[2024-01-25 17:37:50,689] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:37:50,690] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:37:50,690] [INFO] DQC Reference Directory: /var/lib/cwl/stg0b6dedf6-6739-4298-943e-01c7f10a4599/dqc_reference
[2024-01-25 17:37:51,823] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:37:51,824] [INFO] Task started: Prodigal
[2024-01-25 17:37:51,824] [INFO] Running command: gunzip -c /var/lib/cwl/stg0ddae8f4-26ea-45f1-9ec7-8df40af2cc98/GCF_011317445.1_ASM1131744v1_genomic.fna.gz | prodigal -d GCF_011317445.1_ASM1131744v1_genomic.fna/cds.fna -a GCF_011317445.1_ASM1131744v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:38:04,824] [INFO] Task succeeded: Prodigal
[2024-01-25 17:38:04,824] [INFO] Task started: HMMsearch
[2024-01-25 17:38:04,824] [INFO] Running command: hmmsearch --tblout GCF_011317445.1_ASM1131744v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0b6dedf6-6739-4298-943e-01c7f10a4599/dqc_reference/reference_markers.hmm GCF_011317445.1_ASM1131744v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:38:05,079] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:38:05,082] [INFO] Found 6/6 markers.
[2024-01-25 17:38:05,133] [INFO] Query marker FASTA was written to GCF_011317445.1_ASM1131744v1_genomic.fna/markers.fasta
[2024-01-25 17:38:05,133] [INFO] Task started: Blastn
[2024-01-25 17:38:05,133] [INFO] Running command: blastn -query GCF_011317445.1_ASM1131744v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b6dedf6-6739-4298-943e-01c7f10a4599/dqc_reference/reference_markers.fasta -out GCF_011317445.1_ASM1131744v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:38:06,041] [INFO] Task succeeded: Blastn
[2024-01-25 17:38:06,047] [INFO] Selected 14 target genomes.
[2024-01-25 17:38:06,048] [INFO] Target genome list was writen to GCF_011317445.1_ASM1131744v1_genomic.fna/target_genomes.txt
[2024-01-25 17:38:06,052] [INFO] Task started: fastANI
[2024-01-25 17:38:06,052] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ddae8f4-26ea-45f1-9ec7-8df40af2cc98/GCF_011317445.1_ASM1131744v1_genomic.fna.gz --refList GCF_011317445.1_ASM1131744v1_genomic.fna/target_genomes.txt --output GCF_011317445.1_ASM1131744v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:38:19,936] [INFO] Task succeeded: fastANI
[2024-01-25 17:38:19,936] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0b6dedf6-6739-4298-943e-01c7f10a4599/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:38:19,937] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0b6dedf6-6739-4298-943e-01c7f10a4599/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:38:19,951] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:38:19,951] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:38:19,951] [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 xinjiangense	strain=lm93	GCA_009812055.1	2681485	2681485	type	True	79.2984	515	1598	95	below_threshold
Chelativorans alearense	strain=UJN715	GCA_010993735.1	2681495	2681495	type	True	79.1574	525	1598	95	below_threshold
Chelativorans intermedius	strain=LMG 28482	GCA_025398255.1	515947	515947	type	True	78.737	479	1598	95	below_threshold
Nitratireductor pacificus	strain=pht-3B	GCA_000300335.1	1231180	1231180	type	True	78.6159	394	1598	95	below_threshold
Nitratireductor indicus	strain=C115	GCA_000300515.1	721133	721133	type	True	78.6019	343	1598	95	below_threshold
Nitratireductor soli	strain=ZZ-1	GCA_001050155.1	1670619	1670619	type	True	78.3703	411	1598	95	below_threshold
Aquamicrobium defluvii	strain=DSM 11603	GCA_004363725.1	69279	69279	type	True	78.1503	307	1598	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	77.9565	323	1598	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	77.9559	323	1598	95	below_threshold
Mesorhizobium australicum	strain=WSM2073	GCA_000230995.3	536018	536018	type	True	77.8295	319	1598	95	below_threshold
Mesorhizobium sanjuanii	strain=BSA136	GCA_002529485.1	2037900	2037900	type	True	77.6664	326	1598	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	77.6238	364	1598	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	77.5325	369	1598	95	below_threshold
Sphingomonas faeni	strain=MA-olki	GCA_003053745.1	185950	185950	type	True	75.967	57	1598	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:38:19,958] [INFO] DFAST Taxonomy check result was written to GCF_011317445.1_ASM1131744v1_genomic.fna/tc_result.tsv
[2024-01-25 17:38:19,961] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:38:19,961] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:38:19,961] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0b6dedf6-6739-4298-943e-01c7f10a4599/dqc_reference/checkm_data
