[2024-01-25 18:04:35,499] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:04:35,501] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:04:35,501] [INFO] DQC Reference Directory: /var/lib/cwl/stg3ae2777f-c663-48d1-a04d-166501a6ad9d/dqc_reference
[2024-01-25 18:04:36,627] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:04:36,628] [INFO] Task started: Prodigal
[2024-01-25 18:04:36,628] [INFO] Running command: gunzip -c /var/lib/cwl/stg758ccc85-b667-48a7-9d57-c08f85913aa2/GCF_003992725.1_ASM399272v1_genomic.fna.gz | prodigal -d GCF_003992725.1_ASM399272v1_genomic.fna/cds.fna -a GCF_003992725.1_ASM399272v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:04:46,671] [INFO] Task succeeded: Prodigal
[2024-01-25 18:04:46,671] [INFO] Task started: HMMsearch
[2024-01-25 18:04:46,671] [INFO] Running command: hmmsearch --tblout GCF_003992725.1_ASM399272v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3ae2777f-c663-48d1-a04d-166501a6ad9d/dqc_reference/reference_markers.hmm GCF_003992725.1_ASM399272v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:04:46,961] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:04:46,963] [INFO] Found 6/6 markers.
[2024-01-25 18:04:47,001] [INFO] Query marker FASTA was written to GCF_003992725.1_ASM399272v1_genomic.fna/markers.fasta
[2024-01-25 18:04:47,002] [INFO] Task started: Blastn
[2024-01-25 18:04:47,002] [INFO] Running command: blastn -query GCF_003992725.1_ASM399272v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ae2777f-c663-48d1-a04d-166501a6ad9d/dqc_reference/reference_markers.fasta -out GCF_003992725.1_ASM399272v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:04:47,862] [INFO] Task succeeded: Blastn
[2024-01-25 18:04:47,864] [INFO] Selected 18 target genomes.
[2024-01-25 18:04:47,865] [INFO] Target genome list was writen to GCF_003992725.1_ASM399272v1_genomic.fna/target_genomes.txt
[2024-01-25 18:04:47,882] [INFO] Task started: fastANI
[2024-01-25 18:04:47,882] [INFO] Running command: fastANI --query /var/lib/cwl/stg758ccc85-b667-48a7-9d57-c08f85913aa2/GCF_003992725.1_ASM399272v1_genomic.fna.gz --refList GCF_003992725.1_ASM399272v1_genomic.fna/target_genomes.txt --output GCF_003992725.1_ASM399272v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:05:02,455] [INFO] Task succeeded: fastANI
[2024-01-25 18:05:02,455] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3ae2777f-c663-48d1-a04d-166501a6ad9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:05:02,455] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3ae2777f-c663-48d1-a04d-166501a6ad9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:05:02,466] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:05:02,466] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:05:02,466] [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
Rhodomicrobium lacus	strain=JA980	GCA_003992725.1	2498452	2498452	type	True	100.0	1286	1287	95	conclusive
Rhodomicrobium udaipurense	strain=JA643	GCA_016461795.1	1202716	1202716	type	True	87.6872	1002	1287	95	below_threshold
Rhodomicrobium udaipurense	strain=JA643	GCA_000636015.1	1202716	1202716	type	True	87.5757	926	1287	95	below_threshold
Blastochloris sulfoviridis	strain=DSM 729	GCA_008630065.1	50712	50712	type	True	77.3565	178	1287	95	below_threshold
Hyphomicrobium album	strain=XQ2	GCA_009708035.1	2665159	2665159	type	True	77.2339	142	1287	95	below_threshold
Blastochloris tepida	strain=GI	GCA_003966715.1	2233851	2233851	type	True	77.1918	180	1287	95	below_threshold
Pannonibacter phragmitetus	strain=NCTC13350	GCA_900454465.1	121719	121719	suspected-type	True	76.9558	119	1287	95	below_threshold
Pannonibacter phragmitetus	strain=DSM 14782	GCA_000382365.1	121719	121719	suspected-type	True	76.6753	118	1287	95	below_threshold
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	76.6514	164	1287	95	below_threshold
Xanthobacter aminoxidans	strain=ATCC BAA-299	GCA_023571765.1	186280	186280	type	True	76.6238	167	1287	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	76.4999	178	1287	95	below_threshold
Dichotomicrobium thermohalophilum	strain=DSM 5002	GCA_003550175.1	933063	933063	type	True	76.4816	128	1287	95	below_threshold
Kaistia hirudinis	strain=DSM 25966	GCA_014196455.1	1293440	1293440	type	True	76.4369	169	1287	95	below_threshold
Methylobacterium gregans	strain=NBRC 103626	GCA_022179245.1	374424	374424	type	True	76.3891	139	1287	95	below_threshold
Rhizobium wuzhouense	strain=W44	GCA_003205195.1	1986026	1986026	type	True	76.3831	96	1287	95	below_threshold
