[2024-01-24 12:43:54,219] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:43:54,221] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:43:54,221] [INFO] DQC Reference Directory: /var/lib/cwl/stgdb9d9398-1a44-4b99-937b-4fbad20be558/dqc_reference
[2024-01-24 12:43:59,336] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:43:59,337] [INFO] Task started: Prodigal
[2024-01-24 12:43:59,337] [INFO] Running command: gunzip -c /var/lib/cwl/stg4772cf9c-47bb-4418-9678-3e6ff76b9b41/GCF_014643555.1_ASM1464355v1_genomic.fna.gz | prodigal -d GCF_014643555.1_ASM1464355v1_genomic.fna/cds.fna -a GCF_014643555.1_ASM1464355v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:11,537] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:11,537] [INFO] Task started: HMMsearch
[2024-01-24 12:44:11,537] [INFO] Running command: hmmsearch --tblout GCF_014643555.1_ASM1464355v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdb9d9398-1a44-4b99-937b-4fbad20be558/dqc_reference/reference_markers.hmm GCF_014643555.1_ASM1464355v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:11,834] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:11,836] [INFO] Found 6/6 markers.
[2024-01-24 12:44:11,879] [INFO] Query marker FASTA was written to GCF_014643555.1_ASM1464355v1_genomic.fna/markers.fasta
[2024-01-24 12:44:11,879] [INFO] Task started: Blastn
[2024-01-24 12:44:11,879] [INFO] Running command: blastn -query GCF_014643555.1_ASM1464355v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb9d9398-1a44-4b99-937b-4fbad20be558/dqc_reference/reference_markers.fasta -out GCF_014643555.1_ASM1464355v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:12,623] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:12,627] [INFO] Selected 16 target genomes.
[2024-01-24 12:44:12,628] [INFO] Target genome list was writen to GCF_014643555.1_ASM1464355v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:12,673] [INFO] Task started: fastANI
[2024-01-24 12:44:12,674] [INFO] Running command: fastANI --query /var/lib/cwl/stg4772cf9c-47bb-4418-9678-3e6ff76b9b41/GCF_014643555.1_ASM1464355v1_genomic.fna.gz --refList GCF_014643555.1_ASM1464355v1_genomic.fna/target_genomes.txt --output GCF_014643555.1_ASM1464355v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:44:25,162] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:25,163] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdb9d9398-1a44-4b99-937b-4fbad20be558/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:44:25,163] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdb9d9398-1a44-4b99-937b-4fbad20be558/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:44:25,174] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:44:25,174] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:44:25,174] [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
Alteromonas lipolytica	strain=CGMCC 1.15735	GCA_014643555.1	1856405	1856405	type	True	100.0	1653	1655	95	conclusive
Alteromonas lipolytica	strain=JW12	GCA_001758465.1	1856405	1856405	type	True	99.9944	1655	1655	95	conclusive
Alteromonas oceani	strain=S35	GCA_003731635.1	2071609	2071609	type	True	81.8806	817	1655	95	below_threshold
Alteromonas alba	strain=190	GCA_002993365.1	2079529	2079529	type	True	81.4485	794	1655	95	below_threshold
Alteromonas macleodii	strain=ATCC 27126	GCA_000172635.2	28108	28108	type	True	78.9718	135	1655	95	below_threshold
Alteromonas confluentis	strain=KCTC 42603	GCA_001757105.1	1656094	1656094	type	True	78.5393	243	1655	95	below_threshold
Salinimonas iocasae	strain=KX18D6	GCA_006228385.1	2572577	2572577	type	True	78.1919	138	1655	95	below_threshold
Alteromonas antoniana	strain=MD_567	GCA_019249295.1	2803813	2803813	type	True	78.1556	200	1655	95	below_threshold
Alteromonas mediterranea	strain=DE	GCA_000020585.3	314275	314275	type	True	78.037	158	1655	95	below_threshold
Salinimonas profundi	strain=HHU 13199	GCA_014750655.1	2729140	2729140	type	True	78.0066	144	1655	95	below_threshold
Paraglaciecola aquimarina	strain=GGW-M5	GCA_021532655.1	1235557	1235557	type	True	77.1747	69	1655	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:44:25,176] [INFO] DFAST Taxonomy check result was written to GCF_014643555.1_ASM1464355v1_genomic.fna/tc_result.tsv
[2024-01-24 12:44:25,177] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:44:25,177] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:44:25,177] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdb9d9398-1a44-4b99-937b-4fbad20be558/dqc_reference/checkm_data
[2024-01-24 12:44:25,178] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:44:25,231] [INFO] Task started: CheckM
[2024-01-24 12:44:25,232] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014643555.1_ASM1464355v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014643555.1_ASM1464355v1_genomic.fna/checkm_input GCF_014643555.1_ASM1464355v1_genomic.fna/checkm_result
[2024-01-24 12:45:05,109] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:05,111] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.75%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:05,130] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:05,131] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:05,131] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014643555.1_ASM1464355v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:05,132] [INFO] Task started: Blastn
[2024-01-24 12:45:05,132] [INFO] Running command: blastn -query GCF_014643555.1_ASM1464355v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb9d9398-1a44-4b99-937b-4fbad20be558/dqc_reference/reference_markers_gtdb.fasta -out GCF_014643555.1_ASM1464355v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:06,379] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:06,383] [INFO] Selected 6 target genomes.
[2024-01-24 12:45:06,383] [INFO] Target genome list was writen to GCF_014643555.1_ASM1464355v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:06,390] [INFO] Task started: fastANI
[2024-01-24 12:45:06,390] [INFO] Running command: fastANI --query /var/lib/cwl/stg4772cf9c-47bb-4418-9678-3e6ff76b9b41/GCF_014643555.1_ASM1464355v1_genomic.fna.gz --refList GCF_014643555.1_ASM1464355v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014643555.1_ASM1464355v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:12,559] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:12,571] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:45:12,572] [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_001758465.1	s__Alteromonas lipolytica	99.9944	1655	1655	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_003731635.1	s__Alteromonas oceani	81.8809	818	1655	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002993365.1	s__Alteromonas alba	81.4302	797	1655	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222405.1	s__Alteromonas sp018222405	81.3978	764	1655	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002691625.1	s__Alteromonas sp002691625	81.3851	639	1655	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.62	99.31	0.91	0.90	3	-
GCA_002339125.1	s__Alteromonas sp002335925	81.3677	734	1655	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.57	96.36	0.89	0.83	19	-
--------------------------------------------------------------------------------
[2024-01-24 12:45:12,573] [INFO] GTDB search result was written to GCF_014643555.1_ASM1464355v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:12,574] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:12,577] [INFO] DFAST_QC result json was written to GCF_014643555.1_ASM1464355v1_genomic.fna/dqc_result.json
[2024-01-24 12:45:12,577] [INFO] DFAST_QC completed!
[2024-01-24 12:45:12,577] [INFO] Total running time: 0h1m18s