[2023-03-19 04:46:13,870] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:46:13,870] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:46:13,871] [INFO] DQC Reference Directory: /var/lib/cwl/stg846b8272-c113-41a1-bdbb-85d0f937f82a/dqc_reference
[2023-03-19 04:46:14,966] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:46:14,967] [INFO] Task started: Prodigal
[2023-03-19 04:46:14,967] [INFO] Running command: cat /var/lib/cwl/stge1f68920-d5f8-4d04-93b5-49364d4d0c96/OceanDNA-b29993.fa | prodigal -d OceanDNA-b29993/cds.fna -a OceanDNA-b29993/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:46:34,307] [INFO] Task succeeded: Prodigal
[2023-03-19 04:46:34,307] [INFO] Task started: HMMsearch
[2023-03-19 04:46:34,307] [INFO] Running command: hmmsearch --tblout OceanDNA-b29993/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg846b8272-c113-41a1-bdbb-85d0f937f82a/dqc_reference/reference_markers.hmm OceanDNA-b29993/protein.faa > /dev/null
[2023-03-19 04:46:34,503] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:46:34,504] [INFO] Found 6/6 markers.
[2023-03-19 04:46:34,523] [INFO] Query marker FASTA was written to OceanDNA-b29993/markers.fasta
[2023-03-19 04:46:34,524] [INFO] Task started: Blastn
[2023-03-19 04:46:34,524] [INFO] Running command: blastn -query OceanDNA-b29993/markers.fasta -db /var/lib/cwl/stg846b8272-c113-41a1-bdbb-85d0f937f82a/dqc_reference/reference_markers.fasta -out OceanDNA-b29993/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:46:35,155] [INFO] Task succeeded: Blastn
[2023-03-19 04:46:35,155] [INFO] Selected 21 target genomes.
[2023-03-19 04:46:35,156] [INFO] Target genome list was writen to OceanDNA-b29993/target_genomes.txt
[2023-03-19 04:46:35,170] [INFO] Task started: fastANI
[2023-03-19 04:46:35,170] [INFO] Running command: fastANI --query /var/lib/cwl/stge1f68920-d5f8-4d04-93b5-49364d4d0c96/OceanDNA-b29993.fa --refList OceanDNA-b29993/target_genomes.txt --output OceanDNA-b29993/fastani_result.tsv --threads 1
[2023-03-19 04:46:46,891] [INFO] Task succeeded: fastANI
[2023-03-19 04:46:46,892] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg846b8272-c113-41a1-bdbb-85d0f937f82a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:46:46,892] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg846b8272-c113-41a1-bdbb-85d0f937f82a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:46:46,904] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:46:46,904] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 04:46:46,905] [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
Planktotalea frisia	strain=DSM 23709	GCA_003254185.1	696762	696762	type	True	80.2951	581	1010	95	below_threshold
Planktotalea frisia	strain=SH6-1	GCA_001890925.1	696762	696762	type	True	80.2702	572	1010	95	below_threshold
Planktotalea arctica	strain=IMCC9565	GCA_002105285.1	1481893	1481893	type	True	78.6033	428	1010	95	below_threshold
Ascidiaceihabitans donghaensis	strain=CECT 8599	GCA_900302465.1	1510460	1510460	type	True	76.8191	147	1010	95	below_threshold
Octadecabacter ascidiaceicola	strain=CECT 8868	GCA_900185015.1	1655543	1655543	type	True	76.7319	119	1010	95	below_threshold
Octadecabacter temperatus	strain=DSM 26878	GCA_900142425.1	1458307	1458307	type	True	76.6445	116	1010	95	below_threshold
Octadecabacter temperatus	strain=SB1	GCA_001187845.1	1458307	1458307	type	True	76.6408	115	1010	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	76.5542	113	1010	95	below_threshold
Sulfitobacter indolifex	strain=HEL-45	GCA_000172095.1	225422	225422	type	True	76.5029	112	1010	95	below_threshold
Actibacterium pelagium	strain=JN33	GCA_002285415.1	2029103	2029103	type	True	76.4356	82	1010	95	below_threshold
Actibacterium pelagium	strain=CGMCC 1.16012	GCA_014644355.1	2029103	2029103	type	True	76.4176	84	1010	95	below_threshold
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	76.3592	121	1010	95	below_threshold
Shimia marina	strain=CECT 7688	GCA_001458175.1	321267	321267	type	True	76.3363	97	1010	95	below_threshold
