[2024-01-25 18:10:50,321] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:10:50,322] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:10:50,323] [INFO] DQC Reference Directory: /var/lib/cwl/stgd389365b-486c-4014-bcf2-627f2e68c311/dqc_reference
[2024-01-25 18:10:51,479] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:10:51,480] [INFO] Task started: Prodigal
[2024-01-25 18:10:51,480] [INFO] Running command: gunzip -c /var/lib/cwl/stg66d7b349-bba5-4d87-89a6-8ab589c836ff/GCF_014653435.1_ASM1465343v1_genomic.fna.gz | prodigal -d GCF_014653435.1_ASM1465343v1_genomic.fna/cds.fna -a GCF_014653435.1_ASM1465343v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:10:59,329] [INFO] Task succeeded: Prodigal
[2024-01-25 18:10:59,329] [INFO] Task started: HMMsearch
[2024-01-25 18:10:59,329] [INFO] Running command: hmmsearch --tblout GCF_014653435.1_ASM1465343v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd389365b-486c-4014-bcf2-627f2e68c311/dqc_reference/reference_markers.hmm GCF_014653435.1_ASM1465343v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:10:59,567] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:10:59,568] [INFO] Found 6/6 markers.
[2024-01-25 18:10:59,599] [INFO] Query marker FASTA was written to GCF_014653435.1_ASM1465343v1_genomic.fna/markers.fasta
[2024-01-25 18:10:59,599] [INFO] Task started: Blastn
[2024-01-25 18:10:59,599] [INFO] Running command: blastn -query GCF_014653435.1_ASM1465343v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd389365b-486c-4014-bcf2-627f2e68c311/dqc_reference/reference_markers.fasta -out GCF_014653435.1_ASM1465343v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:11:00,281] [INFO] Task succeeded: Blastn
[2024-01-25 18:11:00,284] [INFO] Selected 18 target genomes.
[2024-01-25 18:11:00,284] [INFO] Target genome list was writen to GCF_014653435.1_ASM1465343v1_genomic.fna/target_genomes.txt
[2024-01-25 18:11:00,295] [INFO] Task started: fastANI
[2024-01-25 18:11:00,295] [INFO] Running command: fastANI --query /var/lib/cwl/stg66d7b349-bba5-4d87-89a6-8ab589c836ff/GCF_014653435.1_ASM1465343v1_genomic.fna.gz --refList GCF_014653435.1_ASM1465343v1_genomic.fna/target_genomes.txt --output GCF_014653435.1_ASM1465343v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:11:13,991] [INFO] Task succeeded: fastANI
[2024-01-25 18:11:13,991] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd389365b-486c-4014-bcf2-627f2e68c311/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:11:13,992] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd389365b-486c-4014-bcf2-627f2e68c311/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:11:14,001] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:11:14,001] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:11:14,001] [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 longhuensis	strain=CGMCC 1.7003	GCA_014653435.1	1091037	1091037	type	True	100.0	1302	1304	95	conclusive
Alishewanella tabrizica	strain=KCTC 23723	GCA_014652375.1	671278	671278	type	True	81.5307	605	1304	95	below_threshold
Alishewanella aestuarii	strain=B11	GCA_000280055.1	453835	453835	type	True	79.5155	466	1304	95	below_threshold
Alishewanella agri	strain=BL06	GCA_000272005.1	553384	553384	type	True	79.4423	496	1304	95	below_threshold
Alishewanella jeotgali	strain=KCTC 22429	GCA_000245735.2	545533	545533	type	True	79.4068	490	1304	95	below_threshold
Rheinheimera maricola	strain=MA-13	GCA_017824735.1	2793282	2793282	type	True	78.6605	293	1304	95	below_threshold
Arsukibacterium perlucidum	strain=DSM 18276	GCA_000382165.1	368811	368811	type	True	78.6524	312	1304	95	below_threshold
Rheinheimera maricola	strain=MA-13	GCA_016918075.2	2793282	2793282	type	True	78.6376	295	1304	95	below_threshold
Arsukibacterium indicum	strain=SM2107	GCA_019100565.1	2848612	2848612	type	True	78.5981	314	1304	95	below_threshold
Rheinheimera pleomorphica	strain=PKS7	GCA_011634895.1	2703963	2703963	type	True	78.5652	296	1304	95	below_threshold
Rheinheimera nanhaiensis	strain=E407-8	GCA_000296695.1	1163621	1163621	type	True	78.4102	304	1304	95	below_threshold
Arsukibacterium tuosuense	strain=CGMCC 1.12461	GCA_900215315.1	1323745	1323745	type	True	78.2766	297	1304	95	below_threshold
Rheinheimera baltica	strain=DSM 14885	GCA_000425345.1	67576	67576	type	True	78.2504	261	1304	95	below_threshold
Pararheinheimera mesophila	strain=IITR13	GCA_003862465.1	1547515	1547515	type	True	77.957	160	1304	95	below_threshold
