[2023-03-18 03:09:33,546] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:09:33,546] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:09:33,546] [INFO] DQC Reference Directory: /var/lib/cwl/stg2bb476ae-569e-49b6-a887-7fd4b8efedf8/dqc_reference
[2023-03-18 03:09:34,689] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:09:34,689] [INFO] Task started: Prodigal
[2023-03-18 03:09:34,689] [INFO] Running command: cat /var/lib/cwl/stg9421e683-70bd-43bc-8afa-c091af95a898/OceanDNA-b38337.fa | prodigal -d OceanDNA-b38337/cds.fna -a OceanDNA-b38337/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:10:02,948] [INFO] Task succeeded: Prodigal
[2023-03-18 03:10:02,948] [INFO] Task started: HMMsearch
[2023-03-18 03:10:02,948] [INFO] Running command: hmmsearch --tblout OceanDNA-b38337/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2bb476ae-569e-49b6-a887-7fd4b8efedf8/dqc_reference/reference_markers.hmm OceanDNA-b38337/protein.faa > /dev/null
[2023-03-18 03:10:03,239] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:10:03,240] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg9421e683-70bd-43bc-8afa-c091af95a898/OceanDNA-b38337.fa]
[2023-03-18 03:10:03,267] [INFO] Query marker FASTA was written to OceanDNA-b38337/markers.fasta
[2023-03-18 03:10:03,268] [INFO] Task started: Blastn
[2023-03-18 03:10:03,268] [INFO] Running command: blastn -query OceanDNA-b38337/markers.fasta -db /var/lib/cwl/stg2bb476ae-569e-49b6-a887-7fd4b8efedf8/dqc_reference/reference_markers.fasta -out OceanDNA-b38337/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:10:04,113] [INFO] Task succeeded: Blastn
[2023-03-18 03:10:04,114] [INFO] Selected 16 target genomes.
[2023-03-18 03:10:04,114] [INFO] Target genome list was writen to OceanDNA-b38337/target_genomes.txt
[2023-03-18 03:10:04,123] [INFO] Task started: fastANI
[2023-03-18 03:10:04,123] [INFO] Running command: fastANI --query /var/lib/cwl/stg9421e683-70bd-43bc-8afa-c091af95a898/OceanDNA-b38337.fa --refList OceanDNA-b38337/target_genomes.txt --output OceanDNA-b38337/fastani_result.tsv --threads 1
[2023-03-18 03:10:18,990] [INFO] Task succeeded: fastANI
[2023-03-18 03:10:18,990] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2bb476ae-569e-49b6-a887-7fd4b8efedf8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:10:18,990] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2bb476ae-569e-49b6-a887-7fd4b8efedf8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:10:18,999] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 03:10:19,000] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 03:10:19,000] [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
Halomonas litopenaei	strain=SYSU ZJ2214	GCA_003045775.1	2109328	2109328	type	True	98.3581	1407	1503	95	conclusive
Halomonas halophila	strain=NBRC 102604	GCA_007989465.1	29573	29573	type	True	81.9711	676	1503	95	below_threshold
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	81.9549	657	1503	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	81.8222	725	1503	95	below_threshold
Halomonas campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	81.4455	645	1503	95	below_threshold
Halomonas urmiana	strain=TBZ3	GCA_005780185.1	490901	490901	type	True	81.4323	673	1503	95	below_threshold
Halomonas ventosae	strain=CECT 5797	GCA_004363555.1	229007	229007	type	True	81.3836	685	1503	95	below_threshold
Halomonas organivorans	strain=CECT 5995	GCA_014192055.1	257772	257772	type	True	81.3677	726	1503	95	below_threshold
Halomonas saccharevitans	strain=CGMCC 1.6493	GCA_900116405.1	416872	416872	type	True	81.3557	660	1503	95	below_threshold
Halomonas aestuarii	strain=Hb3	GCA_001886615.1	1897729	1897729	type	True	81.2948	671	1503	95	below_threshold
Halomonas heilongjiangensis	strain=9-2	GCA_003202165.1	1387883	1387883	type	True	81.1022	705	1503	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	80.8615	604	1503	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	80.702	644	1503	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	80.4334	588	1503	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	80.145	524	1503	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	80.0689	598	1503	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 03:10:19,000] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38337/tc_result.tsv
[2023-03-18 03:10:19,000] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:10:19,000] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:10:19,000] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2bb476ae-569e-49b6-a887-7fd4b8efedf8/dqc_reference/checkm_data
[2023-03-18 03:10:19,001] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:10:19,016] [INFO] Task started: CheckM
[2023-03-18 03:10:19,016] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38337/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38337/checkm_input OceanDNA-b38337/checkm_result
[2023-03-18 03:11:27,492] [INFO] Task succeeded: CheckM
[2023-03-18 03:11:27,493] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.32%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 03:11:27,496] [INFO] ===== Completeness check finished =====
[2023-03-18 03:11:27,496] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:11:27,496] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38337/markers.fasta)
[2023-03-18 03:11:27,496] [INFO] Task started: Blastn
[2023-03-18 03:11:27,496] [INFO] Running command: blastn -query OceanDNA-b38337/markers.fasta -db /var/lib/cwl/stg2bb476ae-569e-49b6-a887-7fd4b8efedf8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38337/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:11:28,989] [INFO] Task succeeded: Blastn
[2023-03-18 03:11:28,990] [INFO] Selected 12 target genomes.
[2023-03-18 03:11:28,990] [INFO] Target genome list was writen to OceanDNA-b38337/target_genomes_gtdb.txt
[2023-03-18 03:11:29,038] [INFO] Task started: fastANI
[2023-03-18 03:11:29,039] [INFO] Running command: fastANI --query /var/lib/cwl/stg9421e683-70bd-43bc-8afa-c091af95a898/OceanDNA-b38337.fa --refList OceanDNA-b38337/target_genomes_gtdb.txt --output OceanDNA-b38337/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:11:39,823] [INFO] Task succeeded: fastANI
[2023-03-18 03:11:39,830] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 03:11:39,831] [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_003045775.1	s__Halomonas litopenaei	98.3581	1407	1503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.31	97.80	0.93	0.89	11	conclusive
GCA_002433675.1	s__Halomonas salina_B	94.5349	1092	1503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.49	99.49	0.75	0.75	2	-
GCF_017303055.1	s__Halomonas litopenaei_A	82.7239	1011	1503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265245.1	s__Halomonas smyrnensis	81.9718	656	1503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.45	98.45	0.89	0.89	2	-
GCF_007989465.1	s__Halomonas halophila	81.9547	676	1503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.43	97.59	0.92	0.89	4	-
GCF_003056305.1	s__Halomonas denitrificans	81.7879	729	1503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363755.1	s__Halomonas sp009363755	81.6503	713	1503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014192055.1	s__Halomonas organivorans	81.3769	726	1503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116405.1	s__Halomonas saccharevitans	81.3625	659	1503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002549795.1	s__Halomonas beimenensis	81.3321	706	1503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859505.1	s__Halomonas sp014859505	80.819	537	1503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010977575.1	s__Halomonas_B socia	80.5104	607	1503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 03:11:39,831] [INFO] GTDB search result was written to OceanDNA-b38337/result_gtdb.tsv
[2023-03-18 03:11:39,831] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:11:39,833] [INFO] DFAST_QC result json was written to OceanDNA-b38337/dqc_result.json
[2023-03-18 03:11:39,833] [INFO] DFAST_QC completed!
[2023-03-18 03:11:39,833] [INFO] Total running time: 0h2m6s