[2024-01-24 13:22:02,522] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:02,524] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:02,525] [INFO] DQC Reference Directory: /var/lib/cwl/stg376d0b0f-ce04-49f2-a60c-7068b60a1ddc/dqc_reference
[2024-01-24 13:22:03,916] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:03,918] [INFO] Task started: Prodigal
[2024-01-24 13:22:03,918] [INFO] Running command: gunzip -c /var/lib/cwl/stg854bf80e-24eb-4951-aee6-8c70b15b7f75/GCF_900215315.1_IMG-taxon_2721755863_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900215315.1_IMG-taxon_2721755863_annotated_assembly_genomic.fna/cds.fna -a GCF_900215315.1_IMG-taxon_2721755863_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:14,256] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:14,257] [INFO] Task started: HMMsearch
[2024-01-24 13:22:14,257] [INFO] Running command: hmmsearch --tblout GCF_900215315.1_IMG-taxon_2721755863_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg376d0b0f-ce04-49f2-a60c-7068b60a1ddc/dqc_reference/reference_markers.hmm GCF_900215315.1_IMG-taxon_2721755863_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:14,597] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:14,598] [INFO] Found 6/6 markers.
[2024-01-24 13:22:14,637] [INFO] Query marker FASTA was written to GCF_900215315.1_IMG-taxon_2721755863_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:22:14,637] [INFO] Task started: Blastn
[2024-01-24 13:22:14,637] [INFO] Running command: blastn -query GCF_900215315.1_IMG-taxon_2721755863_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg376d0b0f-ce04-49f2-a60c-7068b60a1ddc/dqc_reference/reference_markers.fasta -out GCF_900215315.1_IMG-taxon_2721755863_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:15,413] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:15,416] [INFO] Selected 14 target genomes.
[2024-01-24 13:22:15,416] [INFO] Target genome list was writen to GCF_900215315.1_IMG-taxon_2721755863_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:22:15,419] [INFO] Task started: fastANI
[2024-01-24 13:22:15,419] [INFO] Running command: fastANI --query /var/lib/cwl/stg854bf80e-24eb-4951-aee6-8c70b15b7f75/GCF_900215315.1_IMG-taxon_2721755863_annotated_assembly_genomic.fna.gz --refList GCF_900215315.1_IMG-taxon_2721755863_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900215315.1_IMG-taxon_2721755863_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:26,444] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:26,444] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg376d0b0f-ce04-49f2-a60c-7068b60a1ddc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:26,445] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg376d0b0f-ce04-49f2-a60c-7068b60a1ddc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:26,458] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:26,460] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:26,460] [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
Arsukibacterium tuosuense	strain=CGMCC 1.12461	GCA_900215315.1	1323745	1323745	type	True	100.0	1332	1332	95	conclusive
Arsukibacterium perlucidum	strain=DSM 18276	GCA_000382165.1	368811	368811	type	True	86.1592	988	1332	95	below_threshold
Arsukibacterium indicum	strain=SM2107	GCA_019100565.1	2848612	2848612	type	True	82.7854	932	1332	95	below_threshold
Rheinheimera pacifica	strain=DSM 17616	GCA_900108485.1	173990	173990	type	True	78.9551	456	1332	95	below_threshold
Rheinheimera maricola	strain=MA-13	GCA_016918075.2	2793282	2793282	type	True	78.8556	382	1332	95	below_threshold
Rheinheimera lutimaris	strain=YQF-2	GCA_013283795.1	2740584	2740584	type	True	78.8214	441	1332	95	below_threshold
Rheinheimera pleomorphica	strain=PKS7	GCA_011634895.1	2703963	2703963	type	True	78.8208	430	1332	95	below_threshold
Rheinheimera hassiensis	strain=LMG 27268	GCA_022436675.1	1193627	1193627	type	True	78.8151	440	1332	95	below_threshold
Rheinheimera nanhaiensis	strain=E407-8	GCA_000296695.1	1163621	1163621	type	True	78.7996	417	1332	95	below_threshold
Rheinheimera maricola	strain=MA-13	GCA_017824735.1	2793282	2793282	type	True	78.7289	391	1332	95	below_threshold
Rheinheimera aquimaris	strain=KCTC 12840	GCA_020531985.1	412437	412437	type	True	78.6358	361	1332	95	below_threshold
Alishewanella longhuensis	strain=CGMCC 1.7003	GCA_014653435.1	1091037	1091037	type	True	78.4811	281	1332	95	below_threshold
Alishewanella agri	strain=BL06	GCA_000272005.1	553384	553384	type	True	78.3853	312	1332	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:26,466] [INFO] DFAST Taxonomy check result was written to GCF_900215315.1_IMG-taxon_2721755863_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:22:26,466] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:26,466] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:26,467] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg376d0b0f-ce04-49f2-a60c-7068b60a1ddc/dqc_reference/checkm_data
[2024-01-24 13:22:26,468] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:26,512] [INFO] Task started: CheckM
[2024-01-24 13:22:26,512] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900215315.1_IMG-taxon_2721755863_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900215315.1_IMG-taxon_2721755863_annotated_assembly_genomic.fna/checkm_input GCF_900215315.1_IMG-taxon_2721755863_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:23:01,330] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:01,332] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:01,353] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:01,354] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:01,354] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900215315.1_IMG-taxon_2721755863_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:23:01,355] [INFO] Task started: Blastn
[2024-01-24 13:23:01,355] [INFO] Running command: blastn -query GCF_900215315.1_IMG-taxon_2721755863_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg376d0b0f-ce04-49f2-a60c-7068b60a1ddc/dqc_reference/reference_markers_gtdb.fasta -out GCF_900215315.1_IMG-taxon_2721755863_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:02,560] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:02,565] [INFO] Selected 7 target genomes.
[2024-01-24 13:23:02,565] [INFO] Target genome list was writen to GCF_900215315.1_IMG-taxon_2721755863_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:02,575] [INFO] Task started: fastANI
[2024-01-24 13:23:02,576] [INFO] Running command: fastANI --query /var/lib/cwl/stg854bf80e-24eb-4951-aee6-8c70b15b7f75/GCF_900215315.1_IMG-taxon_2721755863_annotated_assembly_genomic.fna.gz --refList GCF_900215315.1_IMG-taxon_2721755863_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900215315.1_IMG-taxon_2721755863_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:09,317] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:09,328] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:09,328] [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_900215315.1	s__Arsukibacterium tuosuense	100.0	1332	1332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018402695.1	s__Arsukibacterium sp018402695	87.2145	1070	1332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382165.1	s__Arsukibacterium perlucidum	86.1725	986	1332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019100565.1	s__Arsukibacterium sp019100565	82.7854	932	1332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000987775.1	s__Arsukibacterium ikkense	81.7966	851	1332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002415085.1	s__Arsukibacterium sp002415085	81.6594	863	1332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	99.96	99.86	0.96	0.90	7	-
GCA_002364615.1	s__Arsukibacterium sp002364615	81.48	841	1332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	99.93	99.93	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:09,330] [INFO] GTDB search result was written to GCF_900215315.1_IMG-taxon_2721755863_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:09,331] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:09,335] [INFO] DFAST_QC result json was written to GCF_900215315.1_IMG-taxon_2721755863_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:23:09,335] [INFO] DFAST_QC completed!
[2024-01-24 13:23:09,335] [INFO] Total running time: 0h1m7s