[2024-01-24 13:01:26,639] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:26,641] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:26,641] [INFO] DQC Reference Directory: /var/lib/cwl/stga7271574-05a8-41c9-95ce-24152e22e136/dqc_reference
[2024-01-24 13:01:28,010] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:28,011] [INFO] Task started: Prodigal
[2024-01-24 13:01:28,011] [INFO] Running command: gunzip -c /var/lib/cwl/stgb57c16a4-3085-4d6c-b1b3-7eed9fd1aa12/GCF_900129565.1_IMG-taxon_2675903007_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900129565.1_IMG-taxon_2675903007_annotated_assembly_genomic.fna/cds.fna -a GCF_900129565.1_IMG-taxon_2675903007_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:41,708] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:41,708] [INFO] Task started: HMMsearch
[2024-01-24 13:01:41,708] [INFO] Running command: hmmsearch --tblout GCF_900129565.1_IMG-taxon_2675903007_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga7271574-05a8-41c9-95ce-24152e22e136/dqc_reference/reference_markers.hmm GCF_900129565.1_IMG-taxon_2675903007_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:42,084] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:42,086] [INFO] Found 6/6 markers.
[2024-01-24 13:01:42,143] [INFO] Query marker FASTA was written to GCF_900129565.1_IMG-taxon_2675903007_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:01:42,144] [INFO] Task started: Blastn
[2024-01-24 13:01:42,144] [INFO] Running command: blastn -query GCF_900129565.1_IMG-taxon_2675903007_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga7271574-05a8-41c9-95ce-24152e22e136/dqc_reference/reference_markers.fasta -out GCF_900129565.1_IMG-taxon_2675903007_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:42,943] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:42,947] [INFO] Selected 26 target genomes.
[2024-01-24 13:01:42,947] [INFO] Target genome list was writen to GCF_900129565.1_IMG-taxon_2675903007_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:01:42,975] [INFO] Task started: fastANI
[2024-01-24 13:01:42,975] [INFO] Running command: fastANI --query /var/lib/cwl/stgb57c16a4-3085-4d6c-b1b3-7eed9fd1aa12/GCF_900129565.1_IMG-taxon_2675903007_annotated_assembly_genomic.fna.gz --refList GCF_900129565.1_IMG-taxon_2675903007_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900129565.1_IMG-taxon_2675903007_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:01,290] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:01,291] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga7271574-05a8-41c9-95ce-24152e22e136/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:01,292] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga7271574-05a8-41c9-95ce-24152e22e136/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:01,306] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:02:01,306] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:02:01,307] [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 alba	strain=190	GCA_002993365.1	2079529	2079529	type	True	79.4299	444	1627	95	below_threshold
Alteromonas oceani	strain=S35	GCA_003731635.1	2071609	2071609	type	True	79.2139	459	1627	95	below_threshold
Alteromonas lipolytica	strain=JW12	GCA_001758465.1	1856405	1856405	type	True	79.1228	420	1627	95	below_threshold
Alteromonas lipolytica	strain=CGMCC 1.15735	GCA_014643555.1	1856405	1856405	type	True	79.118	412	1627	95	below_threshold
Alteromonas macleodii	strain=ATCC 27126	GCA_000172635.2	28108	28108	type	True	78.608	160	1627	95	below_threshold
Alteromonas mediterranea	strain=DE	GCA_000020585.3	314275	314275	type	True	78.5081	167	1627	95	below_threshold
Alteromonas abrolhosensis	strain=PEL67E	GCA_001953635.1	1892904	1892904	type	True	78.399	162	1627	95	below_threshold
Alteromonas gracilis	strain=9a2	GCA_002993325.1	1479524	1479524	type	True	78.2929	158	1627	95	below_threshold
Alteromonas confluentis	strain=KCTC 42603	GCA_001757105.1	1656094	1656094	type	True	78.1137	229	1627	95	below_threshold
Alteromonas antoniana	strain=MD_567	GCA_019249295.1	2803813	2803813	type	True	78.0676	194	1627	95	below_threshold
Alteromonas portus	strain=HB161718	GCA_005117025.1	2565549	2565549	type	True	78.0439	170	1627	95	below_threshold
Salinimonas lutimaris	strain=DPSR-4	GCA_005222225.1	914153	914153	type	True	78.0425	182	1627	95	below_threshold
Alteromonas halophila	strain=KCTC 22164	GCA_014651815.1	516698	516698	type	True	77.8164	171	1627	95	below_threshold
