[2024-01-25 20:03:35,547] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:03:35,548] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:03:35,548] [INFO] DQC Reference Directory: /var/lib/cwl/stg60f128c6-3c64-4dba-a2f0-f2fd61dd7d90/dqc_reference
[2024-01-25 20:03:36,736] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:03:36,736] [INFO] Task started: Prodigal
[2024-01-25 20:03:36,736] [INFO] Running command: gunzip -c /var/lib/cwl/stg34b392f7-f716-40dc-ba28-9ea99ae87984/GCF_013327855.1_ASM1332785v1_genomic.fna.gz | prodigal -d GCF_013327855.1_ASM1332785v1_genomic.fna/cds.fna -a GCF_013327855.1_ASM1332785v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:03:49,467] [INFO] Task succeeded: Prodigal
[2024-01-25 20:03:49,467] [INFO] Task started: HMMsearch
[2024-01-25 20:03:49,467] [INFO] Running command: hmmsearch --tblout GCF_013327855.1_ASM1332785v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg60f128c6-3c64-4dba-a2f0-f2fd61dd7d90/dqc_reference/reference_markers.hmm GCF_013327855.1_ASM1332785v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:03:49,794] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:03:49,795] [INFO] Found 6/6 markers.
[2024-01-25 20:03:49,834] [INFO] Query marker FASTA was written to GCF_013327855.1_ASM1332785v1_genomic.fna/markers.fasta
[2024-01-25 20:03:49,835] [INFO] Task started: Blastn
[2024-01-25 20:03:49,835] [INFO] Running command: blastn -query GCF_013327855.1_ASM1332785v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60f128c6-3c64-4dba-a2f0-f2fd61dd7d90/dqc_reference/reference_markers.fasta -out GCF_013327855.1_ASM1332785v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:03:50,693] [INFO] Task succeeded: Blastn
[2024-01-25 20:03:50,696] [INFO] Selected 16 target genomes.
[2024-01-25 20:03:50,697] [INFO] Target genome list was writen to GCF_013327855.1_ASM1332785v1_genomic.fna/target_genomes.txt
[2024-01-25 20:03:50,705] [INFO] Task started: fastANI
[2024-01-25 20:03:50,705] [INFO] Running command: fastANI --query /var/lib/cwl/stg34b392f7-f716-40dc-ba28-9ea99ae87984/GCF_013327855.1_ASM1332785v1_genomic.fna.gz --refList GCF_013327855.1_ASM1332785v1_genomic.fna/target_genomes.txt --output GCF_013327855.1_ASM1332785v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:04:08,665] [INFO] Task succeeded: fastANI
[2024-01-25 20:04:08,665] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg60f128c6-3c64-4dba-a2f0-f2fd61dd7d90/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:04:08,665] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg60f128c6-3c64-4dba-a2f0-f2fd61dd7d90/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:04:08,675] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:04:08,676] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:04:08,676] [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
Phyllobacterium pellucidum	strain=BT25	GCA_013327855.1	2740464	2740464	type	True	100.0	1545	1546	95	conclusive
Phyllobacterium zundukense	strain=Tri-48; RCAM 03910	GCA_002764115.1	1867719	1867719	type	True	80.5455	864	1546	95	below_threshold
Phyllobacterium myrsinacearum	strain=DSM 5892	GCA_002980555.1	28101	28101	type	True	80.045	766	1546	95	below_threshold
Phyllobacterium calauticae	strain=R2-JL	GCA_019991125.1	2817027	2817027	type	True	79.9406	786	1546	95	below_threshold
Phyllobacterium sophorae	strain=CCBAU 03422	GCA_003010965.1	1520277	1520277	type	True	79.8279	845	1546	95	below_threshold
Phyllobacterium brassicacearum	strain=STM 196	GCA_003010955.1	314235	314235	type	True	79.8206	835	1546	95	below_threshold
Phyllobacterium trifolii	strain=CECT 7015	GCA_014192095.1	300193	300193	type	True	79.6134	725	1546	95	below_threshold
Phyllobacterium bourgognense	strain=31-25a	GCA_003337575.1	314236	314236	type	True	79.3553	741	1546	95	below_threshold
Phyllobacterium phragmitis	strain=1N-3	GCA_002980495.1	2670329	2670329	type	True	78.0887	446	1546	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	77.6539	416	1546	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	77.5549	401	1546	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	77.4251	320	1546	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	77.2681	274	1546	95	below_threshold
Brucella pituitosa	strain=CCUG 50899	GCA_008801705.1	571256	571256	type	True	77.2599	207	1546	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	77.2577	275	1546	95	below_threshold
