[2024-01-24 13:22:01,960] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:01,962] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:01,962] [INFO] DQC Reference Directory: /var/lib/cwl/stgdbe0058e-074c-4ec0-9f21-3a99e0dfa657/dqc_reference
[2024-01-24 13:22:03,296] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:03,297] [INFO] Task started: Prodigal
[2024-01-24 13:22:03,297] [INFO] Running command: gunzip -c /var/lib/cwl/stg384db540-4c5a-4f94-9e24-0f6b0faa5b54/GCF_003344765.1_ASM334476v1_genomic.fna.gz | prodigal -d GCF_003344765.1_ASM334476v1_genomic.fna/cds.fna -a GCF_003344765.1_ASM334476v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:15,774] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:15,774] [INFO] Task started: HMMsearch
[2024-01-24 13:22:15,774] [INFO] Running command: hmmsearch --tblout GCF_003344765.1_ASM334476v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdbe0058e-074c-4ec0-9f21-3a99e0dfa657/dqc_reference/reference_markers.hmm GCF_003344765.1_ASM334476v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:16,091] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:16,098] [INFO] Found 6/6 markers.
[2024-01-24 13:22:16,145] [INFO] Query marker FASTA was written to GCF_003344765.1_ASM334476v1_genomic.fna/markers.fasta
[2024-01-24 13:22:16,146] [INFO] Task started: Blastn
[2024-01-24 13:22:16,146] [INFO] Running command: blastn -query GCF_003344765.1_ASM334476v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdbe0058e-074c-4ec0-9f21-3a99e0dfa657/dqc_reference/reference_markers.fasta -out GCF_003344765.1_ASM334476v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:17,064] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:17,068] [INFO] Selected 17 target genomes.
[2024-01-24 13:22:17,068] [INFO] Target genome list was writen to GCF_003344765.1_ASM334476v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:17,079] [INFO] Task started: fastANI
[2024-01-24 13:22:17,079] [INFO] Running command: fastANI --query /var/lib/cwl/stg384db540-4c5a-4f94-9e24-0f6b0faa5b54/GCF_003344765.1_ASM334476v1_genomic.fna.gz --refList GCF_003344765.1_ASM334476v1_genomic.fna/target_genomes.txt --output GCF_003344765.1_ASM334476v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:32,644] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:32,644] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdbe0058e-074c-4ec0-9f21-3a99e0dfa657/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:32,644] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdbe0058e-074c-4ec0-9f21-3a99e0dfa657/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:32,659] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:32,659] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:32,660] [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
Ferruginivarius sediminum	strain=WD2A32	GCA_003344765.1	2661937	2661937	type	True	100.0	1376	1378	95	conclusive
Rhodovibrio sodomensis	strain=DSM 9895	GCA_016583645.1	1088	1088	type	True	78.7621	500	1378	95	below_threshold
Rhodovibrio salinarum	strain=DSM 9154	GCA_000515255.1	1087	1087	type	True	78.5251	413	1378	95	below_threshold
Rhodovibrio salinarum	strain=DSM 9154	GCA_016583505.1	1087	1087	type	True	78.5119	404	1378	95	below_threshold
Limimonas halophila	strain=DSM 25584	GCA_900100655.1	1082479	1082479	type	True	78.2706	380	1378	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	77.676	353	1378	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	77.5467	447	1378	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	77.4928	450	1378	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	76.9528	228	1378	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	76.8702	291	1378	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	76.7789	241	1378	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.4257	278	1378	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	76.3417	204	1378	95	below_threshold
Elioraea tepida	strain=MS-P2	GCA_019203965.1	2843330	2843330	type	True	76.1808	130	1378	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	76.1601	238	1378	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	75.9789	176	1378	95	below_threshold
Bradyrhizobium guangxiense	strain=CCBAU 53363	GCA_004114915.1	1325115	1325115	type	True	75.8415	165	1378	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:32,661] [INFO] DFAST Taxonomy check result was written to GCF_003344765.1_ASM334476v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:32,662] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:32,662] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:32,662] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdbe0058e-074c-4ec0-9f21-3a99e0dfa657/dqc_reference/checkm_data
[2024-01-24 13:22:32,663] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:32,705] [INFO] Task started: CheckM
[2024-01-24 13:22:32,705] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003344765.1_ASM334476v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003344765.1_ASM334476v1_genomic.fna/checkm_input GCF_003344765.1_ASM334476v1_genomic.fna/checkm_result
[2024-01-24 13:23:11,968] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:11,969] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:11,987] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:11,988] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:11,988] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003344765.1_ASM334476v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:11,989] [INFO] Task started: Blastn
[2024-01-24 13:23:11,989] [INFO] Running command: blastn -query GCF_003344765.1_ASM334476v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdbe0058e-074c-4ec0-9f21-3a99e0dfa657/dqc_reference/reference_markers_gtdb.fasta -out GCF_003344765.1_ASM334476v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:13,652] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:13,656] [INFO] Selected 12 target genomes.
[2024-01-24 13:23:13,656] [INFO] Target genome list was writen to GCF_003344765.1_ASM334476v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:13,679] [INFO] Task started: fastANI
[2024-01-24 13:23:13,679] [INFO] Running command: fastANI --query /var/lib/cwl/stg384db540-4c5a-4f94-9e24-0f6b0faa5b54/GCF_003344765.1_ASM334476v1_genomic.fna.gz --refList GCF_003344765.1_ASM334476v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003344765.1_ASM334476v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:25,174] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:25,193] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:25,193] [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_003344765.1	s__Ferruginivarius sediminum	100.0	1376	1378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Rhodovibrionaceae;g__Ferruginivarius	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016583645.1	s__Rhodovibrio sodomensis	78.7702	499	1378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Rhodovibrionaceae;g__Rhodovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000515255.1	s__Rhodovibrio salinarum	78.5279	411	1378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Rhodovibrionaceae;g__Rhodovibrio	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900100655.1	s__Limimonas halophila	78.2669	381	1378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Rhodovibrionaceae;g__Limimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007127165.1	s__SKZV01 sp007127165	78.0202	315	1378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Rhodovibrionaceae;g__SKZV01	95.0	99.42	99.10	0.91	0.89	3	-
GCF_900177295.1	s__Tistlia consotensis	77.4942	451	1378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_008728835.1	s__Hypericibacter adhaerens	76.9289	229	1378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Hypericibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016792765.1	s__SBBV01 sp016792765	76.6038	198	1378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Bin65;f__Bin65;g__SBBV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003130795.1	s__Azospirillum thermophilum	76.5516	342	1378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013365.1	s__Rhodopseudomonas palustris_J	76.3838	164	1378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002068095.1	s__Bradyrhizobium sacchari	75.943	173	1378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.98	99.98	0.99	0.99	3	-
GCF_004114915.1	s__Bradyrhizobium guangxiense	75.8691	167	1378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:25,195] [INFO] GTDB search result was written to GCF_003344765.1_ASM334476v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:25,195] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:25,201] [INFO] DFAST_QC result json was written to GCF_003344765.1_ASM334476v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:25,201] [INFO] DFAST_QC completed!
[2024-01-24 13:23:25,201] [INFO] Total running time: 0h1m23s