[2024-01-24 14:46:35,499] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:35,501] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:35,501] [INFO] DQC Reference Directory: /var/lib/cwl/stg103b938f-81ac-41bc-a9df-7849ecea675e/dqc_reference
[2024-01-24 14:46:37,179] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:37,181] [INFO] Task started: Prodigal
[2024-01-24 14:46:37,181] [INFO] Running command: gunzip -c /var/lib/cwl/stg5bbc3e2d-45b1-4e74-bdab-b9edd84b919d/GCF_014270035.1_ASM1427003v1_genomic.fna.gz | prodigal -d GCF_014270035.1_ASM1427003v1_genomic.fna/cds.fna -a GCF_014270035.1_ASM1427003v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:46:46,782] [INFO] Task succeeded: Prodigal
[2024-01-24 14:46:46,782] [INFO] Task started: HMMsearch
[2024-01-24 14:46:46,782] [INFO] Running command: hmmsearch --tblout GCF_014270035.1_ASM1427003v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg103b938f-81ac-41bc-a9df-7849ecea675e/dqc_reference/reference_markers.hmm GCF_014270035.1_ASM1427003v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:46:47,006] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:46:47,007] [INFO] Found 6/6 markers.
[2024-01-24 14:46:47,043] [INFO] Query marker FASTA was written to GCF_014270035.1_ASM1427003v1_genomic.fna/markers.fasta
[2024-01-24 14:46:47,043] [INFO] Task started: Blastn
[2024-01-24 14:46:47,043] [INFO] Running command: blastn -query GCF_014270035.1_ASM1427003v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg103b938f-81ac-41bc-a9df-7849ecea675e/dqc_reference/reference_markers.fasta -out GCF_014270035.1_ASM1427003v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:46:47,753] [INFO] Task succeeded: Blastn
[2024-01-24 14:46:47,756] [INFO] Selected 28 target genomes.
[2024-01-24 14:46:47,756] [INFO] Target genome list was writen to GCF_014270035.1_ASM1427003v1_genomic.fna/target_genomes.txt
[2024-01-24 14:46:47,845] [INFO] Task started: fastANI
[2024-01-24 14:46:47,845] [INFO] Running command: fastANI --query /var/lib/cwl/stg5bbc3e2d-45b1-4e74-bdab-b9edd84b919d/GCF_014270035.1_ASM1427003v1_genomic.fna.gz --refList GCF_014270035.1_ASM1427003v1_genomic.fna/target_genomes.txt --output GCF_014270035.1_ASM1427003v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:06,253] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:06,254] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg103b938f-81ac-41bc-a9df-7849ecea675e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:06,254] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg103b938f-81ac-41bc-a9df-7849ecea675e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:06,267] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:47:06,268] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:06,268] [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
Neptunicella marina	strain=S27-2	GCA_014270035.1	2125989	2125989	type	True	100.0	1357	1357	95	conclusive
Alteromonas alba	strain=190	GCA_002993365.1	2079529	2079529	type	True	78.5739	109	1357	95	below_threshold
Alteromonas oceani	strain=S35	GCA_003731635.1	2071609	2071609	type	True	78.5228	116	1357	95	below_threshold
Salinimonas lutimaris	strain=DPSR-4	GCA_005222225.1	914153	914153	type	True	77.8763	91	1357	95	below_threshold
Alteromonas facilis	strain=P0213	GCA_002807665.1	2048004	2048004	type	True	77.5645	73	1357	95	below_threshold
Paraglaciecola polaris	strain=LMG 21857	GCA_000315055.1	222814	222814	type	True	77.3562	77	1357	95	below_threshold
Aestuariibacter salexigens	strain=DSM 15300	GCA_000429145.1	226010	226010	type	True	77.2743	74	1357	95	below_threshold
Alteromonas lipolytica	strain=JW12	GCA_001758465.1	1856405	1856405	type	True	77.2394	120	1357	95	below_threshold
Paraneptunicella aestuarii	strain=NBU2194	GCA_019900845.1	2831148	2831148	type	True	77.2339	90	1357	95	below_threshold
Alteromonas halophila	strain=KCTC 22164	GCA_014651815.1	516698	516698	type	True	77.2291	70	1357	95	below_threshold
Planctobacterium marinum	strain=K7	GCA_020687805.1	1631968	1631968	type	True	77.2018	85	1357	95	below_threshold
Paraglaciecola aquimarina	strain=GGW-M5	GCA_021532655.1	1235557	1235557	type	True	77.1864	88	1357	95	below_threshold
Paraglaciecola hydrolytica	strain=S66	GCA_001565895.1	1799789	1799789	type	True	77.0798	128	1357	95	below_threshold
Alteromonas lipolytica	strain=CGMCC 1.15735	GCA_014643555.1	1856405	1856405	type	True	77.0639	115	1357	95	below_threshold
Lacimicrobium alkaliphilum	strain=X13M-12	GCA_002591895.1	1526571	1526571	type	True	76.8802	79	1357	95	below_threshold
Lacimicrobium alkaliphilum	strain=CGMCC 1.12923	GCA_014640135.1	1526571	1526571	type	True	76.804	79	1357	95	below_threshold
Pseudoalteromonas spongiae	strain=UST010723-006	GCA_000238255.4	298657	298657	type	True	76.5863	50	1357	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:06,269] [INFO] DFAST Taxonomy check result was written to GCF_014270035.1_ASM1427003v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:06,270] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:06,270] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:06,270] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg103b938f-81ac-41bc-a9df-7849ecea675e/dqc_reference/checkm_data
