[2023-06-18 20:29:48,411] [INFO] DFAST_QC pipeline started.
[2023-06-18 20:29:48,414] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 20:29:48,414] [INFO] DQC Reference Directory: /var/lib/cwl/stg9b2f3ae4-9030-4b38-a252-67fd6db2c2ce/dqc_reference
[2023-06-18 20:29:49,712] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 20:29:49,713] [INFO] Task started: Prodigal
[2023-06-18 20:29:49,713] [INFO] Running command: gunzip -c /var/lib/cwl/stg0429a327-1589-434d-9798-733840830a71/GCA_018607995.1_ASM1860799v1_genomic.fna.gz | prodigal -d GCA_018607995.1_ASM1860799v1_genomic.fna/cds.fna -a GCA_018607995.1_ASM1860799v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 20:30:00,632] [INFO] Task succeeded: Prodigal
[2023-06-18 20:30:00,632] [INFO] Task started: HMMsearch
[2023-06-18 20:30:00,632] [INFO] Running command: hmmsearch --tblout GCA_018607995.1_ASM1860799v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9b2f3ae4-9030-4b38-a252-67fd6db2c2ce/dqc_reference/reference_markers.hmm GCA_018607995.1_ASM1860799v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 20:30:00,909] [INFO] Task succeeded: HMMsearch
[2023-06-18 20:30:00,916] [INFO] Found 6/6 markers.
[2023-06-18 20:30:00,957] [INFO] Query marker FASTA was written to GCA_018607995.1_ASM1860799v1_genomic.fna/markers.fasta
[2023-06-18 20:30:00,958] [INFO] Task started: Blastn
[2023-06-18 20:30:00,958] [INFO] Running command: blastn -query GCA_018607995.1_ASM1860799v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b2f3ae4-9030-4b38-a252-67fd6db2c2ce/dqc_reference/reference_markers.fasta -out GCA_018607995.1_ASM1860799v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 20:30:01,723] [INFO] Task succeeded: Blastn
[2023-06-18 20:30:01,733] [INFO] Selected 21 target genomes.
[2023-06-18 20:30:01,734] [INFO] Target genome list was writen to GCA_018607995.1_ASM1860799v1_genomic.fna/target_genomes.txt
[2023-06-18 20:30:01,738] [INFO] Task started: fastANI
[2023-06-18 20:30:01,739] [INFO] Running command: fastANI --query /var/lib/cwl/stg0429a327-1589-434d-9798-733840830a71/GCA_018607995.1_ASM1860799v1_genomic.fna.gz --refList GCA_018607995.1_ASM1860799v1_genomic.fna/target_genomes.txt --output GCA_018607995.1_ASM1860799v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 20:30:14,610] [INFO] Task succeeded: fastANI
[2023-06-18 20:30:14,610] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9b2f3ae4-9030-4b38-a252-67fd6db2c2ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 20:30:14,611] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9b2f3ae4-9030-4b38-a252-67fd6db2c2ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 20:30:14,632] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 20:30:14,632] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 20:30:14,632] [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	79.9974	557	1025	95	below_threshold
Planktotalea frisia	strain=SH6-1	GCA_001890925.1	696762	696762	type	True	79.9631	558	1025	95	below_threshold
Planktotalea arctica	strain=IMCC9565	GCA_002105285.1	1481893	1481893	type	True	78.4255	428	1025	95	below_threshold
Ascidiaceihabitans donghaensis	strain=CECT 8599	GCA_900302465.1	1510460	1510460	type	True	76.9275	126	1025	95	below_threshold
Sulfitobacter donghicola	strain=KCTC 12864	GCA_000622405.1	421000	421000	type	True	76.8463	125	1025	95	below_threshold
Sulfitobacter donghicola	strain=JCM 14565	GCA_000712275.1	421000	421000	type	True	76.7704	123	1025	95	below_threshold
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	76.7429	107	1025	95	below_threshold
Octadecabacter ascidiaceicola	strain=CECT 8868	GCA_900185015.1	1655543	1655543	type	True	76.7332	113	1025	95	below_threshold
Sulfitobacter indolifex	strain=HEL-45	GCA_000172095.1	225422	225422	type	True	76.6282	110	1025	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	76.5838	113	1025	95	below_threshold
Shimia marina	strain=DSM 26895	GCA_900112745.1	321267	321267	type	True	76.3849	91	1025	95	below_threshold
Shimia marina	strain=CECT 7688	GCA_001458175.1	321267	321267	type	True	76.3243	95	1025	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	76.2968	93	1025	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	76.2176	96	1025	95	below_threshold