Pararheinheimera mesophila	strain=IITR-13	GCA_000986865.1	1547515	1547515	type	True	77.6859	152	1304	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:11:14,003] [INFO] DFAST Taxonomy check result was written to GCF_014653435.1_ASM1465343v1_genomic.fna/tc_result.tsv
[2024-01-25 18:11:14,003] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:11:14,003] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:11:14,004] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd389365b-486c-4014-bcf2-627f2e68c311/dqc_reference/checkm_data
[2024-01-25 18:11:14,004] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:11:14,043] [INFO] Task started: CheckM
[2024-01-25 18:11:14,043] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014653435.1_ASM1465343v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014653435.1_ASM1465343v1_genomic.fna/checkm_input GCF_014653435.1_ASM1465343v1_genomic.fna/checkm_result
[2024-01-25 18:11:40,728] [INFO] Task succeeded: CheckM
[2024-01-25 18:11:40,729] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:11:40,750] [INFO] ===== Completeness check finished =====
[2024-01-25 18:11:40,750] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:11:40,750] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014653435.1_ASM1465343v1_genomic.fna/markers.fasta)
[2024-01-25 18:11:40,750] [INFO] Task started: Blastn
[2024-01-25 18:11:40,750] [INFO] Running command: blastn -query GCF_014653435.1_ASM1465343v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd389365b-486c-4014-bcf2-627f2e68c311/dqc_reference/reference_markers_gtdb.fasta -out GCF_014653435.1_ASM1465343v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:11:41,800] [INFO] Task succeeded: Blastn
[2024-01-25 18:11:41,803] [INFO] Selected 14 target genomes.
[2024-01-25 18:11:41,803] [INFO] Target genome list was writen to GCF_014653435.1_ASM1465343v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:11:41,818] [INFO] Task started: fastANI
[2024-01-25 18:11:41,818] [INFO] Running command: fastANI --query /var/lib/cwl/stg66d7b349-bba5-4d87-89a6-8ab589c836ff/GCF_014653435.1_ASM1465343v1_genomic.fna.gz --refList GCF_014653435.1_ASM1465343v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014653435.1_ASM1465343v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:11:52,702] [INFO] Task succeeded: fastANI
[2024-01-25 18:11:52,711] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:11:52,711] [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_014653435.1	s__Alishewanella longhuensis	100.0	1302	1304	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alishewanella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014652375.1	s__Alishewanella tabrizica	81.5432	605	1304	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alishewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000280055.1	s__Alishewanella aestuarii	79.5388	465	1304	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alishewanella	95.6353	96.26	96.26	0.87	0.87	2	-
GCF_000272005.1	s__Alishewanella agri	79.4623	494	1304	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alishewanella	95.0	96.64	95.87	0.84	0.80	3	-
GCF_000245735.1	s__Alishewanella jeotgali	79.4266	488	1304	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alishewanella	95.6353	N/A	N/A	N/A	N/A	1	-
GCF_017824735.1	s__Rheinheimera sp017824735	78.6605	293	1304	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000382165.1	s__Arsukibacterium perlucidum	78.6388	313	1304	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	78.6115	314	1304	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001513785.1	s__Rheinheimera sp001513785	78.5892	335	1304	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011634895.1	s__Rheinheimera pleomorphica	78.5652	296	1304	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000296695.1	s__Rheinheimera nanhaiensis	78.4102	304	1304	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	78.2887	296	1304	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425345.1	s__Rheinheimera baltica	78.2676	259	1304	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003990335.1	s__Pararheinheimera sp003990335	77.5194	173	1304	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:11:52,713] [INFO] GTDB search result was written to GCF_014653435.1_ASM1465343v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:11:52,713] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:11:52,718] [INFO] DFAST_QC result json was written to GCF_014653435.1_ASM1465343v1_genomic.fna/dqc_result.json
[2024-01-25 18:11:52,719] [INFO] DFAST_QC completed!
[2024-01-25 18:11:52,719] [INFO] Total running time: 0h1m2s