[2024-01-24 12:07:18,847] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:07:18,848] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:07:18,849] [INFO] DQC Reference Directory: /var/lib/cwl/stg4199e875-6dce-4d88-adab-02438dcd554e/dqc_reference
[2024-01-24 12:07:20,038] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:07:20,039] [INFO] Task started: Prodigal
[2024-01-24 12:07:20,039] [INFO] Running command: gunzip -c /var/lib/cwl/stg9e43d5c6-5600-4010-b149-26aa29a582a3/GCF_014925325.1_ASM1492532v1_genomic.fna.gz | prodigal -d GCF_014925325.1_ASM1492532v1_genomic.fna/cds.fna -a GCF_014925325.1_ASM1492532v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:07:34,920] [INFO] Task succeeded: Prodigal
[2024-01-24 12:07:34,920] [INFO] Task started: HMMsearch
[2024-01-24 12:07:34,921] [INFO] Running command: hmmsearch --tblout GCF_014925325.1_ASM1492532v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4199e875-6dce-4d88-adab-02438dcd554e/dqc_reference/reference_markers.hmm GCF_014925325.1_ASM1492532v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:07:35,254] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:07:35,256] [INFO] Found 6/6 markers.
[2024-01-24 12:07:35,309] [INFO] Query marker FASTA was written to GCF_014925325.1_ASM1492532v1_genomic.fna/markers.fasta
[2024-01-24 12:07:35,309] [INFO] Task started: Blastn
[2024-01-24 12:07:35,309] [INFO] Running command: blastn -query GCF_014925325.1_ASM1492532v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4199e875-6dce-4d88-adab-02438dcd554e/dqc_reference/reference_markers.fasta -out GCF_014925325.1_ASM1492532v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:36,055] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:36,059] [INFO] Selected 22 target genomes.
[2024-01-24 12:07:36,059] [INFO] Target genome list was writen to GCF_014925325.1_ASM1492532v1_genomic.fna/target_genomes.txt
[2024-01-24 12:07:36,068] [INFO] Task started: fastANI
[2024-01-24 12:07:36,068] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e43d5c6-5600-4010-b149-26aa29a582a3/GCF_014925325.1_ASM1492532v1_genomic.fna.gz --refList GCF_014925325.1_ASM1492532v1_genomic.fna/target_genomes.txt --output GCF_014925325.1_ASM1492532v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:54,305] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:54,306] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4199e875-6dce-4d88-adab-02438dcd554e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:54,306] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4199e875-6dce-4d88-adab-02438dcd554e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:54,323] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:07:54,323] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:54,324] [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
Pseudoalteromonas luteoviolacea	strain=CH130	GCA_014925325.1	43657	43657	suspected-type	True	100.0	1994	1996	95	conclusive
Pseudoalteromonas luteoviolacea	strain=DSM 6061	GCA_001625655.1	43657	43657	suspected-type	True	99.9549	1884	1996	95	conclusive
Pseudoalteromonas galatheae	strain=S4498	GCA_005886105.2	579562	579562	type	True	79.4342	284	1996	95	below_threshold
Pseudoalteromonas piscicida	strain=JCM 20779	GCA_000238315.4	43662	43662	type	True	79.4301	282	1996	95	below_threshold
Pseudoalteromonas piscicida	strain=ATCC 15057	GCA_000382005.1	43662	43662	type	True	79.2414	278	1996	95	below_threshold
Pseudoalteromonas flavipulchra	strain=LMG 20361	GCA_014596995.1	137779	137779	suspected-type	True	79.2317	270	1996	95	below_threshold
Pseudoalteromonas phenolica	strain=O-BC30	GCA_014925335.1	161398	161398	suspected-type	True	79.2251	306	1996	95	below_threshold
Pseudoalteromonas peptidolytica	strain=F12-50-A1	GCA_014858745.1	61150	61150	type	True	79.2006	264	1996	95	below_threshold
Pseudoalteromonas byunsanensis	strain=JCM 12483	GCA_001854475.1	327939	327939	type	True	79.13	255	1996	95	below_threshold
Pseudoalteromonas phenolica	strain=KCTC 12086	GCA_001444405.1	161398	161398	suspected-type	True	79.0854	310	1996	95	below_threshold
Pseudoalteromonas caenipelagi	strain=JBTF-M23	GCA_013140855.1	2726988	2726988	type	True	79.0798	266	1996	95	below_threshold
Pseudoalteromonas amylolytica	strain=JW1	GCA_001854605.1	1859457	1859457	type	True	79.0748	270	1996	95	below_threshold
Pseudoalteromonas peptidolytica	strain=DSM 14001	GCA_012641745.1	61150	61150	type	True	79.0741	263	1996	95	below_threshold
