[2024-01-24 14:28:17,882] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:17,886] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:17,886] [INFO] DQC Reference Directory: /var/lib/cwl/stg4889868f-3aca-4636-8872-672d1bdcf7af/dqc_reference
[2024-01-24 14:28:20,482] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:20,483] [INFO] Task started: Prodigal
[2024-01-24 14:28:20,483] [INFO] Running command: gunzip -c /var/lib/cwl/stg87db422f-62a8-4dac-a027-d54b87146ff7/GCF_000272005.1_ASM27200v1_genomic.fna.gz | prodigal -d GCF_000272005.1_ASM27200v1_genomic.fna/cds.fna -a GCF_000272005.1_ASM27200v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:29,142] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:29,143] [INFO] Task started: HMMsearch
[2024-01-24 14:28:29,143] [INFO] Running command: hmmsearch --tblout GCF_000272005.1_ASM27200v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4889868f-3aca-4636-8872-672d1bdcf7af/dqc_reference/reference_markers.hmm GCF_000272005.1_ASM27200v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:29,458] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:29,460] [INFO] Found 6/6 markers.
[2024-01-24 14:28:29,496] [INFO] Query marker FASTA was written to GCF_000272005.1_ASM27200v1_genomic.fna/markers.fasta
[2024-01-24 14:28:29,497] [INFO] Task started: Blastn
[2024-01-24 14:28:29,497] [INFO] Running command: blastn -query GCF_000272005.1_ASM27200v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4889868f-3aca-4636-8872-672d1bdcf7af/dqc_reference/reference_markers.fasta -out GCF_000272005.1_ASM27200v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:30,328] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:30,332] [INFO] Selected 14 target genomes.
[2024-01-24 14:28:30,332] [INFO] Target genome list was writen to GCF_000272005.1_ASM27200v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:30,338] [INFO] Task started: fastANI
[2024-01-24 14:28:30,338] [INFO] Running command: fastANI --query /var/lib/cwl/stg87db422f-62a8-4dac-a027-d54b87146ff7/GCF_000272005.1_ASM27200v1_genomic.fna.gz --refList GCF_000272005.1_ASM27200v1_genomic.fna/target_genomes.txt --output GCF_000272005.1_ASM27200v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:41,633] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:41,633] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4889868f-3aca-4636-8872-672d1bdcf7af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:41,634] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4889868f-3aca-4636-8872-672d1bdcf7af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:41,645] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:28:41,646] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:28:41,646] [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
Alishewanella agri	strain=BL06	GCA_000272005.1	553384	553384	type	True	100.0	1146	1147	95	conclusive
Alishewanella aestuarii	strain=B11	GCA_000280055.1	453835	453835	type	True	89.6827	812	1147	95	below_threshold
Alishewanella jeotgali	strain=KCTC 22429	GCA_000245735.2	545533	545533	type	True	89.2746	834	1147	95	below_threshold
Alishewanella longhuensis	strain=CGMCC 1.7003	GCA_014653435.1	1091037	1091037	type	True	79.7551	482	1147	95	below_threshold
Rheinheimera nanhaiensis	strain=E407-8	GCA_000296695.1	1163621	1163621	type	True	79.2622	381	1147	95	below_threshold
Alishewanella tabrizica	strain=KCTC 23723	GCA_014652375.1	671278	671278	type	True	79.2495	374	1147	95	below_threshold
Rheinheimera pacifica	strain=DSM 17616	GCA_900108485.1	173990	173990	type	True	79.1861	378	1147	95	below_threshold
Arsukibacterium tuosuense	strain=CGMCC 1.12461	GCA_900215315.1	1323745	1323745	type	True	78.4538	315	1147	95	below_threshold
Rheinheimera lutimaris	strain=YQF-2	GCA_013283795.1	2740584	2740584	type	True	78.3463	341	1147	95	below_threshold
Rheinheimera hassiensis	strain=LMG 27268	GCA_022436675.1	1193627	1193627	type	True	78.3255	330	1147	95	below_threshold
Pararheinheimera mesophila	strain=IITR13	GCA_003862465.1	1547515	1547515	type	True	77.7193	203	1147	95	below_threshold
Pararheinheimera mesophila	strain=IITR-13	GCA_000986865.1	1547515	1547515	type	True	77.6283	197	1147	95	below_threshold
