[2024-01-24 13:48:42,027] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:42,030] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:42,030] [INFO] DQC Reference Directory: /var/lib/cwl/stg38732f87-4780-4e7e-9435-965a29f49927/dqc_reference
[2024-01-24 13:48:43,285] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:48:43,286] [INFO] Task started: Prodigal
[2024-01-24 13:48:43,286] [INFO] Running command: gunzip -c /var/lib/cwl/stgd9745f7d-7e0e-4740-8ba7-237512487fe1/GCF_003075035.1_ASM307503v1_genomic.fna.gz | prodigal -d GCF_003075035.1_ASM307503v1_genomic.fna/cds.fna -a GCF_003075035.1_ASM307503v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:48:54,866] [INFO] Task succeeded: Prodigal
[2024-01-24 13:48:54,866] [INFO] Task started: HMMsearch
[2024-01-24 13:48:54,867] [INFO] Running command: hmmsearch --tblout GCF_003075035.1_ASM307503v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg38732f87-4780-4e7e-9435-965a29f49927/dqc_reference/reference_markers.hmm GCF_003075035.1_ASM307503v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:48:55,132] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:48:55,133] [INFO] Found 6/6 markers.
[2024-01-24 13:48:55,165] [INFO] Query marker FASTA was written to GCF_003075035.1_ASM307503v1_genomic.fna/markers.fasta
[2024-01-24 13:48:55,166] [INFO] Task started: Blastn
[2024-01-24 13:48:55,166] [INFO] Running command: blastn -query GCF_003075035.1_ASM307503v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38732f87-4780-4e7e-9435-965a29f49927/dqc_reference/reference_markers.fasta -out GCF_003075035.1_ASM307503v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:56,059] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:56,062] [INFO] Selected 14 target genomes.
[2024-01-24 13:48:56,062] [INFO] Target genome list was writen to GCF_003075035.1_ASM307503v1_genomic.fna/target_genomes.txt
[2024-01-24 13:48:56,083] [INFO] Task started: fastANI
[2024-01-24 13:48:56,083] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9745f7d-7e0e-4740-8ba7-237512487fe1/GCF_003075035.1_ASM307503v1_genomic.fna.gz --refList GCF_003075035.1_ASM307503v1_genomic.fna/target_genomes.txt --output GCF_003075035.1_ASM307503v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:06,234] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:06,234] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg38732f87-4780-4e7e-9435-965a29f49927/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:06,235] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg38732f87-4780-4e7e-9435-965a29f49927/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:06,246] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:49:06,246] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:49:06,246] [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 psychrotolerans	strain=LAM-WHM-ZC	GCA_001870485.1	1414654	1414654	type	True	82.0365	741	1305	95	below_threshold
Zobellella denitrificans	strain=ZD1	GCA_002237365.1	347534	347534	type	True	81.7718	695	1305	95	below_threshold
Zobellella endophytica	strain=59N8	GCA_003012775.1	2116700	2116700	type	True	81.7419	759	1305	95	below_threshold
Oceanisphaera arctica	strain=KCTC 23013	GCA_014652055.1	641510	641510	type	True	81.3949	735	1305	95	below_threshold
Oceanisphaera arctica	strain=V1-41	GCA_002936955.1	641510	641510	type	True	81.3792	713	1305	95	below_threshold
Oceanisphaera litoralis	strain=DSM 15406	GCA_016907015.1	225144	225144	type	True	81.331	625	1305	95	below_threshold
Zobellella taiwanensis	strain=JCM 13381	GCA_003012795.1	347535	347535	type	True	81.3105	675	1305	95	below_threshold
Oceanimonas marisflavi	strain=102-Na3	GCA_003049725.1	2059724	2059724	type	True	80.7311	637	1305	95	below_threshold
Oceanimonas doudoroffii	strain=ATCC 27123	GCA_002242685.1	84158	84158	type	True	80.7029	687	1305	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.7116	115	1305	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.4223	149	1305	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	76.3292	130	1305	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	76.231	102	1305	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	76.1581	119	1305	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:06,247] [INFO] DFAST Taxonomy check result was written to GCF_003075035.1_ASM307503v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:06,248] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:06,248] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:06,248] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg38732f87-4780-4e7e-9435-965a29f49927/dqc_reference/checkm_data
[2024-01-24 13:49:06,249] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:06,293] [INFO] Task started: CheckM
[2024-01-24 13:49:06,293] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003075035.1_ASM307503v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003075035.1_ASM307503v1_genomic.fna/checkm_input GCF_003075035.1_ASM307503v1_genomic.fna/checkm_result
[2024-01-24 13:49:43,174] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:43,175] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:43,194] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:43,194] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:43,195] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003075035.1_ASM307503v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:43,195] [INFO] Task started: Blastn
[2024-01-24 13:49:43,195] [INFO] Running command: blastn -query GCF_003075035.1_ASM307503v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38732f87-4780-4e7e-9435-965a29f49927/dqc_reference/reference_markers_gtdb.fasta -out GCF_003075035.1_ASM307503v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:44,744] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:44,750] [INFO] Selected 11 target genomes.
[2024-01-24 13:49:44,750] [INFO] Target genome list was writen to GCF_003075035.1_ASM307503v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:44,775] [INFO] Task started: fastANI
[2024-01-24 13:49:44,776] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9745f7d-7e0e-4740-8ba7-237512487fe1/GCF_003075035.1_ASM307503v1_genomic.fna.gz --refList GCF_003075035.1_ASM307503v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003075035.1_ASM307503v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:54,681] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:54,693] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:54,694] [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_003075035.1	s__Zobellella_A maritima	100.0	1305	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Zobellella_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001870485.1	s__Oceanisphaera psychrotolerans	81.9994	745	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002237365.1	s__Zobellella denitrificans	81.7557	698	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Zobellella	95.0	98.78	98.78	0.93	0.93	2	-
GCF_003012775.1	s__Zobellella_C endophytica	81.7533	757	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Zobellella_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016746085.1	s__CGMCC-1-18722 sp016746085	81.4989	767	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__CGMCC-1-18722	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907015.1	s__Oceanisphaera litoralis	81.3202	626	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003012795.1	s__Zobellella_D taiwanensis	81.3045	675	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Zobellella_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000243075.1	s__Oceanimonas sp000243075	80.8515	635	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003049725.1	s__Oceanimonas marisflavi	80.742	636	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002242685.1	s__Oceanimonas doudoroffii	80.71	685	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanimonas	95.0	98.80	98.80	0.94	0.94	2	-
GCA_018222825.1	s__Oceanisphaera sp018222825	80.6176	513	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanisphaera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:49:54,699] [INFO] GTDB search result was written to GCF_003075035.1_ASM307503v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:54,699] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:54,703] [INFO] DFAST_QC result json was written to GCF_003075035.1_ASM307503v1_genomic.fna/dqc_result.json
[2024-01-24 13:49:54,703] [INFO] DFAST_QC completed!
[2024-01-24 13:49:54,703] [INFO] Total running time: 0h1m13s