Actibacterium pelagium	strain=JN33	GCA_002285415.1	2029103	2029103	type	True	76.2133	73	1025	95	below_threshold
Actibacterium pelagium	strain=CGMCC 1.16012	GCA_014644355.1	2029103	2029103	type	True	76.1184	74	1025	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	75.8883	56	1025	95	below_threshold
Roseovarius gahaiensis	strain=GH877	GCA_011601345.1	2716691	2716691	type	True	75.7248	86	1025	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 20:30:14,635] [INFO] DFAST Taxonomy check result was written to GCA_018607995.1_ASM1860799v1_genomic.fna/tc_result.tsv
[2023-06-18 20:30:14,636] [INFO] ===== Taxonomy check completed =====
[2023-06-18 20:30:14,636] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 20:30:14,636] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9b2f3ae4-9030-4b38-a252-67fd6db2c2ce/dqc_reference/checkm_data
[2023-06-18 20:30:14,637] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 20:30:14,670] [INFO] Task started: CheckM
[2023-06-18 20:30:14,670] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018607995.1_ASM1860799v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018607995.1_ASM1860799v1_genomic.fna/checkm_input GCA_018607995.1_ASM1860799v1_genomic.fna/checkm_result
[2023-06-18 20:30:50,908] [INFO] Task succeeded: CheckM
[2023-06-18 20:30:50,909] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.16%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 20:30:50,929] [INFO] ===== Completeness check finished =====
[2023-06-18 20:30:50,930] [INFO] ===== Start GTDB Search =====
[2023-06-18 20:30:50,930] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018607995.1_ASM1860799v1_genomic.fna/markers.fasta)
[2023-06-18 20:30:50,931] [INFO] Task started: Blastn
[2023-06-18 20:30:50,931] [INFO] Running command: blastn -query GCA_018607995.1_ASM1860799v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b2f3ae4-9030-4b38-a252-67fd6db2c2ce/dqc_reference/reference_markers_gtdb.fasta -out GCA_018607995.1_ASM1860799v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 20:30:52,105] [INFO] Task succeeded: Blastn
[2023-06-18 20:30:52,109] [INFO] Selected 12 target genomes.
[2023-06-18 20:30:52,110] [INFO] Target genome list was writen to GCA_018607995.1_ASM1860799v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 20:30:52,117] [INFO] Task started: fastANI
[2023-06-18 20:30:52,117] [INFO] Running command: fastANI --query /var/lib/cwl/stg0429a327-1589-434d-9798-733840830a71/GCA_018607995.1_ASM1860799v1_genomic.fna.gz --refList GCA_018607995.1_ASM1860799v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018607995.1_ASM1860799v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 20:31:00,064] [INFO] Task succeeded: fastANI
[2023-06-18 20:31:00,081] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 20:31:00,081] [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	100.0	1024	1025	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	92.1585	897	1025	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	79.9531	559	1025	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	78.6054	446	1025	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	78.4258	429	1025	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900302465.1	s__Ascidiaceihabitans donghaensis	76.9072	127	1025	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143545.1	s__Yoonia sp900143545	76.6248	103	1025	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001292625.1	s__Shimia sp001292625	76.3818	117	1025	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335585.1	s__Sulfitobacter sp003335585	76.2728	101	1025	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	76.205	98	1025	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	75.7376	87	1025	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 20:31:00,083] [INFO] GTDB search result was written to GCA_018607995.1_ASM1860799v1_genomic.fna/result_gtdb.tsv
[2023-06-18 20:31:00,083] [INFO] ===== GTDB Search completed =====
[2023-06-18 20:31:00,086] [INFO] DFAST_QC result json was written to GCA_018607995.1_ASM1860799v1_genomic.fna/dqc_result.json
[2023-06-18 20:31:00,087] [INFO] DFAST_QC completed!
[2023-06-18 20:31:00,087] [INFO] Total running time: 0h1m12s