[2024-01-24 11:26:11,701] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:11,704] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:11,704] [INFO] DQC Reference Directory: /var/lib/cwl/stg9850e6e7-9948-49b2-8c88-2f4023d41ad0/dqc_reference
[2024-01-24 11:26:13,018] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:13,019] [INFO] Task started: Prodigal
[2024-01-24 11:26:13,019] [INFO] Running command: gunzip -c /var/lib/cwl/stg7f528a63-cabb-4665-b443-5fd1d427b751/GCF_024397575.1_ASM2439757v1_genomic.fna.gz | prodigal -d GCF_024397575.1_ASM2439757v1_genomic.fna/cds.fna -a GCF_024397575.1_ASM2439757v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:27,228] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:27,228] [INFO] Task started: HMMsearch
[2024-01-24 11:26:27,228] [INFO] Running command: hmmsearch --tblout GCF_024397575.1_ASM2439757v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9850e6e7-9948-49b2-8c88-2f4023d41ad0/dqc_reference/reference_markers.hmm GCF_024397575.1_ASM2439757v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:27,519] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:27,520] [INFO] Found 6/6 markers.
[2024-01-24 11:26:27,560] [INFO] Query marker FASTA was written to GCF_024397575.1_ASM2439757v1_genomic.fna/markers.fasta
[2024-01-24 11:26:27,561] [INFO] Task started: Blastn
[2024-01-24 11:26:27,561] [INFO] Running command: blastn -query GCF_024397575.1_ASM2439757v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9850e6e7-9948-49b2-8c88-2f4023d41ad0/dqc_reference/reference_markers.fasta -out GCF_024397575.1_ASM2439757v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:28,604] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:28,608] [INFO] Selected 9 target genomes.
[2024-01-24 11:26:28,608] [INFO] Target genome list was writen to GCF_024397575.1_ASM2439757v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:28,612] [INFO] Task started: fastANI
[2024-01-24 11:26:28,612] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f528a63-cabb-4665-b443-5fd1d427b751/GCF_024397575.1_ASM2439757v1_genomic.fna.gz --refList GCF_024397575.1_ASM2439757v1_genomic.fna/target_genomes.txt --output GCF_024397575.1_ASM2439757v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:38,624] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:38,625] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9850e6e7-9948-49b2-8c88-2f4023d41ad0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:38,625] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9850e6e7-9948-49b2-8c88-2f4023d41ad0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:38,634] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:26:38,634] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:26:38,634] [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
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	100.0	1518	1522	95	inconclusive
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_900114065.1	1211807	1211807	type	True	99.9993	1518	1522	95	inconclusive
Stutzerimonas chloritidismutans	strain=AW-1	GCA_000495915.1	203192	203192	type	True	96.7245	1278	1522	95	inconclusive
Pseudomonas songnenensis	strain=NEAU-ST5-5	GCA_003696315.1	1176259	1176259	type	True	89.1889	1204	1522	95	below_threshold
Pseudomonas songnenensis	strain=DSM 27560T	GCA_024448495.1	1176259	1176259	type	True	89.1211	1205	1522	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	88.6862	1228	1522	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	88.6488	1216	1522	95	below_threshold
Stutzerimonas stutzeri	strain=FDAARGOS_875	GCA_016028655.1	316	316	type	True	87.701	1225	1522	95	below_threshold
Stutzerimonas stutzeri	strain=CGMCC 1.1803	GCA_000219605.1	316	316	type	True	87.6503	1227	1522	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:38,636] [INFO] DFAST Taxonomy check result was written to GCF_024397575.1_ASM2439757v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:38,636] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:38,636] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:38,637] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9850e6e7-9948-49b2-8c88-2f4023d41ad0/dqc_reference/checkm_data
[2024-01-24 11:26:38,638] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:38,685] [INFO] Task started: CheckM
[2024-01-24 11:26:38,685] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024397575.1_ASM2439757v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024397575.1_ASM2439757v1_genomic.fna/checkm_input GCF_024397575.1_ASM2439757v1_genomic.fna/checkm_result
[2024-01-24 11:27:20,783] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:20,785] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:20,805] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:20,806] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:20,806] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024397575.1_ASM2439757v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:20,807] [INFO] Task started: Blastn
[2024-01-24 11:27:20,807] [INFO] Running command: blastn -query GCF_024397575.1_ASM2439757v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9850e6e7-9948-49b2-8c88-2f4023d41ad0/dqc_reference/reference_markers_gtdb.fasta -out GCF_024397575.1_ASM2439757v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:22,686] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:22,689] [INFO] Selected 10 target genomes.
[2024-01-24 11:27:22,689] [INFO] Target genome list was writen to GCF_024397575.1_ASM2439757v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:22,697] [INFO] Task started: fastANI
[2024-01-24 11:27:22,697] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f528a63-cabb-4665-b443-5fd1d427b751/GCF_024397575.1_ASM2439757v1_genomic.fna.gz --refList GCF_024397575.1_ASM2439757v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024397575.1_ASM2439757v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:33,018] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:33,031] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:33,031] [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_900114065.1	s__Pseudomonas_A kunmingensis	99.9993	1518	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.08	97.31	97.18	0.87	0.86	3	conclusive
GCF_013409135.1	s__Pseudomonas_A kunmingensis_A	97.0592	1328	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.08	97.66	97.10	0.91	0.87	14	-
GCF_003935375.1	s__Pseudomonas_A xanthomarina_A	96.9975	1324	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.0614	97.25	97.14	0.91	0.88	14	-
GCF_014764705.1	s__Pseudomonas_A sp002692525	96.9062	1308	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.0332	98.20	97.14	0.91	0.83	13	-
GCA_007713455.1	s__Pseudomonas_A sp007713455	96.8071	1352	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.0636	N/A	N/A	N/A	N/A	1	-
GCF_002929225.1	s__Pseudomonas_A stutzeri_U	96.7492	1380	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.0711	97.19	97.19	0.89	0.89	2	-
GCF_000495915.1	s__Pseudomonas_A chloritidismutans	96.7245	1278	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	96.9847	97.37	97.19	0.88	0.85	8	-
GCF_000935215.1	s__Pseudomonas_A stutzeri_AD	96.5303	1229	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	96.8359	97.48	96.93	0.86	0.84	3	-
GCF_000341615.1	s__Pseudomonas_A stutzeri_G	93.3702	1273	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.57	97.27	0.90	0.83	4	-
GCA_002840055.1	s__Pseudomonas_D sp002840055	79.8306	214	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:33,034] [INFO] GTDB search result was written to GCF_024397575.1_ASM2439757v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:33,034] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:33,037] [INFO] DFAST_QC result json was written to GCF_024397575.1_ASM2439757v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:33,038] [INFO] DFAST_QC completed!
[2024-01-24 11:27:33,038] [INFO] Total running time: 0h1m21s