[2024-01-24 13:32:55,979] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:55,981] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:55,981] [INFO] DQC Reference Directory: /var/lib/cwl/stg4be0f261-9b45-48ef-aeb9-8abd307dc07e/dqc_reference
[2024-01-24 13:32:57,296] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:57,297] [INFO] Task started: Prodigal
[2024-01-24 13:32:57,297] [INFO] Running command: gunzip -c /var/lib/cwl/stg849a668a-32af-46c4-8b29-e2bb029495d2/GCF_002879535.1_ASM287953v2_genomic.fna.gz | prodigal -d GCF_002879535.1_ASM287953v2_genomic.fna/cds.fna -a GCF_002879535.1_ASM287953v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:33:17,234] [INFO] Task succeeded: Prodigal
[2024-01-24 13:33:17,234] [INFO] Task started: HMMsearch
[2024-01-24 13:33:17,234] [INFO] Running command: hmmsearch --tblout GCF_002879535.1_ASM287953v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4be0f261-9b45-48ef-aeb9-8abd307dc07e/dqc_reference/reference_markers.hmm GCF_002879535.1_ASM287953v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:33:17,600] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:33:17,601] [INFO] Found 6/6 markers.
[2024-01-24 13:33:17,660] [INFO] Query marker FASTA was written to GCF_002879535.1_ASM287953v2_genomic.fna/markers.fasta
[2024-01-24 13:33:17,661] [INFO] Task started: Blastn
[2024-01-24 13:33:17,661] [INFO] Running command: blastn -query GCF_002879535.1_ASM287953v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg4be0f261-9b45-48ef-aeb9-8abd307dc07e/dqc_reference/reference_markers.fasta -out GCF_002879535.1_ASM287953v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:18,763] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:18,766] [INFO] Selected 10 target genomes.
[2024-01-24 13:33:18,767] [INFO] Target genome list was writen to GCF_002879535.1_ASM287953v2_genomic.fna/target_genomes.txt
[2024-01-24 13:33:18,771] [INFO] Task started: fastANI
[2024-01-24 13:33:18,771] [INFO] Running command: fastANI --query /var/lib/cwl/stg849a668a-32af-46c4-8b29-e2bb029495d2/GCF_002879535.1_ASM287953v2_genomic.fna.gz --refList GCF_002879535.1_ASM287953v2_genomic.fna/target_genomes.txt --output GCF_002879535.1_ASM287953v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:35,547] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:35,547] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4be0f261-9b45-48ef-aeb9-8abd307dc07e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:35,548] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4be0f261-9b45-48ef-aeb9-8abd307dc07e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:35,563] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:33:35,563] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:35,563] [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 intechi	strain=BD68	GCA_002879535.2	537601	537601	type	True	100.0	1971	1996	95	conclusive
Mesorhizobium jarvisii	strain=LMG 28313	GCA_003601985.1	1777867	1777867	type	True	93.7208	1645	1996	95	below_threshold
Mesorhizobium jarvisii	strain=ATCC 33669	GCA_013170785.1	1777867	1777867	type	True	93.617	1740	1996	95	below_threshold
Mesorhizobium japonicum	strain=MAFF 303099	GCA_000009625.1	2066070	2066070	type	True	93.0361	1658	1996	95	below_threshold
Mesorhizobium carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	90.5808	1589	1996	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	87.191	1421	1996	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	84.3989	1250	1996	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	78.9904	588	1996	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	78.8784	573	1996	95	below_threshold
Chelativorans intermedius	strain=LMG 28482	GCA_025398255.1	515947	515947	type	True	78.1297	480	1996	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:35,565] [INFO] DFAST Taxonomy check result was written to GCF_002879535.1_ASM287953v2_genomic.fna/tc_result.tsv
[2024-01-24 13:33:35,566] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:35,566] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:35,566] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4be0f261-9b45-48ef-aeb9-8abd307dc07e/dqc_reference/checkm_data
[2024-01-24 13:33:35,567] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:35,630] [INFO] Task started: CheckM
[2024-01-24 13:33:35,630] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002879535.1_ASM287953v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002879535.1_ASM287953v2_genomic.fna/checkm_input GCF_002879535.1_ASM287953v2_genomic.fna/checkm_result
[2024-01-24 13:34:29,440] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:29,441] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:29,465] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:29,465] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:29,466] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002879535.1_ASM287953v2_genomic.fna/markers.fasta)
[2024-01-24 13:34:29,466] [INFO] Task started: Blastn
[2024-01-24 13:34:29,466] [INFO] Running command: blastn -query GCF_002879535.1_ASM287953v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg4be0f261-9b45-48ef-aeb9-8abd307dc07e/dqc_reference/reference_markers_gtdb.fasta -out GCF_002879535.1_ASM287953v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:31,642] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:31,647] [INFO] Selected 9 target genomes.
[2024-01-24 13:34:31,647] [INFO] Target genome list was writen to GCF_002879535.1_ASM287953v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:31,656] [INFO] Task started: fastANI
[2024-01-24 13:34:31,656] [INFO] Running command: fastANI --query /var/lib/cwl/stg849a668a-32af-46c4-8b29-e2bb029495d2/GCF_002879535.1_ASM287953v2_genomic.fna.gz --refList GCF_002879535.1_ASM287953v2_genomic.fna/target_genomes_gtdb.txt --output GCF_002879535.1_ASM287953v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:46,537] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:46,552] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:46,552] [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_002879535.1	s__Mesorhizobium intechi	100.0	1972	1996	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002295115.1	s__Mesorhizobium sp002295115	93.8806	1662	1996	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.79	96.42	0.94	0.85	9	-
GCF_003601985.1	s__Mesorhizobium jarvisii	93.722	1645	1996	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.40	98.93	0.96	0.91	10	-
GCF_016467435.1	s__Mesorhizobium sp016467435	93.5709	1605	1996	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.58	98.58	0.95	0.95	2	-
GCF_000009625.1	s__Mesorhizobium japonicum	93.0079	1661	1996	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.35	97.93	0.93	0.85	23	-
GCF_016756495.1	s__Mesorhizobium sp016756495	92.0047	1673	1996	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000688075.1	s__Mesorhizobium sp000688075	90.2202	1543	1996	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013170805.1	s__Mesorhizobium sp013170805	90.1825	1610	1996	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013170825.1	s__Mesorhizobium sp013170825	90.0792	1579	1996	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 13:34:46,554] [INFO] GTDB search result was written to GCF_002879535.1_ASM287953v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:46,554] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:46,558] [INFO] DFAST_QC result json was written to GCF_002879535.1_ASM287953v2_genomic.fna/dqc_result.json
[2024-01-24 13:34:46,558] [INFO] DFAST_QC completed!
[2024-01-24 13:34:46,558] [INFO] Total running time: 0h1m51s