[2024-01-24 14:05:00,963] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:00,965] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:00,965] [INFO] DQC Reference Directory: /var/lib/cwl/stga218ad97-6b76-4412-b071-8a6e7eeec1f9/dqc_reference
[2024-01-24 14:05:02,139] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:02,140] [INFO] Task started: Prodigal
[2024-01-24 14:05:02,140] [INFO] Running command: gunzip -c /var/lib/cwl/stg57e88337-eab8-4dc9-a4e6-d431e9e7bf2c/GCF_014643915.1_ASM1464391v1_genomic.fna.gz | prodigal -d GCF_014643915.1_ASM1464391v1_genomic.fna/cds.fna -a GCF_014643915.1_ASM1464391v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:11,554] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:11,554] [INFO] Task started: HMMsearch
[2024-01-24 14:05:11,555] [INFO] Running command: hmmsearch --tblout GCF_014643915.1_ASM1464391v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga218ad97-6b76-4412-b071-8a6e7eeec1f9/dqc_reference/reference_markers.hmm GCF_014643915.1_ASM1464391v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:11,778] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:11,779] [INFO] Found 6/6 markers.
[2024-01-24 14:05:11,807] [INFO] Query marker FASTA was written to GCF_014643915.1_ASM1464391v1_genomic.fna/markers.fasta
[2024-01-24 14:05:11,807] [INFO] Task started: Blastn
[2024-01-24 14:05:11,807] [INFO] Running command: blastn -query GCF_014643915.1_ASM1464391v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga218ad97-6b76-4412-b071-8a6e7eeec1f9/dqc_reference/reference_markers.fasta -out GCF_014643915.1_ASM1464391v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:12,596] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:12,599] [INFO] Selected 17 target genomes.
[2024-01-24 14:05:12,600] [INFO] Target genome list was writen to GCF_014643915.1_ASM1464391v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:12,625] [INFO] Task started: fastANI
[2024-01-24 14:05:12,625] [INFO] Running command: fastANI --query /var/lib/cwl/stg57e88337-eab8-4dc9-a4e6-d431e9e7bf2c/GCF_014643915.1_ASM1464391v1_genomic.fna.gz --refList GCF_014643915.1_ASM1464391v1_genomic.fna/target_genomes.txt --output GCF_014643915.1_ASM1464391v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:05:23,497] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:23,497] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga218ad97-6b76-4412-b071-8a6e7eeec1f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:05:23,497] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga218ad97-6b76-4412-b071-8a6e7eeec1f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:05:23,507] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:05:23,507] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:05:23,507] [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 marina	strain=CGMCC 1.15923	GCA_014643915.1	2017550	2017550	type	True	100.0	1084	1087	95	conclusive
Oceanisphaera arctica	strain=V1-41	GCA_002936955.1	641510	641510	type	True	81.7342	693	1087	95	below_threshold
Oceanisphaera arctica	strain=KCTC 23013	GCA_014652055.1	641510	641510	type	True	81.7204	705	1087	95	below_threshold
Oceanisphaera litoralis	strain=DSM 15406	GCA_016907015.1	225144	225144	type	True	81.1917	647	1087	95	below_threshold
Oceanisphaera psychrotolerans	strain=LAM-WHM-ZC	GCA_001870485.1	1414654	1414654	type	True	81.0175	651	1087	95	below_threshold
Oceanisphaera profunda	strain=SM1222	GCA_002157895.1	1416627	1416627	type	True	79.6777	571	1087	95	below_threshold
Oceanimonas marisflavi	strain=102-Na3	GCA_003049725.1	2059724	2059724	type	True	79.2561	507	1087	95	below_threshold
Oceanimonas smirnovii	strain=ATCC BAA-899	GCA_000381965.1	264574	264574	type	True	78.8444	514	1087	95	below_threshold
Shewanella litorisediminis	strain=CCUG 62411	GCA_023349165.1	1173586	1173586	type	True	76.4725	91	1087	95	below_threshold
Leminorella grimontii	strain=JCM 5902	GCA_024343555.1	82981	82981	type	True	76.0818	57	1087	95	below_threshold
Shewanella corallii	strain=DSM 21332	GCA_023349125.1	560080	560080	type	True	76.0598	62	1087	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:05:23,509] [INFO] DFAST Taxonomy check result was written to GCF_014643915.1_ASM1464391v1_genomic.fna/tc_result.tsv
[2024-01-24 14:05:23,509] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:05:23,509] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:05:23,509] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga218ad97-6b76-4412-b071-8a6e7eeec1f9/dqc_reference/checkm_data
[2024-01-24 14:05:23,510] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:05:23,544] [INFO] Task started: CheckM
[2024-01-24 14:05:23,544] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014643915.1_ASM1464391v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014643915.1_ASM1464391v1_genomic.fna/checkm_input GCF_014643915.1_ASM1464391v1_genomic.fna/checkm_result
[2024-01-24 14:05:55,684] [INFO] Task succeeded: CheckM
[2024-01-24 14:05:55,686] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:05:55,717] [INFO] ===== Completeness check finished =====
[2024-01-24 14:05:55,718] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:05:55,718] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014643915.1_ASM1464391v1_genomic.fna/markers.fasta)
[2024-01-24 14:05:55,719] [INFO] Task started: Blastn
[2024-01-24 14:05:55,719] [INFO] Running command: blastn -query GCF_014643915.1_ASM1464391v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga218ad97-6b76-4412-b071-8a6e7eeec1f9/dqc_reference/reference_markers_gtdb.fasta -out GCF_014643915.1_ASM1464391v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:56,990] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:56,993] [INFO] Selected 13 target genomes.
[2024-01-24 14:05:56,994] [INFO] Target genome list was writen to GCF_014643915.1_ASM1464391v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:05:57,007] [INFO] Task started: fastANI
[2024-01-24 14:05:57,007] [INFO] Running command: fastANI --query /var/lib/cwl/stg57e88337-eab8-4dc9-a4e6-d431e9e7bf2c/GCF_014643915.1_ASM1464391v1_genomic.fna.gz --refList GCF_014643915.1_ASM1464391v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014643915.1_ASM1464391v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:06,859] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:06,870] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:06,871] [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_014643915.1	s__Oceanisphaera marina	100.0	1084	1087	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_018222825.1	s__Oceanisphaera sp018222825	81.7509	575	1087	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	81.73	694	1087	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	81.1927	646	1087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001870485.1	s__Oceanisphaera psychrotolerans	81.0311	650	1087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002157895.1	s__Oceanisphaera profunda	79.6785	571	1087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003049725.1	s__Oceanimonas marisflavi	79.2892	503	1087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018883865.1	s__Oceanisphaera merdipullorum	79.0345	396	1087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003012775.1	s__Zobellella_C endophytica	78.9844	507	1087	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_000381965.1	s__Oceanimonas smirnovii	78.8492	514	1087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013155275.1	s__Brenneria sp013155275	76.4835	71	1087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria	95.0	99.39	99.39	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:06,872] [INFO] GTDB search result was written to GCF_014643915.1_ASM1464391v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:06,873] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:06,876] [INFO] DFAST_QC result json was written to GCF_014643915.1_ASM1464391v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:06,876] [INFO] DFAST_QC completed!
[2024-01-24 14:06:06,876] [INFO] Total running time: 0h1m6s