Pseudochrobactrum asaccharolyticum	strain=DSM 25619	GCA_003314995.1	354351	354351	type	True	76.5093	105	1546	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:04:08,677] [INFO] DFAST Taxonomy check result was written to GCF_013327855.1_ASM1332785v1_genomic.fna/tc_result.tsv
[2024-01-25 20:04:08,678] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:04:08,678] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:04:08,678] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg60f128c6-3c64-4dba-a2f0-f2fd61dd7d90/dqc_reference/checkm_data
[2024-01-25 20:04:08,679] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:04:08,724] [INFO] Task started: CheckM
[2024-01-25 20:04:08,724] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013327855.1_ASM1332785v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013327855.1_ASM1332785v1_genomic.fna/checkm_input GCF_013327855.1_ASM1332785v1_genomic.fna/checkm_result
[2024-01-25 20:04:46,608] [INFO] Task succeeded: CheckM
[2024-01-25 20:04:46,609] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:04:46,624] [INFO] ===== Completeness check finished =====
[2024-01-25 20:04:46,624] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:04:46,625] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013327855.1_ASM1332785v1_genomic.fna/markers.fasta)
[2024-01-25 20:04:46,625] [INFO] Task started: Blastn
[2024-01-25 20:04:46,625] [INFO] Running command: blastn -query GCF_013327855.1_ASM1332785v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60f128c6-3c64-4dba-a2f0-f2fd61dd7d90/dqc_reference/reference_markers_gtdb.fasta -out GCF_013327855.1_ASM1332785v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:04:48,063] [INFO] Task succeeded: Blastn
[2024-01-25 20:04:48,066] [INFO] Selected 11 target genomes.
[2024-01-25 20:04:48,066] [INFO] Target genome list was writen to GCF_013327855.1_ASM1332785v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:04:48,080] [INFO] Task started: fastANI
[2024-01-25 20:04:48,080] [INFO] Running command: fastANI --query /var/lib/cwl/stg34b392f7-f716-40dc-ba28-9ea99ae87984/GCF_013327855.1_ASM1332785v1_genomic.fna.gz --refList GCF_013327855.1_ASM1332785v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013327855.1_ASM1332785v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:05:01,165] [INFO] Task succeeded: fastANI
[2024-01-25 20:05:01,172] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:05:01,173] [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_013327855.1	s__Phyllobacterium pellucidum	100.0	1545	1546	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	97.81	96.22	0.94	0.90	6	conclusive
GCA_900473175.1	s__Phyllobacterium sp900473175	81.0407	969	1546	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002764115.1	s__Phyllobacterium zundukense	80.5526	863	1546	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900539805.1	s__Phyllobacterium sp900539805	79.9695	747	1546	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	96.69	96.69	0.93	0.93	2	-
GCF_003010965.1	s__Phyllobacterium sophorae	79.8183	847	1546	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	99.00	98.48	0.92	0.90	3	-
GCF_003010955.1	s__Phyllobacterium brassicacearum	79.8142	836	1546	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014192095.1	s__Phyllobacterium trifolii	79.613	725	1546	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	99.32	99.28	0.88	0.88	4	-
GCF_003337575.1	s__Phyllobacterium bourgognense	79.3553	741	1546	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104355.1	s__Phyllobacterium sp900104355	79.2094	633	1546	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001558695.1	s__Paramesorhizobium deserti	78.2418	480	1546	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Paramesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002980495.1	s__Paramesorhizobium phragmitis	78.0804	447	1546	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Paramesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:05:01,174] [INFO] GTDB search result was written to GCF_013327855.1_ASM1332785v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:05:01,175] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:05:01,178] [INFO] DFAST_QC result json was written to GCF_013327855.1_ASM1332785v1_genomic.fna/dqc_result.json
[2024-01-25 20:05:01,178] [INFO] DFAST_QC completed!
[2024-01-25 20:05:01,178] [INFO] Total running time: 0h1m26s