Bosea caraganae	strain=RCAM 04680	GCA_003351345.1	2763117	2763117	type	True	76.3442	198	1287	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	76.1703	165	1287	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:05:02,468] [INFO] DFAST Taxonomy check result was written to GCF_003992725.1_ASM399272v1_genomic.fna/tc_result.tsv
[2024-01-25 18:05:02,468] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:05:02,469] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:05:02,469] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3ae2777f-c663-48d1-a04d-166501a6ad9d/dqc_reference/checkm_data
[2024-01-25 18:05:02,470] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:05:02,512] [INFO] Task started: CheckM
[2024-01-25 18:05:02,512] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003992725.1_ASM399272v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003992725.1_ASM399272v1_genomic.fna/checkm_input GCF_003992725.1_ASM399272v1_genomic.fna/checkm_result
[2024-01-25 18:05:33,356] [INFO] Task succeeded: CheckM
[2024-01-25 18:05:33,360] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:05:33,386] [INFO] ===== Completeness check finished =====
[2024-01-25 18:05:33,386] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:05:33,386] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003992725.1_ASM399272v1_genomic.fna/markers.fasta)
[2024-01-25 18:05:33,386] [INFO] Task started: Blastn
[2024-01-25 18:05:33,386] [INFO] Running command: blastn -query GCF_003992725.1_ASM399272v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ae2777f-c663-48d1-a04d-166501a6ad9d/dqc_reference/reference_markers_gtdb.fasta -out GCF_003992725.1_ASM399272v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:05:35,192] [INFO] Task succeeded: Blastn
[2024-01-25 18:05:35,195] [INFO] Selected 9 target genomes.
[2024-01-25 18:05:35,195] [INFO] Target genome list was writen to GCF_003992725.1_ASM399272v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:05:35,222] [INFO] Task started: fastANI
[2024-01-25 18:05:35,222] [INFO] Running command: fastANI --query /var/lib/cwl/stg758ccc85-b667-48a7-9d57-c08f85913aa2/GCF_003992725.1_ASM399272v1_genomic.fna.gz --refList GCF_003992725.1_ASM399272v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003992725.1_ASM399272v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:05:43,863] [INFO] Task succeeded: fastANI
[2024-01-25 18:05:43,869] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:05:43,870] [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_003992725.1	s__Rhodomicrobium lacus	100.0	1286	1287	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodomicrobiaceae;g__Rhodomicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000166055.1	s__Rhodomicrobium vannielii	87.6798	1014	1287	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodomicrobiaceae;g__Rhodomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000636015.1	s__Rhodomicrobium udaipurense	87.5789	925	1287	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodomicrobiaceae;g__Rhodomicrobium	95.0	98.25	96.51	0.94	0.88	3	-
GCF_018619475.1	s__Rhodomicrobium sp018619475	86.7523	880	1287	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodomicrobiaceae;g__Rhodomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003153975.1	s__Rhodomicrobium sp003153975	77.5687	304	1287	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodomicrobiaceae;g__Rhodomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002198715.1	s__R-RK-3 sp002198715	77.3064	240	1287	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodomicrobiaceae;g__R-RK-3	95.0	99.98	99.98	0.99	0.99	2	-
GCF_003550175.1	s__Dichotomicrobium thermohalophilum	76.4816	128	1287	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodomicrobiaceae;g__Dichotomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900465755.1	s__Allorhizobium sp900465755	76.3155	97	1287	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813725.1	s__Leisingera sp000813725	75.6419	56	1287	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:05:43,872] [INFO] GTDB search result was written to GCF_003992725.1_ASM399272v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:05:43,872] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:05:43,875] [INFO] DFAST_QC result json was written to GCF_003992725.1_ASM399272v1_genomic.fna/dqc_result.json
[2024-01-25 18:05:43,875] [INFO] DFAST_QC completed!
[2024-01-25 18:05:43,875] [INFO] Total running time: 0h1m8s