[2024-01-25 18:04:35,644] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:04:35,646] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:04:35,646] [INFO] DQC Reference Directory: /var/lib/cwl/stgf20f229e-ffb7-4122-a4cb-307acbec7978/dqc_reference
[2024-01-25 18:04:36,786] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:04:36,787] [INFO] Task started: Prodigal
[2024-01-25 18:04:36,787] [INFO] Running command: gunzip -c /var/lib/cwl/stg6fbd434e-8983-43c4-b1e5-bfbc7f9ea647/GCF_002157895.1_ASM215789v1_genomic.fna.gz | prodigal -d GCF_002157895.1_ASM215789v1_genomic.fna/cds.fna -a GCF_002157895.1_ASM215789v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:04:44,674] [INFO] Task succeeded: Prodigal
[2024-01-25 18:04:44,674] [INFO] Task started: HMMsearch
[2024-01-25 18:04:44,674] [INFO] Running command: hmmsearch --tblout GCF_002157895.1_ASM215789v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf20f229e-ffb7-4122-a4cb-307acbec7978/dqc_reference/reference_markers.hmm GCF_002157895.1_ASM215789v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:04:44,920] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:04:44,921] [INFO] Found 6/6 markers.
[2024-01-25 18:04:44,947] [INFO] Query marker FASTA was written to GCF_002157895.1_ASM215789v1_genomic.fna/markers.fasta
[2024-01-25 18:04:44,947] [INFO] Task started: Blastn
[2024-01-25 18:04:44,948] [INFO] Running command: blastn -query GCF_002157895.1_ASM215789v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf20f229e-ffb7-4122-a4cb-307acbec7978/dqc_reference/reference_markers.fasta -out GCF_002157895.1_ASM215789v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:04:45,678] [INFO] Task succeeded: Blastn
[2024-01-25 18:04:45,681] [INFO] Selected 19 target genomes.
[2024-01-25 18:04:45,681] [INFO] Target genome list was writen to GCF_002157895.1_ASM215789v1_genomic.fna/target_genomes.txt
[2024-01-25 18:04:45,698] [INFO] Task started: fastANI
[2024-01-25 18:04:45,698] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fbd434e-8983-43c4-b1e5-bfbc7f9ea647/GCF_002157895.1_ASM215789v1_genomic.fna.gz --refList GCF_002157895.1_ASM215789v1_genomic.fna/target_genomes.txt --output GCF_002157895.1_ASM215789v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:04:59,847] [INFO] Task succeeded: fastANI
[2024-01-25 18:04:59,848] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf20f229e-ffb7-4122-a4cb-307acbec7978/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:04:59,848] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf20f229e-ffb7-4122-a4cb-307acbec7978/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:04:59,857] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:04:59,857] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:04:59,858] [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
Oceanisphaera profunda	strain=SM1222	GCA_002157895.1	1416627	1416627	type	True	100.0	1169	1169	95	conclusive
Oceanisphaera avium	strain=AMac2203	GCA_002157875.1	1903694	1903694	type	True	80.5569	558	1169	95	below_threshold
Oceanisphaera marina	strain=CGMCC 1.15923	GCA_014643915.1	2017550	2017550	type	True	79.6025	567	1169	95	below_threshold
Vibrio stylophorae	strain=CECT 7929	GCA_921293875.1	659351	659351	type	True	79.5334	54	1169	95	below_threshold
Oceanisphaera pacifica	strain=DM8	GCA_017498065.1	2818389	2818389	type	True	79.191	497	1169	95	below_threshold
Shewanella baltica	strain=NCTC10735	GCA_900456975.1	62322	62322	type	True	78.6743	71	1169	95	below_threshold
Oceanisphaera arctica	strain=V1-41	GCA_002936955.1	641510	641510	type	True	78.5676	368	1169	95	below_threshold
Oceanisphaera arctica	strain=KCTC 23013	GCA_014652055.1	641510	641510	type	True	78.5394	379	1169	95	below_threshold
Oceanisphaera litoralis	strain=DSM 15406	GCA_016907015.1	225144	225144	type	True	78.5064	323	1169	95	below_threshold
Oceanisphaera psychrotolerans	strain=LAM-WHM-ZC	GCA_001870485.1	1414654	1414654	type	True	78.0721	315	1169	95	below_threshold
Oceanimonas baumannii	strain=ATCC 700832	GCA_002245495.1	129578	129578	type	True	77.1987	234	1169	95	below_threshold
Oceanimonas baumannii	strain=DSM 15594	GCA_004365405.1	129578	129578	type	True	77.1891	238	1169	95	below_threshold
Shewanella litorisediminis	strain=CCUG 62411	GCA_023349165.1	1173586	1173586	type	True	76.5822	55	1169	95	below_threshold
