989065.1	s__RXIW01 sp003989065	76.0461	52	584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__RXIW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104805.1	s__Pseudomonas_K oryzae	75.9538	57	584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101755.1	s__Pseudomonas_E alcaliphila	75.9215	53	584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.74	97.49	0.95	0.92	3	-
GCF_001512295.1	s__Pseudomonas_B sp001512295	75.9073	54	584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004521985.1	s__Pseudomonas_E khazarica	75.7839	61	584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.35	98.01	0.91	0.87	12	-
--------------------------------------------------------------------------------
[2023-03-15 10:47:14,816] [INFO] GTDB search result was written to OceanDNA-b34223/result_gtdb.tsv
[2023-03-15 10:47:14,816] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:47:14,818] [INFO] DFAST_QC result json was written to OceanDNA-b34223/dqc_result.json
[2023-03-15 10:47:14,818] [INFO] DFAST_QC completed!
[2023-03-15 10:47:14,818] [INFO] Total running time: 0h1m23s