[2024-01-24 13:10:19,552] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:10:19,554] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:10:19,554] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8309117-da05-48a3-bd85-d886fa513b8d/dqc_reference
[2024-01-24 13:10:20,764] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:10:20,765] [INFO] Task started: Prodigal
[2024-01-24 13:10:20,765] [INFO] Running command: gunzip -c /var/lib/cwl/stg94c30d15-009c-4b04-af45-b81cf1ae3efa/GCF_900105655.1_IMG-taxon_2667527386_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900105655.1_IMG-taxon_2667527386_annotated_assembly_genomic.fna/cds.fna -a GCF_900105655.1_IMG-taxon_2667527386_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:32,881] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:32,882] [INFO] Task started: HMMsearch
[2024-01-24 13:10:32,882] [INFO] Running command: hmmsearch --tblout GCF_900105655.1_IMG-taxon_2667527386_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8309117-da05-48a3-bd85-d886fa513b8d/dqc_reference/reference_markers.hmm GCF_900105655.1_IMG-taxon_2667527386_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:33,193] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:33,195] [INFO] Found 6/6 markers.
[2024-01-24 13:10:33,234] [INFO] Query marker FASTA was written to GCF_900105655.1_IMG-taxon_2667527386_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:10:33,235] [INFO] Task started: Blastn
[2024-01-24 13:10:33,235] [INFO] Running command: blastn -query GCF_900105655.1_IMG-taxon_2667527386_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8309117-da05-48a3-bd85-d886fa513b8d/dqc_reference/reference_markers.fasta -out GCF_900105655.1_IMG-taxon_2667527386_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:34,202] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:34,206] [INFO] Selected 22 target genomes.
[2024-01-24 13:10:34,207] [INFO] Target genome list was writen to GCF_900105655.1_IMG-taxon_2667527386_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:10:34,217] [INFO] Task started: fastANI
[2024-01-24 13:10:34,217] [INFO] Running command: fastANI --query /var/lib/cwl/stg94c30d15-009c-4b04-af45-b81cf1ae3efa/GCF_900105655.1_IMG-taxon_2667527386_annotated_assembly_genomic.fna.gz --refList GCF_900105655.1_IMG-taxon_2667527386_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900105655.1_IMG-taxon_2667527386_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:50,570] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:50,571] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8309117-da05-48a3-bd85-d886fa513b8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:50,572] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8309117-da05-48a3-bd85-d886fa513b8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:50,596] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:10:50,597] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:10:50,597] [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 yangmingensis	strain=DSM 24213	GCA_900114825.1	1720063	1720063	type	True	78.9448	393	1265	95	below_threshold
Halopseudomonas litoralis	strain=2SM5	GCA_900105005.1	797277	797277	type	True	78.7279	329	1265	95	below_threshold
Halopseudomonas pachastrellae	strain=JCM 12285	GCA_900114765.1	254161	254161	type	True	78.6083	383	1265	95	below_threshold
Halopseudomonas bauzanensis	strain=CGMCC 1.9095	GCA_900114735.1	653930	653930	type	True	78.6066	354	1265	95	below_threshold
Halopseudomonas aestusnigri	strain=CECT 8317	GCA_900108005.1	857252	857252	type	True	78.5976	369	1265	95	below_threshold
Halopseudomonas bauzanensis	strain=DSM 22558	GCA_900111225.1	653930	653930	type	True	78.5964	359	1265	95	below_threshold
Halopseudomonas aestusnigri	strain=VGXO14	GCA_002197985.1	857252	857252	type	True	78.5956	373	1265	95	below_threshold
Halopseudomonas pachastrellae	strain=CCUG 46540	GCA_001989375.1	254161	254161	type	True	78.444	377	1265	95	below_threshold
Pseudomonas profundi	strain=M5	GCA_008638305.1	1981513	1981513	type	True	78.3361	298	1265	95	below_threshold
Halopseudomonas salina	strain=CGMCC 1.12482	GCA_014637955.1	1323744	1323744	type	True	78.302	338	1265	95	below_threshold
Halopseudomonas salina	strain=XCD-X85	GCA_008641105.1	1323744	1323744	type	True	78.2345	339	1265	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=DSM 6698	GCA_003851905.1	587851	587753	type	True	77.7889	200	1265	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=NBRC 3521	GCA_000813225.1	587851	587753	type	True	77.5739	194	1265	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	77.5479	240	1265	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	77.5472	176	1265	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=LMG 1245	GCA_001269575.1	587851	587753	type	True	77.4868	191	1265	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=CCUG 712	GCA_008801625.1	587851	587753	type	True	77.485	198	1265	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	77.472	224	1265	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_013373895.1	2740516	2740516	type	True	77.4594	169	1265	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_021602025.1	2740516	2740516	type	True	77.3425	176	1265	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	77.2506	181	1265	95	below_threshold