Pseudoalteromonas peptidolytica	strain=NBRC 101021	GCA_007989895.1	61150	61150	type	True	79.0469	242	1996	95	below_threshold
Pseudoalteromonas rubra	strain=DSM 6842	GCA_000238295.4	43658	43658	suspected-type	True	78.9029	340	1996	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	78.3428	184	1996	95	below_threshold
Vibrio comitans	strain=LMG 23416	GCA_024346835.1	413401	413401	type	True	78.2369	51	1996	95	below_threshold
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	78.2253	69	1996	95	below_threshold
Pseudoalteromonas rhizosphaerae	strain=RA15	GCA_902498845.1	2518973	2518973	type	True	78.1992	192	1996	95	below_threshold
Vibrio kanaloae	strain=LMG 20539	GCA_024347535.1	170673	170673	type	True	78.0566	57	1996	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:54,325] [INFO] DFAST Taxonomy check result was written to GCF_014925325.1_ASM1492532v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:54,326] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:54,326] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:54,326] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4199e875-6dce-4d88-adab-02438dcd554e/dqc_reference/checkm_data
[2024-01-24 12:07:54,328] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:54,387] [INFO] Task started: CheckM
[2024-01-24 12:07:54,387] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014925325.1_ASM1492532v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014925325.1_ASM1492532v1_genomic.fna/checkm_input GCF_014925325.1_ASM1492532v1_genomic.fna/checkm_result
[2024-01-24 12:08:41,668] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:41,670] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:41,693] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:41,693] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:41,694] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014925325.1_ASM1492532v1_genomic.fna/markers.fasta)
[2024-01-24 12:08:41,694] [INFO] Task started: Blastn
[2024-01-24 12:08:41,694] [INFO] Running command: blastn -query GCF_014925325.1_ASM1492532v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4199e875-6dce-4d88-adab-02438dcd554e/dqc_reference/reference_markers_gtdb.fasta -out GCF_014925325.1_ASM1492532v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:42,785] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:42,793] [INFO] Selected 7 target genomes.
[2024-01-24 12:08:42,793] [INFO] Target genome list was writen to GCF_014925325.1_ASM1492532v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:42,798] [INFO] Task started: fastANI
[2024-01-24 12:08:42,798] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e43d5c6-5600-4010-b149-26aa29a582a3/GCF_014925325.1_ASM1492532v1_genomic.fna.gz --refList GCF_014925325.1_ASM1492532v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014925325.1_ASM1492532v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:52,604] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:52,614] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:52,615] [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_001625655.1	s__Pseudoalteromonas luteoviolacea	99.9549	1884	1996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.50	98.88	0.97	0.94	4	conclusive
GCF_001625595.1	s__Pseudoalteromonas luteoviolacea_A	83.5115	1101	1996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.64	99.64	0.92	0.92	2	-
GCF_001696455.1	s__Pseudoalteromonas luteoviolacea_C	83.32	1202	1996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.80	98.80	0.96	0.96	2	-
GCF_001625575.1	s__Pseudoalteromonas luteoviolacea_E	83.1899	1188	1996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.25	97.25	0.92	0.92	2	-
GCF_001625695.1	s__Pseudoalteromonas luteoviolacea_B	81.5068	763	1996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.59	99.39	0.98	0.96	4	-
GCF_000814765.1	s__Pseudoalteromonas luteoviolacea_H	81.3347	774	1996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	95.23	95.23	0.92	0.92	2	-
GCF_001625565.1	s__Pseudoalteromonas luteoviolacea_F	81.0598	814	1996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:52,616] [INFO] GTDB search result was written to GCF_014925325.1_ASM1492532v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:52,617] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:52,621] [INFO] DFAST_QC result json was written to GCF_014925325.1_ASM1492532v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:52,621] [INFO] DFAST_QC completed!
[2024-01-24 12:08:52,621] [INFO] Total running time: 0h1m34s