Shimia marina	strain=DSM 26895	GCA_900112745.1	321267	321267	type	True	76.2642	97	1010	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	76.2207	58	1010	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	76.2095	109	1010	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	76.1896	108	1010	95	below_threshold
Roseovarius gahaiensis	strain=GH877	GCA_011601345.1	2716691	2716691	type	True	75.8866	86	1010	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	75.272	54	1010	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:46:46,905] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29993/tc_result.tsv
[2023-03-19 04:46:46,905] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:46:46,905] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:46:46,905] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg846b8272-c113-41a1-bdbb-85d0f937f82a/dqc_reference/checkm_data
[2023-03-19 04:46:46,906] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:46:46,911] [INFO] Task started: CheckM
[2023-03-19 04:46:46,911] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29993/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29993/checkm_input OceanDNA-b29993/checkm_result
[2023-03-19 04:47:36,904] [INFO] Task succeeded: CheckM
[2023-03-19 04:47:36,905] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:47:36,934] [INFO] ===== Completeness check finished =====
[2023-03-19 04:47:36,934] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:47:36,934] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29993/markers.fasta)
[2023-03-19 04:47:36,936] [INFO] Task started: Blastn
[2023-03-19 04:47:36,936] [INFO] Running command: blastn -query OceanDNA-b29993/markers.fasta -db /var/lib/cwl/stg846b8272-c113-41a1-bdbb-85d0f937f82a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29993/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:47:38,025] [INFO] Task succeeded: Blastn
[2023-03-19 04:47:38,029] [INFO] Selected 12 target genomes.
[2023-03-19 04:47:38,029] [INFO] Target genome list was writen to OceanDNA-b29993/target_genomes_gtdb.txt
[2023-03-19 04:47:38,042] [INFO] Task started: fastANI
[2023-03-19 04:47:38,042] [INFO] Running command: fastANI --query /var/lib/cwl/stge1f68920-d5f8-4d04-93b5-49364d4d0c96/OceanDNA-b29993.fa --refList OceanDNA-b29993/target_genomes_gtdb.txt --output OceanDNA-b29993/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:47:46,097] [INFO] Task succeeded: fastANI
[2023-03-19 04:47:46,104] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 04:47:46,105] [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_018607995.1	s__Planktotalea sp018607995	99.9519	966	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktotalea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000156115.1	s__Planktotalea sp000156115	92.1971	894	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktotalea	95.0	99.77	99.74	0.95	0.90	3	-
GCF_001890925.1	s__Planktotalea frisia	80.3006	569	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktotalea	95.0	99.35	98.99	0.94	0.89	4	-
GCA_018607965.1	s__Planktotalea sp018607965	78.6308	438	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002105285.1	s__Planktotalea arctica	78.6129	427	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143545.1	s__Yoonia sp900143545	76.8304	110	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900302465.1	s__Ascidiaceihabitans donghaensis	76.8191	147	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001187845.1	s__Octadecabacter temperatus	76.6423	116	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003335585.1	s__Sulfitobacter sp003335585	76.5043	105	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	76.2095	109	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCF_011601345.1	s__Roseovarius gahaiensis	75.8972	87	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:47:46,105] [INFO] GTDB search result was written to OceanDNA-b29993/result_gtdb.tsv
[2023-03-19 04:47:46,105] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:47:46,107] [INFO] DFAST_QC result json was written to OceanDNA-b29993/dqc_result.json
[2023-03-19 04:47:46,107] [INFO] DFAST_QC completed!
[2023-03-19 04:47:46,107] [INFO] Total running time: 0h1m32s