[2024-01-24 13:55:15,340] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:15,342] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:15,342] [INFO] DQC Reference Directory: /var/lib/cwl/stg122e035f-91cc-4657-9a93-66627be2f0f0/dqc_reference
[2024-01-24 13:55:16,569] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:16,570] [INFO] Task started: Prodigal
[2024-01-24 13:55:16,570] [INFO] Running command: gunzip -c /var/lib/cwl/stgf3659789-0ce2-41a3-87dc-9751f60cfc64/GCF_008807375.1_ASM880737v1_genomic.fna.gz | prodigal -d GCF_008807375.1_ASM880737v1_genomic.fna/cds.fna -a GCF_008807375.1_ASM880737v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:36,785] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:36,786] [INFO] Task started: HMMsearch
[2024-01-24 13:55:36,786] [INFO] Running command: hmmsearch --tblout GCF_008807375.1_ASM880737v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg122e035f-91cc-4657-9a93-66627be2f0f0/dqc_reference/reference_markers.hmm GCF_008807375.1_ASM880737v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:37,112] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:37,113] [INFO] Found 6/6 markers.
[2024-01-24 13:55:37,161] [INFO] Query marker FASTA was written to GCF_008807375.1_ASM880737v1_genomic.fna/markers.fasta
[2024-01-24 13:55:37,161] [INFO] Task started: Blastn
[2024-01-24 13:55:37,161] [INFO] Running command: blastn -query GCF_008807375.1_ASM880737v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg122e035f-91cc-4657-9a93-66627be2f0f0/dqc_reference/reference_markers.fasta -out GCF_008807375.1_ASM880737v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:38,337] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:38,341] [INFO] Selected 18 target genomes.
[2024-01-24 13:55:38,341] [INFO] Target genome list was writen to GCF_008807375.1_ASM880737v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:38,364] [INFO] Task started: fastANI
[2024-01-24 13:55:38,364] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3659789-0ce2-41a3-87dc-9751f60cfc64/GCF_008807375.1_ASM880737v1_genomic.fna.gz --refList GCF_008807375.1_ASM880737v1_genomic.fna/target_genomes.txt --output GCF_008807375.1_ASM880737v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:02,515] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:02,515] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg122e035f-91cc-4657-9a93-66627be2f0f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:02,516] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg122e035f-91cc-4657-9a93-66627be2f0f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:02,531] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:56:02,531] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:56:02,531] [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
Pseudomonas furukawaii	strain=KF707	GCA_002355475.1	1149133	1149133	type	True	86.7632	1437	2018	95	below_threshold
Pseudomonas furukawaii	strain=KF707	GCA_000262065.3	1149133	1149133	type	True	86.7619	1422	2018	95	below_threshold
Pseudomonas tohonis	strain=TUM18999	GCA_012767755.2	2725477	2725477	type	True	85.1829	1304	2018	95	below_threshold
Pseudomonas otitidis	strain=DSM 17224	GCA_900111835.1	319939	319939	suspected-type	True	84.837	1249	2018	95	below_threshold
Pseudomonas delhiensis	strain=RLD-1	GCA_900187975.1	366289	366289	type	True	83.5022	1199	2018	95	below_threshold
Pseudomonas delhiensis	strain=CCM 7361	GCA_900099945.1	366289	366289	type	True	83.4884	1195	2018	95	below_threshold
Pseudomonas alcaligenes	strain=NCTC10367	GCA_900455475.1	43263	43263	type	True	83.3007	980	2018	95	below_threshold
Pseudomonas alcaligenes	strain=NBRC 14159	GCA_000467105.1	43263	43263	type	True	83.2794	960	2018	95	below_threshold
Pseudomonas knackmussii	strain=B13	GCA_000689415.1	65741	65741	type	True	82.9662	1152	2018	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	82.8593	1013	2018	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	82.6979	1047	2018	95	below_threshold
Pseudomonas thermotolerans	strain=DSM 14292	GCA_000364625.1	157784	157784	type	True	82.6291	884	2018	95	below_threshold
Pseudomonas campi	strain=S1-A32-2	GCA_013200955.2	2731681	2731681	type	True	82.6254	910	2018	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	82.4294	1041	2018	95	below_threshold
Pseudomonas ullengensis	strain=UL070	GCA_014174475.1	2759166	2759166	type	True	82.4195	984	2018	95	below_threshold
[Pseudomonas] nosocomialis	strain=A31/70	GCA_005876855.1	1056496	1056496	type	True	81.1261	766	2018	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	81.1106	732	2018	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	81.0285	713	2018	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:02,533] [INFO] DFAST Taxonomy check result was written to GCF_008807375.1_ASM880737v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:02,534] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:02,534] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:02,534] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg122e035f-91cc-4657-9a93-66627be2f0f0/dqc_reference/checkm_data
[2024-01-24 13:56:02,535] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:02,597] [INFO] Task started: CheckM
[2024-01-24 13:56:02,597] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008807375.1_ASM880737v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008807375.1_ASM880737v1_genomic.fna/checkm_input GCF_008807375.1_ASM880737v1_genomic.fna/checkm_result
[2024-01-24 13:57:03,529] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:03,530] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:03,552] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:03,553] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:03,553] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008807375.1_ASM880737v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:03,554] [INFO] Task started: Blastn
[2024-01-24 13:57:03,554] [INFO] Running command: blastn -query GCF_008807375.1_ASM880737v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg122e035f-91cc-4657-9a93-66627be2f0f0/dqc_reference/reference_markers_gtdb.fasta -out GCF_008807375.1_ASM880737v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:05,493] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:05,497] [INFO] Selected 9 target genomes.
[2024-01-24 13:57:05,498] [INFO] Target genome list was writen to GCF_008807375.1_ASM880737v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:05,510] [INFO] Task started: fastANI
[2024-01-24 13:57:05,510] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3659789-0ce2-41a3-87dc-9751f60cfc64/GCF_008807375.1_ASM880737v1_genomic.fna.gz --refList GCF_008807375.1_ASM880737v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008807375.1_ASM880737v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:20,498] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:20,506] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:20,506] [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_008807375.1	s__Pseudomonas_F lalkuanensis	100.0	2016	2018	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014700075.1	s__Pseudomonas_F sp014700075	93.9485	1675	2018	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013393345.1	s__Pseudomonas_F resinovorans_C	89.3722	1605	2018	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	95.04	95.04	0.90	0.90	2	-
GCF_000412695.1	s__Pseudomonas_F resinovorans_A	88.7159	1563	2018	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000949385.2	s__Pseudomonas_F sp000949385	88.607	1528	2018	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001708505.1	s__Pseudomonas_F sp001708505	88.5439	1485	2018	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003626975.1	s__Pseudomonas_F sp003626975	88.3652	1575	2018	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	99.49	99.49	0.93	0.93	2	-
GCF_002355475.1	s__Pseudomonas_F furukawaii	86.8192	1431	2018	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	99.26	98.53	0.90	0.84	3	-
GCF_900111835.1	s__Pseudomonas_F otitidis	84.8341	1250	2018	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	96.35	95.43	0.89	0.84	21	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:20,508] [INFO] GTDB search result was written to GCF_008807375.1_ASM880737v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:20,508] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:20,513] [INFO] DFAST_QC result json was written to GCF_008807375.1_ASM880737v1_genomic.fna/dqc_result.json
[2024-01-24 13:57:20,513] [INFO] DFAST_QC completed!
[2024-01-24 13:57:20,514] [INFO] Total running time: 0h2m5s