Shewanella corallii	strain=DSM 21332	GCA_023349125.1	560080	560080	type	True	76.2182	52	1169	95	below_threshold
Shewanella jiangmenensis	strain=JM162201	GCA_018596335.1	2837387	2837387	type	True	76.0819	63	1169	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:04:59,859] [INFO] DFAST Taxonomy check result was written to GCF_002157895.1_ASM215789v1_genomic.fna/tc_result.tsv
[2024-01-25 18:04:59,859] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:04:59,859] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:04:59,860] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf20f229e-ffb7-4122-a4cb-307acbec7978/dqc_reference/checkm_data
[2024-01-25 18:04:59,860] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:04:59,897] [INFO] Task started: CheckM
[2024-01-25 18:04:59,897] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002157895.1_ASM215789v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002157895.1_ASM215789v1_genomic.fna/checkm_input GCF_002157895.1_ASM215789v1_genomic.fna/checkm_result
[2024-01-25 18:05:26,332] [INFO] Task succeeded: CheckM
[2024-01-25 18:05:26,333] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:05:26,350] [INFO] ===== Completeness check finished =====
[2024-01-25 18:05:26,351] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:05:26,351] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002157895.1_ASM215789v1_genomic.fna/markers.fasta)
[2024-01-25 18:05:26,351] [INFO] Task started: Blastn
[2024-01-25 18:05:26,351] [INFO] Running command: blastn -query GCF_002157895.1_ASM215789v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf20f229e-ffb7-4122-a4cb-307acbec7978/dqc_reference/reference_markers_gtdb.fasta -out GCF_002157895.1_ASM215789v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:05:27,573] [INFO] Task succeeded: Blastn
[2024-01-25 18:05:27,576] [INFO] Selected 11 target genomes.
[2024-01-25 18:05:27,576] [INFO] Target genome list was writen to GCF_002157895.1_ASM215789v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:05:27,586] [INFO] Task started: fastANI
[2024-01-25 18:05:27,587] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fbd434e-8983-43c4-b1e5-bfbc7f9ea647/GCF_002157895.1_ASM215789v1_genomic.fna.gz --refList GCF_002157895.1_ASM215789v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002157895.1_ASM215789v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:05:36,240] [INFO] Task succeeded: fastANI
[2024-01-25 18:05:36,248] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:05:36,248] [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_002157895.1	s__Oceanisphaera profunda	100.0	1169	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanisphaera	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018883865.1	s__Oceanisphaera merdipullorum	83.2326	646	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002157875.1	s__Oceanisphaera avium	80.5654	557	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643915.1	s__Oceanisphaera marina	79.6193	564	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017498065.1	s__Oceanisphaera sp017498065	79.1761	497	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002936955.1	s__Oceanisphaera arctica	78.5891	366	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanisphaera	95.0	99.99	99.99	0.99	0.99	2	-
GCF_016907015.1	s__Oceanisphaera litoralis	78.5227	321	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012518835.1	s__Oceanisphaera sp012518835	78.0483	298	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003075035.1	s__Zobellella_A maritima	77.663	208	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Zobellella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002245495.1	s__Oceanimonas baumannii	77.2132	235	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanimonas	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:05:36,250] [INFO] GTDB search result was written to GCF_002157895.1_ASM215789v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:05:36,250] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:05:36,254] [INFO] DFAST_QC result json was written to GCF_002157895.1_ASM215789v1_genomic.fna/dqc_result.json
[2024-01-25 18:05:36,254] [INFO] DFAST_QC completed!
[2024-01-25 18:05:36,254] [INFO] Total running time: 0h1m1s