[2024-01-24 11:35:05,938] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:05,941] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:05,941] [INFO] DQC Reference Directory: /var/lib/cwl/stg5dc26559-d731-4c7d-885f-504f945c3ce3/dqc_reference
[2024-01-24 11:35:07,209] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:07,210] [INFO] Task started: Prodigal
[2024-01-24 11:35:07,210] [INFO] Running command: gunzip -c /var/lib/cwl/stg0e390e86-7478-4537-96c7-200c797d2f11/GCF_019097855.1_ASM1909785v1_genomic.fna.gz | prodigal -d GCF_019097855.1_ASM1909785v1_genomic.fna/cds.fna -a GCF_019097855.1_ASM1909785v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:20,015] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:20,016] [INFO] Task started: HMMsearch
[2024-01-24 11:35:20,016] [INFO] Running command: hmmsearch --tblout GCF_019097855.1_ASM1909785v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5dc26559-d731-4c7d-885f-504f945c3ce3/dqc_reference/reference_markers.hmm GCF_019097855.1_ASM1909785v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:20,328] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:20,329] [INFO] Found 6/6 markers.
[2024-01-24 11:35:20,367] [INFO] Query marker FASTA was written to GCF_019097855.1_ASM1909785v1_genomic.fna/markers.fasta
[2024-01-24 11:35:20,367] [INFO] Task started: Blastn
[2024-01-24 11:35:20,368] [INFO] Running command: blastn -query GCF_019097855.1_ASM1909785v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5dc26559-d731-4c7d-885f-504f945c3ce3/dqc_reference/reference_markers.fasta -out GCF_019097855.1_ASM1909785v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:21,477] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:21,480] [INFO] Selected 20 target genomes.
[2024-01-24 11:35:21,480] [INFO] Target genome list was writen to GCF_019097855.1_ASM1909785v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:21,488] [INFO] Task started: fastANI
[2024-01-24 11:35:21,488] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e390e86-7478-4537-96c7-200c797d2f11/GCF_019097855.1_ASM1909785v1_genomic.fna.gz --refList GCF_019097855.1_ASM1909785v1_genomic.fna/target_genomes.txt --output GCF_019097855.1_ASM1909785v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:44,048] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:44,048] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5dc26559-d731-4c7d-885f-504f945c3ce3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:44,048] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5dc26559-d731-4c7d-885f-504f945c3ce3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:44,062] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:44,062] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:44,062] [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 aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	100.0	1411	1414	95	conclusive
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	90.0448	1093	1414	95	below_threshold
Pseudomonas linyingensis	strain=LMG 25967	GCA_900109175.1	915471	915471	type	True	89.9775	1092	1414	95	below_threshold
Pseudomonas oryzae	strain=KCTC 32247	GCA_900104805.1	1392877	1392877	type	True	88.7557	1059	1414	95	below_threshold
Azotobacter chroococcum subsp. isscasi	strain=P205	GCA_004327895.1	2528971	353	type	True	83.8464	792	1414	95	below_threshold
Azotobacter beijerinckii	strain=DSM 378	GCA_900110885.1	170623	170623	type	True	83.8251	758	1414	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	83.3991	762	1414	95	below_threshold
Pseudomonas thermotolerans	strain=DSM 14292	GCA_000364625.1	157784	157784	type	True	82.8676	709	1414	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	82.7404	776	1414	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	82.6217	748	1414	95	below_threshold
Pseudomonas flexibilis	strain=ATCC 29606	GCA_900155995.1	706570	706570	type	True	82.5025	667	1414	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	82.2167	748	1414	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	82.1423	633	1414	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_012987025.1	287	287	type	True	82.1071	749	1414	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_900167195.1	287	287	type	True	82.051	754	1414	95	below_threshold
Pseudomonas indica	strain=NBRC 103045	GCA_002091635.1	137658	137658	type	True	81.8458	706	1414	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:44,064] [INFO] DFAST Taxonomy check result was written to GCF_019097855.1_ASM1909785v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:44,065] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:44,065] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:44,065] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5dc26559-d731-4c7d-885f-504f945c3ce3/dqc_reference/checkm_data
[2024-01-24 11:35:44,066] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:44,114] [INFO] Task started: CheckM
[2024-01-24 11:35:44,114] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019097855.1_ASM1909785v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019097855.1_ASM1909785v1_genomic.fna/checkm_input GCF_019097855.1_ASM1909785v1_genomic.fna/checkm_result
[2024-01-24 11:36:23,283] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:23,285] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:23,315] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:23,315] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:23,316] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019097855.1_ASM1909785v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:23,316] [INFO] Task started: Blastn
[2024-01-24 11:36:23,316] [INFO] Running command: blastn -query GCF_019097855.1_ASM1909785v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5dc26559-d731-4c7d-885f-504f945c3ce3/dqc_reference/reference_markers_gtdb.fasta -out GCF_019097855.1_ASM1909785v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:25,166] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:25,171] [INFO] Selected 13 target genomes.
[2024-01-24 11:36:25,171] [INFO] Target genome list was writen to GCF_019097855.1_ASM1909785v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:25,181] [INFO] Task started: fastANI
[2024-01-24 11:36:25,181] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e390e86-7478-4537-96c7-200c797d2f11/GCF_019097855.1_ASM1909785v1_genomic.fna.gz --refList GCF_019097855.1_ASM1909785v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019097855.1_ASM1909785v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:37,922] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:37,931] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:37,932] [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_019097855.1	s__Pseudomonas_K sp019097855	100.0	1411	1414	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900115715.1	s__Pseudomonas_K sagittaria	90.0193	1095	1414	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109175.1	s__Pseudomonas_K linyingensis	89.9981	1089	1414	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004801855.1	s__Pseudomonas_K sp004801855	89.2678	966	1414	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	98.38	98.38	0.89	0.89	2	-
GCF_900104805.1	s__Pseudomonas_K oryzae	88.7385	1060	1414	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105885.1	s__Pseudomonas_K guangdongensis	87.4988	809	1414	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	98.99	98.99	0.99	0.99	2	-
GCF_900110885.1	s__Azotobacter beijerinckii	83.8341	758	1414	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Azotobacter	95.0	97.34	96.47	0.86	0.85	5	-
GCF_000802425.1	s__Pseudomonas_H flexibilis	82.4818	661	1414	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_H	95.0	99.07	98.74	0.94	0.90	5	-
GCF_001457615.1	s__Pseudomonas aeruginosa	82.161	757	1414	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.12	97.38	0.94	0.84	5623	-
GCA_018816095.1	s__Pseudomonas_E sp018816095	79.4981	482	1414	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.20	96.15	0.83	0.82	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:37,934] [INFO] GTDB search result was written to GCF_019097855.1_ASM1909785v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:37,934] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:37,938] [INFO] DFAST_QC result json was written to GCF_019097855.1_ASM1909785v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:37,938] [INFO] DFAST_QC completed!
[2024-01-24 11:36:37,938] [INFO] Total running time: 0h1m32s