[2024-01-24 12:06:12,361] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:12,368] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:12,368] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4b97fe3-ecf8-4453-a757-9a219ed26145/dqc_reference
[2024-01-24 12:06:13,625] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:13,626] [INFO] Task started: Prodigal
[2024-01-24 12:06:13,626] [INFO] Running command: gunzip -c /var/lib/cwl/stgb4cd7f63-26da-492d-8a42-7caee22af5e7/GCF_025398255.1_ASM2539825v1_genomic.fna.gz | prodigal -d GCF_025398255.1_ASM2539825v1_genomic.fna/cds.fna -a GCF_025398255.1_ASM2539825v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:26,855] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:26,855] [INFO] Task started: HMMsearch
[2024-01-24 12:06:26,855] [INFO] Running command: hmmsearch --tblout GCF_025398255.1_ASM2539825v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4b97fe3-ecf8-4453-a757-9a219ed26145/dqc_reference/reference_markers.hmm GCF_025398255.1_ASM2539825v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:27,135] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:27,136] [INFO] Found 6/6 markers.
[2024-01-24 12:06:27,176] [INFO] Query marker FASTA was written to GCF_025398255.1_ASM2539825v1_genomic.fna/markers.fasta
[2024-01-24 12:06:27,177] [INFO] Task started: Blastn
[2024-01-24 12:06:27,177] [INFO] Running command: blastn -query GCF_025398255.1_ASM2539825v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4b97fe3-ecf8-4453-a757-9a219ed26145/dqc_reference/reference_markers.fasta -out GCF_025398255.1_ASM2539825v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:28,171] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:28,174] [INFO] Selected 13 target genomes.
[2024-01-24 12:06:28,175] [INFO] Target genome list was writen to GCF_025398255.1_ASM2539825v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:28,181] [INFO] Task started: fastANI
[2024-01-24 12:06:28,181] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4cd7f63-26da-492d-8a42-7caee22af5e7/GCF_025398255.1_ASM2539825v1_genomic.fna.gz --refList GCF_025398255.1_ASM2539825v1_genomic.fna/target_genomes.txt --output GCF_025398255.1_ASM2539825v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:43,806] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:43,807] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4b97fe3-ecf8-4453-a757-9a219ed26145/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:43,807] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4b97fe3-ecf8-4453-a757-9a219ed26145/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:43,819] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:43,819] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:43,819] [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
Chelativorans intermedius	strain=LMG 28482	GCA_025398255.1	515947	515947	type	True	100.0	1346	1347	95	conclusive
Chelativorans xinjiangense	strain=lm93	GCA_009812055.1	2681485	2681485	type	True	82.8505	872	1347	95	below_threshold
Chelativorans alearense	strain=UJN715	GCA_010993735.1	2681495	2681495	type	True	82.5669	865	1347	95	below_threshold
Nitratireductor pacificus	strain=pht-3B	GCA_000300335.1	1231180	1231180	type	True	79.9778	615	1347	95	below_threshold
Nitratireductor soli	strain=ZZ-1	GCA_001050155.1	1670619	1670619	type	True	79.8252	643	1347	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	78.99	560	1347	95	below_threshold
Aquamicrobium defluvii	strain=DSM 11603	GCA_004363725.1	69279	69279	type	True	78.859	468	1347	95	below_threshold
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	78.5943	549	1347	95	below_threshold
Nitratireductor indicus	strain=C115	GCA_000300515.1	721133	721133	type	True	78.5359	446	1347	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	78.2867	514	1347	95	below_threshold
Aminobacter ciceronei	strain=DSM 15910	GCA_014138625.1	150723	150723	type	True	78.2264	508	1347	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	78.0122	448	1347	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	77.9962	450	1347	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:43,821] [INFO] DFAST Taxonomy check result was written to GCF_025398255.1_ASM2539825v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:43,824] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:43,824] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:43,824] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4b97fe3-ecf8-4453-a757-9a219ed26145/dqc_reference/checkm_data
[2024-01-24 12:06:43,825] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:43,869] [INFO] Task started: CheckM
[2024-01-24 12:06:43,870] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025398255.1_ASM2539825v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025398255.1_ASM2539825v1_genomic.fna/checkm_input GCF_025398255.1_ASM2539825v1_genomic.fna/checkm_result
[2024-01-24 12:07:30,999] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:31,003] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:31,027] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:31,027] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:31,027] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025398255.1_ASM2539825v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:31,028] [INFO] Task started: Blastn
[2024-01-24 12:07:31,028] [INFO] Running command: blastn -query GCF_025398255.1_ASM2539825v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4b97fe3-ecf8-4453-a757-9a219ed26145/dqc_reference/reference_markers_gtdb.fasta -out GCF_025398255.1_ASM2539825v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:32,812] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:32,815] [INFO] Selected 19 target genomes.
[2024-01-24 12:07:32,815] [INFO] Target genome list was writen to GCF_025398255.1_ASM2539825v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:32,830] [INFO] Task started: fastANI
[2024-01-24 12:07:32,830] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4cd7f63-26da-492d-8a42-7caee22af5e7/GCF_025398255.1_ASM2539825v1_genomic.fna.gz --refList GCF_025398255.1_ASM2539825v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025398255.1_ASM2539825v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:50,175] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:50,192] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:07:50,192] [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_009812055.1	s__Chelativorans xinjiangense	82.8217	874	1347	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Chelativorans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993735.1	s__Chelativorans alearense	82.5402	869	1347	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Chelativorans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003577315.1	s__Aquamicrobium_A sp003577315	80.0189	501	1347	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000300335.1	s__Nitratireductor pacificus	79.9729	616	1347	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001050155.1	s__Nitratireductor soli	79.841	641	1347	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305835.1	s__RCIO01 sp017305835	79.5731	551	1347	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255295.1	s__Nitratireductor aquimarinus	79.1985	552	1347	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	98.42	98.07	0.93	0.92	7	-
GCF_007829525.1	s__VLJP01 sp007829525	79.1528	470	1347	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__VLJP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001014615.2	s__Aquamicrobium_A sp001014615	79.0883	554	1347	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007922615.2	s__Nitratireductor_D sp007922615	79.0082	528	1347	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011317445.1	s__Chelativorans multitrophicus	79.0001	448	1347	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Chelativorans	95.0	99.92	99.90	0.98	0.98	3	-
GCF_008180155.1	s__Aquamicrobium_A microcysteis	78.7504	504	1347	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018823835.1	s__RCIZ01 sp018823835	78.6112	503	1347	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIZ01	95.0	99.96	99.89	0.99	0.96	11	-
GCF_003289945.1	s__Mesorhizobium hawassense	78.5902	550	1347	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518985.1	s__Chelativorans sp000518985	78.5607	481	1347	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Chelativorans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000300515.1	s__Nitratireductor indicus	78.5396	445	1347	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	99.99	99.99	1.00	1.00	2	-
GCA_001896885.1	s__65-79 sp001896885	78.4455	486	1347	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__65-79	95.0	99.97	99.97	0.97	0.97	2	-
GCF_902809845.1	s__Chelativorans sp902809845	78.0808	384	1347	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Chelativorans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001603335.1	s__Alpha-05 sp001603335	77.6545	86	1347	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Alpha-05	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:50,194] [INFO] GTDB search result was written to GCF_025398255.1_ASM2539825v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:50,195] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:50,199] [INFO] DFAST_QC result json was written to GCF_025398255.1_ASM2539825v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:50,199] [INFO] DFAST_QC completed!
[2024-01-24 12:07:50,199] [INFO] Total running time: 0h1m38s