Pseudomonas karstica	strain=CCM 7891	GCA_009707515.1	1055468	1055468	type	True	76.9984	154	1265	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:50,599] [INFO] DFAST Taxonomy check result was written to GCF_900105655.1_IMG-taxon_2667527386_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:10:50,608] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:50,608] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:50,609] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8309117-da05-48a3-bd85-d886fa513b8d/dqc_reference/checkm_data
[2024-01-24 13:10:50,611] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:50,655] [INFO] Task started: CheckM
[2024-01-24 13:10:50,655] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900105655.1_IMG-taxon_2667527386_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900105655.1_IMG-taxon_2667527386_annotated_assembly_genomic.fna/checkm_input GCF_900105655.1_IMG-taxon_2667527386_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:11:29,922] [INFO] Task succeeded: CheckM
[2024-01-24 13:11:29,923] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:11:29,946] [INFO] ===== Completeness check finished =====
[2024-01-24 13:11:29,947] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:11:29,947] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900105655.1_IMG-taxon_2667527386_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:11:29,948] [INFO] Task started: Blastn
[2024-01-24 13:11:29,948] [INFO] Running command: blastn -query GCF_900105655.1_IMG-taxon_2667527386_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8309117-da05-48a3-bd85-d886fa513b8d/dqc_reference/reference_markers_gtdb.fasta -out GCF_900105655.1_IMG-taxon_2667527386_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:31,522] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:31,526] [INFO] Selected 17 target genomes.
[2024-01-24 13:11:31,527] [INFO] Target genome list was writen to GCF_900105655.1_IMG-taxon_2667527386_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:31,555] [INFO] Task started: fastANI
[2024-01-24 13:11:31,556] [INFO] Running command: fastANI --query /var/lib/cwl/stg94c30d15-009c-4b04-af45-b81cf1ae3efa/GCF_900105655.1_IMG-taxon_2667527386_annotated_assembly_genomic.fna.gz --refList GCF_900105655.1_IMG-taxon_2667527386_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900105655.1_IMG-taxon_2667527386_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:45,000] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:45,017] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:45,018] [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_900105655.1	s__Pseudomonas_D salegens	100.0	1264	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_007117785.1	s__Pseudomonas_D sp007117785	84.4009	533	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007692485.1	s__Pseudomonas_D sp007692485	82.3514	656	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114825.1	s__Pseudomonas_D yangmingensis	78.9094	393	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003586265.1	s__Pseudomonas_D jilinensis	78.8938	456	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	97.07	95.47	0.89	0.88	3	-
GCF_000939975.1	s__Pseudomonas_D saudimassiliensis	78.8928	343	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900105255.1	s__Pseudomonas_D sabulinigri	78.7832	385	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002979975.1	s__Pseudomonas_D sp002979975	78.7572	365	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009497895.1	s__Pseudomonas_D pelagia_A	78.7545	403	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000410875.1	s__Pseudomonas_D pelagia	78.7128	369	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008365385.1	s__Pseudomonas_D laoshanensis	78.6571	377	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	96.00	95.95	0.96	0.95	3	-
GCF_014219065.1	s__Pseudomonas_D xiamenensis	78.6444	370	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002197985.1	s__Pseudomonas_D aestusnigri	78.596	373	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	97.11	96.74	0.91	0.81	25	-
GCF_900114735.1	s__Pseudomonas_D bauzanensis	78.595	355	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	99.15	98.30	0.96	0.91	3	-
GCA_019116555.1	s__Pseudomonas_D excrementavium	78.3998	278	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008641105.1	s__Pseudomonas_D salina	78.2523	339	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	100.00	100.00	0.99	0.99	2	-
GCF_013385425.1	s__Pseudomonas_E gingeri_D	77.3019	193	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.70	98.70	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:45,019] [INFO] GTDB search result was written to GCF_900105655.1_IMG-taxon_2667527386_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:45,020] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:45,025] [INFO] DFAST_QC result json was written to GCF_900105655.1_IMG-taxon_2667527386_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:11:45,025] [INFO] DFAST_QC completed!
[2024-01-24 13:11:45,025] [INFO] Total running time: 0h1m25s