[2024-01-25 17:38:19,962] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:38:20,013] [INFO] Task started: CheckM
[2024-01-25 17:38:20,013] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011317445.1_ASM1131744v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011317445.1_ASM1131744v1_genomic.fna/checkm_input GCF_011317445.1_ASM1131744v1_genomic.fna/checkm_result
[2024-01-25 17:38:57,725] [INFO] Task succeeded: CheckM
[2024-01-25 17:38:57,726] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:38:57,746] [INFO] ===== Completeness check finished =====
[2024-01-25 17:38:57,746] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:38:57,746] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011317445.1_ASM1131744v1_genomic.fna/markers.fasta)
[2024-01-25 17:38:57,746] [INFO] Task started: Blastn
[2024-01-25 17:38:57,746] [INFO] Running command: blastn -query GCF_011317445.1_ASM1131744v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b6dedf6-6739-4298-943e-01c7f10a4599/dqc_reference/reference_markers_gtdb.fasta -out GCF_011317445.1_ASM1131744v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:38:59,581] [INFO] Task succeeded: Blastn
[2024-01-25 17:38:59,584] [INFO] Selected 16 target genomes.
[2024-01-25 17:38:59,584] [INFO] Target genome list was writen to GCF_011317445.1_ASM1131744v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:38:59,592] [INFO] Task started: fastANI
[2024-01-25 17:38:59,593] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ddae8f4-26ea-45f1-9ec7-8df40af2cc98/GCF_011317445.1_ASM1131744v1_genomic.fna.gz --refList GCF_011317445.1_ASM1131744v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011317445.1_ASM1131744v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:39:16,692] [INFO] Task succeeded: fastANI
[2024-01-25 17:39:16,703] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:39:16,703] [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_011317445.1	s__Chelativorans multitrophicus	100.0	1598	1598	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Chelativorans	95.0	99.92	99.90	0.98	0.98	3	conclusive
GCF_000518985.1	s__Chelativorans sp000518985	80.6708	724	1598	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Chelativorans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009812055.1	s__Chelativorans xinjiangense	79.312	513	1598	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	79.1395	527	1598	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Chelativorans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000300335.1	s__Nitratireductor pacificus	78.5951	396	1598	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	78.3547	414	1598	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001014615.2	s__Aquamicrobium_A sp001014615	78.2198	386	1598	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_007829525.1	s__VLJP01 sp007829525	77.9975	382	1598	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__VLJP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003934165.1	s__Pseudaminobacter arsenicus	77.9513	316	1598	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007922615.2	s__Nitratireductor_D sp007922615	77.7671	322	1598	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_004791165.1	s__Mesorhizobium sp004791165	77.7344	338	1598	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.22	95.93	0.90	0.87	21	-
GCF_006439515.1	s__Mesorhizobium sp006439515	77.6298	343	1598	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.05	98.05	0.91	0.91	2	-
GCA_003963455.1	s__Mesorhizobium sp003963455	77.1365	281	1598	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799755.1	s__Rhizobium tropici_A	76.99	229	1598	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.89	99.82	0.97	0.95	4	-
GCF_001428605.1	s__Rhizorhabdus sp001428605	76.1652	86	1598	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	99.98	99.98	0.99	0.99	3	-
GCA_019237215.1	s__VAZQ01 sp019237215	75.8304	96	1598	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__VAZQ01	95.0	98.63	98.51	0.77	0.77	4	-
--------------------------------------------------------------------------------
[2024-01-25 17:39:16,704] [INFO] GTDB search result was written to GCF_011317445.1_ASM1131744v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:39:16,705] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:39:16,708] [INFO] DFAST_QC result json was written to GCF_011317445.1_ASM1131744v1_genomic.fna/dqc_result.json
[2024-01-25 17:39:16,708] [INFO] DFAST_QC completed!
[2024-01-25 17:39:16,708] [INFO] Total running time: 0h1m26s