[2024-01-24 11:26:54,310] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:54,314] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:54,314] [INFO] DQC Reference Directory: /var/lib/cwl/stg4fcbc906-6d15-4133-89e0-e8411d875a09/dqc_reference
[2024-01-24 11:26:58,220] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:58,221] [INFO] Task started: Prodigal
[2024-01-24 11:26:58,222] [INFO] Running command: gunzip -c /var/lib/cwl/stg0c3c9445-19db-44be-985d-ab73d19ad5c6/GCF_003290025.1_ASM329002v1_genomic.fna.gz | prodigal -d GCF_003290025.1_ASM329002v1_genomic.fna/cds.fna -a GCF_003290025.1_ASM329002v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:14,624] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:14,625] [INFO] Task started: HMMsearch
[2024-01-24 11:27:14,625] [INFO] Running command: hmmsearch --tblout GCF_003290025.1_ASM329002v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4fcbc906-6d15-4133-89e0-e8411d875a09/dqc_reference/reference_markers.hmm GCF_003290025.1_ASM329002v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:14,929] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:14,930] [INFO] Found 6/6 markers.
[2024-01-24 11:27:14,979] [INFO] Query marker FASTA was written to GCF_003290025.1_ASM329002v1_genomic.fna/markers.fasta
[2024-01-24 11:27:14,979] [INFO] Task started: Blastn
[2024-01-24 11:27:14,979] [INFO] Running command: blastn -query GCF_003290025.1_ASM329002v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4fcbc906-6d15-4133-89e0-e8411d875a09/dqc_reference/reference_markers.fasta -out GCF_003290025.1_ASM329002v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:15,914] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:15,918] [INFO] Selected 19 target genomes.
[2024-01-24 11:27:15,918] [INFO] Target genome list was writen to GCF_003290025.1_ASM329002v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:15,925] [INFO] Task started: fastANI
[2024-01-24 11:27:15,925] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c3c9445-19db-44be-985d-ab73d19ad5c6/GCF_003290025.1_ASM329002v1_genomic.fna.gz --refList GCF_003290025.1_ASM329002v1_genomic.fna/target_genomes.txt --output GCF_003290025.1_ASM329002v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:32,557] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:32,558] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4fcbc906-6d15-4133-89e0-e8411d875a09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:32,559] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4fcbc906-6d15-4133-89e0-e8411d875a09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:32,577] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:32,578] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:32,578] [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
Pseudogemmobacter bohemicus	strain=Cd-10	GCA_003290025.1	2250708	2250708	type	True	99.997	1826	1860	95	conclusive
Pseudogemmobacter hezensis	strain=D13-10-4-6	GCA_013155295.1	2737662	2737662	type	True	83.4948	968	1860	95	below_threshold
Gemmobacter serpentinus	strain=HB-1	GCA_008973825.1	2652247	2652247	type	True	79.0262	588	1860	95	below_threshold
Gemmobacter caeruleus	strain=N8	GCA_008271655.1	2595004	2595004	type	True	78.817	598	1860	95	below_threshold
Gemmobacter caeni	strain=DSM 21823	GCA_003054195.1	589035	589035	type	True	78.6008	569	1860	95	below_threshold
Gemmobacter aquatilis	strain=DSM 3857	GCA_900110025.1	933059	933059	type	True	78.5402	562	1860	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	78.2883	457	1860	95	below_threshold
Gemmobacter lanyuensis	strain=KCTC 23714	GCA_014652355.1	1054497	1054497	type	True	78.1275	485	1860	95	below_threshold
Gemmobacter nectariphilus	strain=DSM 15620	GCA_000429765.1	220343	220343	type	True	78.0004	483	1860	95	below_threshold
Rhodobacter calidifons	strain=M37P	GCA_011174775.1	2715277	2715277	type	True	77.9794	481	1860	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	77.8849	404	1860	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	77.8375	492	1860	95	below_threshold
Gemmobacter aquaticus	strain=CGMCC 1.7029	GCA_014645295.1	490185	490185	type	True	77.7641	407	1860	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009908165.1	1465486	1465486	type	True	77.7486	446	1860	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009881095.1	1465486	1465486	type	True	77.7037	459	1860	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	77.7017	429	1860	95	below_threshold
Frigidibacter albus	strain=CGMCC 1.13995	GCA_014640395.1	1465486	1465486	type	True	77.6917	457	1860	95	below_threshold
Gemmobacter aquaticus	strain=A1-9	GCA_007859075.1	490185	490185	type	True	77.6895	417	1860	95	below_threshold
[Luteovulum] sphaeroides subsp. megalophilum	strain=DSM 18937	GCA_900188265.1	418630	1063	type	True	77.6809	437	1860	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:32,580] [INFO] DFAST Taxonomy check result was written to GCF_003290025.1_ASM329002v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:32,581] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:32,582] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:32,582] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4fcbc906-6d15-4133-89e0-e8411d875a09/dqc_reference/checkm_data
[2024-01-24 11:27:32,584] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:32,640] [INFO] Task started: CheckM
[2024-01-24 11:27:32,641] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003290025.1_ASM329002v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003290025.1_ASM329002v1_genomic.fna/checkm_input GCF_003290025.1_ASM329002v1_genomic.fna/checkm_result
[2024-01-24 11:28:27,067] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:27,069] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:27,092] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:27,093] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:27,093] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003290025.1_ASM329002v1_genomic.fna/markers.fasta)
[2024-01-24 11:28:27,094] [INFO] Task started: Blastn
[2024-01-24 11:28:27,094] [INFO] Running command: blastn -query GCF_003290025.1_ASM329002v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4fcbc906-6d15-4133-89e0-e8411d875a09/dqc_reference/reference_markers_gtdb.fasta -out GCF_003290025.1_ASM329002v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:28,945] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:28,949] [INFO] Selected 6 target genomes.
[2024-01-24 11:28:28,949] [INFO] Target genome list was writen to GCF_003290025.1_ASM329002v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:28,955] [INFO] Task started: fastANI
[2024-01-24 11:28:28,955] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c3c9445-19db-44be-985d-ab73d19ad5c6/GCF_003290025.1_ASM329002v1_genomic.fna.gz --refList GCF_003290025.1_ASM329002v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003290025.1_ASM329002v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:36,258] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:36,267] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:36,267] [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_003290025.1	s__Pseudogemmobacter bohemicus	99.997	1825	1860	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudogemmobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016405985.1	s__Pseudogemmobacter sp016405985	86.366	1202	1860	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudogemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105075.1	s__Pseudogemmobacter sp900105075	85.8905	1129	1860	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudogemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013155295.1	s__Pseudogemmobacter sp013155295	83.4661	972	1860	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudogemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900609055.1	s__Pseudogemmobacter humi	81.9484	861	1860	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudogemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013298485.1	s__JAAFHS01 sp013298485	77.1708	220	1860	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAAFHS01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:36,269] [INFO] GTDB search result was written to GCF_003290025.1_ASM329002v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:36,269] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:36,272] [INFO] DFAST_QC result json was written to GCF_003290025.1_ASM329002v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:36,273] [INFO] DFAST_QC completed!
[2024-01-24 11:28:36,273] [INFO] Total running time: 0h1m42s