Shewanella jiangmenensis	strain=JM162201	GCA_018596335.1	2837387	2837387	type	True	76.3091	62	1147	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:41,647] [INFO] DFAST Taxonomy check result was written to GCF_000272005.1_ASM27200v1_genomic.fna/tc_result.tsv
[2024-01-24 14:28:41,648] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:41,648] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:41,648] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4889868f-3aca-4636-8872-672d1bdcf7af/dqc_reference/checkm_data
[2024-01-24 14:28:41,650] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:41,686] [INFO] Task started: CheckM
[2024-01-24 14:28:41,686] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000272005.1_ASM27200v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000272005.1_ASM27200v1_genomic.fna/checkm_input GCF_000272005.1_ASM27200v1_genomic.fna/checkm_result
[2024-01-24 14:29:12,503] [INFO] Task succeeded: CheckM
[2024-01-24 14:29:12,504] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:29:12,523] [INFO] ===== Completeness check finished =====
[2024-01-24 14:29:12,524] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:29:12,524] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000272005.1_ASM27200v1_genomic.fna/markers.fasta)
[2024-01-24 14:29:12,525] [INFO] Task started: Blastn
[2024-01-24 14:29:12,525] [INFO] Running command: blastn -query GCF_000272005.1_ASM27200v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4889868f-3aca-4636-8872-672d1bdcf7af/dqc_reference/reference_markers_gtdb.fasta -out GCF_000272005.1_ASM27200v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:29:13,788] [INFO] Task succeeded: Blastn
[2024-01-24 14:29:13,791] [INFO] Selected 12 target genomes.
[2024-01-24 14:29:13,792] [INFO] Target genome list was writen to GCF_000272005.1_ASM27200v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:29:13,803] [INFO] Task started: fastANI
[2024-01-24 14:29:13,803] [INFO] Running command: fastANI --query /var/lib/cwl/stg87db422f-62a8-4dac-a027-d54b87146ff7/GCF_000272005.1_ASM27200v1_genomic.fna.gz --refList GCF_000272005.1_ASM27200v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000272005.1_ASM27200v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:29:23,840] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:23,852] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:29:23,852] [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_000272005.1	s__Alishewanella agri	100.0	1146	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alishewanella	95.0	96.64	95.87	0.84	0.80	3	conclusive
GCF_000280055.1	s__Alishewanella aestuarii	89.6827	812	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alishewanella	95.6353	96.26	96.26	0.87	0.87	2	-
GCF_000245735.1	s__Alishewanella jeotgali	89.3053	833	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alishewanella	95.6353	N/A	N/A	N/A	N/A	1	-
GCF_014653435.1	s__Alishewanella longhuensis	79.7659	481	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alishewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000296695.1	s__Rheinheimera nanhaiensis	79.2622	381	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652375.1	s__Alishewanella tabrizica	79.2559	373	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alishewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108485.1	s__Rheinheimera pacifica	79.1924	377	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002840125.1	s__Rheinheimera sp002840125	78.9043	363	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215315.1	s__Arsukibacterium tuosuense	78.4538	315	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013283795.1	s__Rheinheimera sp013283795	78.3348	342	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018826295.1	s__Rheinheimera sp018826295	78.2673	336	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	99.95	99.91	0.97	0.92	5	-
GCA_008015325.1	s__Pararheinheimera sp008015325	77.1925	186	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:29:23,855] [INFO] GTDB search result was written to GCF_000272005.1_ASM27200v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:29:23,856] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:29:23,860] [INFO] DFAST_QC result json was written to GCF_000272005.1_ASM27200v1_genomic.fna/dqc_result.json
[2024-01-24 14:29:23,861] [INFO] DFAST_QC completed!
[2024-01-24 14:29:23,861] [INFO] Total running time: 0h1m6s