[2024-01-24 14:47:06,271] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:06,308] [INFO] Task started: CheckM
[2024-01-24 14:47:06,308] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014270035.1_ASM1427003v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014270035.1_ASM1427003v1_genomic.fna/checkm_input GCF_014270035.1_ASM1427003v1_genomic.fna/checkm_result
[2024-01-24 14:47:38,556] [INFO] Task succeeded: CheckM
[2024-01-24 14:47:38,557] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:47:38,575] [INFO] ===== Completeness check finished =====
[2024-01-24 14:47:38,576] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:47:38,576] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014270035.1_ASM1427003v1_genomic.fna/markers.fasta)
[2024-01-24 14:47:38,576] [INFO] Task started: Blastn
[2024-01-24 14:47:38,576] [INFO] Running command: blastn -query GCF_014270035.1_ASM1427003v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg103b938f-81ac-41bc-a9df-7849ecea675e/dqc_reference/reference_markers_gtdb.fasta -out GCF_014270035.1_ASM1427003v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:39,681] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:39,684] [INFO] Selected 27 target genomes.
[2024-01-24 14:47:39,684] [INFO] Target genome list was writen to GCF_014270035.1_ASM1427003v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:47:39,709] [INFO] Task started: fastANI
[2024-01-24 14:47:39,709] [INFO] Running command: fastANI --query /var/lib/cwl/stg5bbc3e2d-45b1-4e74-bdab-b9edd84b919d/GCF_014270035.1_ASM1427003v1_genomic.fna.gz --refList GCF_014270035.1_ASM1427003v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014270035.1_ASM1427003v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:01,824] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:01,842] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:01,842] [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_014270035.1	s__Neptunicella marina	100.0	1357	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Neptunicella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002993365.1	s__Alteromonas alba	78.5815	108	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009796765.1	s__Paraglaciecola sp009796765	77.8664	73	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001660395.1	s__XY-R5 sp001660395	77.6966	136	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__XY-R5	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004329715.1	s__JS7-9 sp004329715	77.5678	126	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__JS7-9	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002807665.1	s__Alteromonas_E facilis	77.5608	72	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000597705.1	s__Alteromonas sp000597705	77.5146	72	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.20	99.20	0.96	0.96	2	-
GCF_018861065.1	s__Paraglaciecola arctica_B	77.4579	68	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000315055.1	s__Paraglaciecola polaris	77.4229	75	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018531185.1	s__Bowmanella sp018531185	77.3395	100	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Bowmanella	95.0	96.11	96.11	0.88	0.88	2	-
GCF_006538345.1	s__Alteromonas sp006538345	77.3091	53	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000429145.1	s__Aestuariibacter salexigens	77.27	74	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aestuariibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651815.1	s__Alteromonas halophila	77.2668	67	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129565.1	s__Alteromonas aggregata	77.172	94	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.34	96.39	0.91	0.85	11	-
GCF_000314995.1	s__Paraglaciecola arctica	77.1056	82	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009906955.1	s__Paraglaciecola mesophila_A	77.0837	92	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001565895.1	s__Paraglaciecola hydrolytica	77.0417	129	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009796745.1	s__Paraglaciecola sp009796745	77.0233	92	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003203515.1	s__Glaciecola sp003203515	76.8879	52	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002292215.1	s__Glaciecola sp002292215	76.5326	53	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	99.49	98.83	0.91	0.88	4	-
GCF_001466725.1	s__Lacimicrobium alkaliphilum_B	76.402	100	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Lacimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004005375.1	s__Pararheinheimera sp004005375	76.3851	66	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018825965.1	s__Pararheinheimera sp018825965	76.3457	66	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	99.98	99.95	0.98	0.97	7	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:01,843] [INFO] GTDB search result was written to GCF_014270035.1_ASM1427003v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:01,844] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:01,848] [INFO] DFAST_QC result json was written to GCF_014270035.1_ASM1427003v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:01,848] [INFO] DFAST_QC completed!
[2024-01-24 14:48:01,848] [INFO] Total running time: 0h1m26s