Paraglaciecola mesophila	strain=KMM 241	GCA_000315015.1	197222	197222	type	True	77.2459	75	1627	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:01,308] [INFO] DFAST Taxonomy check result was written to GCF_900129565.1_IMG-taxon_2675903007_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:02:01,309] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:01,309] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:01,310] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga7271574-05a8-41c9-95ce-24152e22e136/dqc_reference/checkm_data
[2024-01-24 13:02:01,311] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:01,360] [INFO] Task started: CheckM
[2024-01-24 13:02:01,360] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900129565.1_IMG-taxon_2675903007_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900129565.1_IMG-taxon_2675903007_annotated_assembly_genomic.fna/checkm_input GCF_900129565.1_IMG-taxon_2675903007_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:02:42,478] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:42,480] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:42,505] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:42,506] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:42,506] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900129565.1_IMG-taxon_2675903007_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:02:42,507] [INFO] Task started: Blastn
[2024-01-24 13:02:42,507] [INFO] Running command: blastn -query GCF_900129565.1_IMG-taxon_2675903007_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga7271574-05a8-41c9-95ce-24152e22e136/dqc_reference/reference_markers_gtdb.fasta -out GCF_900129565.1_IMG-taxon_2675903007_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:43,510] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:43,514] [INFO] Selected 16 target genomes.
[2024-01-24 13:02:43,514] [INFO] Target genome list was writen to GCF_900129565.1_IMG-taxon_2675903007_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:43,535] [INFO] Task started: fastANI
[2024-01-24 13:02:43,535] [INFO] Running command: fastANI --query /var/lib/cwl/stgb57c16a4-3085-4d6c-b1b3-7eed9fd1aa12/GCF_900129565.1_IMG-taxon_2675903007_annotated_assembly_genomic.fna.gz --refList GCF_900129565.1_IMG-taxon_2675903007_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900129565.1_IMG-taxon_2675903007_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:56,017] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:56,033] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:56,033] [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_900129565.1	s__Alteromonas aggregata	100.0	1624	1627	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.34	96.39	0.91	0.85	11	conclusive
GCA_017794925.1	s__Alteromonas sp017794925	87.1266	1122	1627	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006494365.1	s__Alteromonas mangrovi	82.421	976	1627	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	79.4264	444	1627	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003731635.1	s__Alteromonas oceani	79.2002	460	1627	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001758465.1	s__Alteromonas lipolytica	79.1335	419	1627	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.99	99.99	1.00	1.00	2	-
GCA_002339125.1	s__Alteromonas sp002335925	79.0818	402	1627	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.57	96.36	0.89	0.83	19	-
GCF_001885075.1	s__Alteromonas sp001885075	78.534	169	1627	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000020585.3	s__Alteromonas mediterranea	78.4858	168	1627	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.15	97.41	0.86	0.82	24	-
GCA_013373625.1	s__Alteromonas sp013373625	78.3836	341	1627	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222225.1	s__Alteromonas lutimaris	78.0872	179	1627	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003367475.1	s__Alteromonas aestuariivivens	77.8786	179	1627	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015644725.1	s__Alteromonas sp015644725	77.663	153	1627	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:56,035] [INFO] GTDB search result was written to GCF_900129565.1_IMG-taxon_2675903007_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:56,035] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:56,040] [INFO] DFAST_QC result json was written to GCF_900129565.1_IMG-taxon_2675903007_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:02:56,040] [INFO] DFAST_QC completed!
[2024-01-24 13:02:56,040] [INFO] Total running time: 0h1m29s