[2024-01-24 13:22:10,536] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:10,540] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:10,540] [INFO] DQC Reference Directory: /var/lib/cwl/stgdb9fd590-ab38-418c-9228-96f716f11e56/dqc_reference
[2024-01-24 13:22:11,794] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:11,795] [INFO] Task started: Prodigal
[2024-01-24 13:22:11,795] [INFO] Running command: gunzip -c /var/lib/cwl/stgc4023b5e-811b-467d-a740-a504ac35b7cd/GCF_003601985.1_ASM360198v1_genomic.fna.gz | prodigal -d GCF_003601985.1_ASM360198v1_genomic.fna/cds.fna -a GCF_003601985.1_ASM360198v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:32,172] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:32,173] [INFO] Task started: HMMsearch
[2024-01-24 13:22:32,173] [INFO] Running command: hmmsearch --tblout GCF_003601985.1_ASM360198v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdb9fd590-ab38-418c-9228-96f716f11e56/dqc_reference/reference_markers.hmm GCF_003601985.1_ASM360198v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:32,496] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:32,498] [INFO] Found 6/6 markers.
[2024-01-24 13:22:32,550] [INFO] Query marker FASTA was written to GCF_003601985.1_ASM360198v1_genomic.fna/markers.fasta
[2024-01-24 13:22:32,551] [INFO] Task started: Blastn
[2024-01-24 13:22:32,551] [INFO] Running command: blastn -query GCF_003601985.1_ASM360198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb9fd590-ab38-418c-9228-96f716f11e56/dqc_reference/reference_markers.fasta -out GCF_003601985.1_ASM360198v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:33,568] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:33,571] [INFO] Selected 11 target genomes.
[2024-01-24 13:22:33,572] [INFO] Target genome list was writen to GCF_003601985.1_ASM360198v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:33,586] [INFO] Task started: fastANI
[2024-01-24 13:22:33,587] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4023b5e-811b-467d-a740-a504ac35b7cd/GCF_003601985.1_ASM360198v1_genomic.fna.gz --refList GCF_003601985.1_ASM360198v1_genomic.fna/target_genomes.txt --output GCF_003601985.1_ASM360198v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:51,003] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:51,004] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdb9fd590-ab38-418c-9228-96f716f11e56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:51,004] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdb9fd590-ab38-418c-9228-96f716f11e56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:51,021] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:22:51,021] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:51,021] [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
Mesorhizobium jarvisii	strain=LMG 28313	GCA_003601985.1	1777867	1777867	type	True	100.0	2191	2192	95	conclusive
Mesorhizobium jarvisii	strain=ATCC 33669	GCA_013170785.1	1777867	1777867	type	True	99.9933	2189	2192	95	conclusive
Mesorhizobium japonicum	strain=MAFF 303099	GCA_000009625.1	2066070	2066070	type	True	94.3409	1846	2192	95	below_threshold
Mesorhizobium intechi	strain=BD68	GCA_002879535.2	537601	537601	type	True	93.7104	1610	2192	95	below_threshold
Mesorhizobium carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	91.6049	1810	2192	95	below_threshold
Mesorhizobium erdmanii	strain=USDA 3471	GCA_000472705.1	1777866	1777866	type	True	90.1239	1691	2192	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	87.6164	1589	2192	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	84.7837	1327	2192	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	79.2945	704	2192	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	79.2807	706	2192	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	78.9958	655	2192	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:51,022] [INFO] DFAST Taxonomy check result was written to GCF_003601985.1_ASM360198v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:51,023] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:51,023] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:51,023] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdb9fd590-ab38-418c-9228-96f716f11e56/dqc_reference/checkm_data
[2024-01-24 13:22:51,024] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:51,085] [INFO] Task started: CheckM
[2024-01-24 13:22:51,086] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003601985.1_ASM360198v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003601985.1_ASM360198v1_genomic.fna/checkm_input GCF_003601985.1_ASM360198v1_genomic.fna/checkm_result
[2024-01-24 13:23:49,566] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:49,568] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:49,597] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:49,597] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:49,598] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003601985.1_ASM360198v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:49,598] [INFO] Task started: Blastn
[2024-01-24 13:23:49,598] [INFO] Running command: blastn -query GCF_003601985.1_ASM360198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb9fd590-ab38-418c-9228-96f716f11e56/dqc_reference/reference_markers_gtdb.fasta -out GCF_003601985.1_ASM360198v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:51,672] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:51,676] [INFO] Selected 9 target genomes.
[2024-01-24 13:23:51,676] [INFO] Target genome list was writen to GCF_003601985.1_ASM360198v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:52,049] [INFO] Task started: fastANI
[2024-01-24 13:23:52,050] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4023b5e-811b-467d-a740-a504ac35b7cd/GCF_003601985.1_ASM360198v1_genomic.fna.gz --refList GCF_003601985.1_ASM360198v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003601985.1_ASM360198v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:08,389] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:08,405] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:08,406] [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_003601985.1	s__Mesorhizobium jarvisii	100.0	2192	2192	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.40	98.93	0.96	0.91	10	conclusive
GCF_002295115.1	s__Mesorhizobium sp002295115	94.3665	1836	2192	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.79	96.42	0.94	0.85	9	-
GCF_000009625.1	s__Mesorhizobium japonicum	94.3409	1846	2192	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.35	97.93	0.93	0.85	23	-
GCF_016467435.1	s__Mesorhizobium sp016467435	94.0519	1789	2192	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.58	98.58	0.95	0.95	2	-
GCF_002879535.1	s__Mesorhizobium intechi	93.708	1611	2192	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016756495.1	s__Mesorhizobium sp016756495	92.8421	1861	2192	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900199455.1	s__Mesorhizobium carmichaelinearum	91.6129	1809	2192	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003353565.1	s__Mesorhizobium sp003353565	91.3688	1755	2192	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013170825.1	s__Mesorhizobium sp013170825	90.4146	1681	2192	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	95.36	95.35	0.82	0.81	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:24:08,407] [INFO] GTDB search result was written to GCF_003601985.1_ASM360198v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:08,408] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:08,412] [INFO] DFAST_QC result json was written to GCF_003601985.1_ASM360198v1_genomic.fna/dqc_result.json
[2024-01-24 13:24:08,413] [INFO] DFAST_QC completed!
[2024-01-24 13:24:08,413] [INFO] Total running time: 0h1m58s