[2024-01-24 13:49:45,153] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:45,156] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:45,156] [INFO] DQC Reference Directory: /var/lib/cwl/stgc287696f-4339-4099-b826-d17a1ac9dd90/dqc_reference
[2024-01-24 13:49:46,479] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:46,480] [INFO] Task started: Prodigal
[2024-01-24 13:49:46,480] [INFO] Running command: gunzip -c /var/lib/cwl/stg52070ea5-1845-4409-9a81-85c93aef44a7/GCF_016461795.1_ASM1646179v1_genomic.fna.gz | prodigal -d GCF_016461795.1_ASM1646179v1_genomic.fna/cds.fna -a GCF_016461795.1_ASM1646179v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:57,656] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:57,656] [INFO] Task started: HMMsearch
[2024-01-24 13:49:57,656] [INFO] Running command: hmmsearch --tblout GCF_016461795.1_ASM1646179v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc287696f-4339-4099-b826-d17a1ac9dd90/dqc_reference/reference_markers.hmm GCF_016461795.1_ASM1646179v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:57,932] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:57,934] [INFO] Found 6/6 markers.
[2024-01-24 13:49:57,986] [INFO] Query marker FASTA was written to GCF_016461795.1_ASM1646179v1_genomic.fna/markers.fasta
[2024-01-24 13:49:57,987] [INFO] Task started: Blastn
[2024-01-24 13:49:57,987] [INFO] Running command: blastn -query GCF_016461795.1_ASM1646179v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc287696f-4339-4099-b826-d17a1ac9dd90/dqc_reference/reference_markers.fasta -out GCF_016461795.1_ASM1646179v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:58,917] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:58,921] [INFO] Selected 19 target genomes.
[2024-01-24 13:49:58,921] [INFO] Target genome list was writen to GCF_016461795.1_ASM1646179v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:58,928] [INFO] Task started: fastANI
[2024-01-24 13:49:58,928] [INFO] Running command: fastANI --query /var/lib/cwl/stg52070ea5-1845-4409-9a81-85c93aef44a7/GCF_016461795.1_ASM1646179v1_genomic.fna.gz --refList GCF_016461795.1_ASM1646179v1_genomic.fna/target_genomes.txt --output GCF_016461795.1_ASM1646179v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:14,404] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:14,405] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc287696f-4339-4099-b826-d17a1ac9dd90/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:14,405] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc287696f-4339-4099-b826-d17a1ac9dd90/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:14,437] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:50:14,437] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:14,438] [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 udaipurense	strain=JA643	GCA_016461795.1	1202716	1202716	type	True	100.0	1180	1184	95	conclusive
Rhodomicrobium udaipurense	strain=JA643	GCA_000636015.1	1202716	1202716	type	True	99.869	1042	1184	95	conclusive
Rhodomicrobium lacus	strain=JA980	GCA_003992725.1	2498452	2498452	type	True	87.7717	985	1184	95	below_threshold
Hyphomicrobium nitrativorans	strain=NL23	GCA_000503895.1	1427356	1427356	type	True	77.1329	126	1184	95	below_threshold
Hyphomicrobium album	strain=XQ2	GCA_009708035.1	2665159	2665159	type	True	76.8946	142	1184	95	below_threshold
Blastochloris tepida	strain=GI	GCA_003966715.1	2233851	2233851	type	True	76.8784	194	1184	95	below_threshold
Blastochloris sulfoviridis	strain=DSM 729	GCA_008630065.1	50712	50712	type	True	76.7921	195	1184	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	76.7149	123	1184	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	76.6501	194	1184	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	76.5953	196	1184	95	below_threshold
Dichotomicrobium thermohalophilum	strain=DSM 5002	GCA_003550175.1	933063	933063	type	True	76.5548	133	1184	95	below_threshold
Methylobacterium mesophilicum	strain=NBRC 15688	GCA_022179445.1	39956	39956	type	True	76.5123	141	1184	95	below_threshold
Kaistia hirudinis	strain=DSM 25966	GCA_014196455.1	1293440	1293440	type	True	76.4555	172	1184	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	76.445	160	1184	95	below_threshold
Salinarimonas ramus	strain=CGMCC 1.9161	GCA_014645695.1	690164	690164	type	True	76.4199	188	1184	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	76.3416	181	1184	95	below_threshold
Methylobacterium gregans	strain=NBRC 103626	GCA_022179245.1	374424	374424	type	True	76.3173	156	1184	95	below_threshold
Skermanella aerolata	strain=5416T-32	GCA_000936425.1	393310	393310	type	True	75.8616	118	1184	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:14,439] [INFO] DFAST Taxonomy check result was written to GCF_016461795.1_ASM1646179v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:14,440] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:14,440] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:14,440] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc287696f-4339-4099-b826-d17a1ac9dd90/dqc_reference/checkm_data
[2024-01-24 13:50:14,441] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:14,483] [INFO] Task started: CheckM
[2024-01-24 13:50:14,483] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016461795.1_ASM1646179v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016461795.1_ASM1646179v1_genomic.fna/checkm_input GCF_016461795.1_ASM1646179v1_genomic.fna/checkm_result
[2024-01-24 13:50:47,864] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:47,865] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:47,887] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:47,887] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:47,888] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016461795.1_ASM1646179v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:47,888] [INFO] Task started: Blastn
[2024-01-24 13:50:47,888] [INFO] Running command: blastn -query GCF_016461795.1_ASM1646179v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc287696f-4339-4099-b826-d17a1ac9dd90/dqc_reference/reference_markers_gtdb.fasta -out GCF_016461795.1_ASM1646179v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:49,620] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:49,625] [INFO] Selected 9 target genomes.
[2024-01-24 13:50:49,625] [INFO] Target genome list was writen to GCF_016461795.1_ASM1646179v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:49,676] [INFO] Task started: fastANI
[2024-01-24 13:50:49,676] [INFO] Running command: fastANI --query /var/lib/cwl/stg52070ea5-1845-4409-9a81-85c93aef44a7/GCF_016461795.1_ASM1646179v1_genomic.fna.gz --refList GCF_016461795.1_ASM1646179v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016461795.1_ASM1646179v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:57,845] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:57,854] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:57,854] [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_000636015.1	s__Rhodomicrobium udaipurense	99.869	1042	1184	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodomicrobiaceae;g__Rhodomicrobium	95.0	98.25	96.51	0.94	0.88	3	conclusive
GCF_000166055.1	s__Rhodomicrobium vannielii	94.8737	1047	1184	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodomicrobiaceae;g__Rhodomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018619475.1	s__Rhodomicrobium sp018619475	88.6568	891	1184	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodomicrobiaceae;g__Rhodomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003992725.1	s__Rhodomicrobium lacus	87.7588	987	1184	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	77.7409	313	1184	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	77.2505	240	1184	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	76.5548	133	1184	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodomicrobiaceae;g__Dichotomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000936425.1	s__Skermanella aerolata	75.8616	118	1184	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	99.99	99.99	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:57,856] [INFO] GTDB search result was written to GCF_016461795.1_ASM1646179v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:57,857] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:57,863] [INFO] DFAST_QC result json was written to GCF_016461795.1_ASM1646179v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:57,864] [INFO] DFAST_QC completed!
[2024-01-24 13:50:57,864] [INFO] Total running time: 0h1m13s