[2024-01-24 11:20:19,098] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:19,100] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:19,100] [INFO] DQC Reference Directory: /var/lib/cwl/stg536d29ff-af09-4b4b-bc52-76f1d371c097/dqc_reference
[2024-01-24 11:20:20,301] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:20,302] [INFO] Task started: Prodigal
[2024-01-24 11:20:20,302] [INFO] Running command: gunzip -c /var/lib/cwl/stg4e5c0e4b-6df8-47c4-9504-092f4309ee1a/GCF_024448505.1_ASM2444850v1_genomic.fna.gz | prodigal -d GCF_024448505.1_ASM2444850v1_genomic.fna/cds.fna -a GCF_024448505.1_ASM2444850v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:31,930] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:31,930] [INFO] Task started: HMMsearch
[2024-01-24 11:20:31,930] [INFO] Running command: hmmsearch --tblout GCF_024448505.1_ASM2444850v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg536d29ff-af09-4b4b-bc52-76f1d371c097/dqc_reference/reference_markers.hmm GCF_024448505.1_ASM2444850v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:32,249] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:32,251] [INFO] Found 6/6 markers.
[2024-01-24 11:20:32,289] [INFO] Query marker FASTA was written to GCF_024448505.1_ASM2444850v1_genomic.fna/markers.fasta
[2024-01-24 11:20:32,289] [INFO] Task started: Blastn
[2024-01-24 11:20:32,290] [INFO] Running command: blastn -query GCF_024448505.1_ASM2444850v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg536d29ff-af09-4b4b-bc52-76f1d371c097/dqc_reference/reference_markers.fasta -out GCF_024448505.1_ASM2444850v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:33,322] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:33,326] [INFO] Selected 10 target genomes.
[2024-01-24 11:20:33,327] [INFO] Target genome list was writen to GCF_024448505.1_ASM2444850v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:33,332] [INFO] Task started: fastANI
[2024-01-24 11:20:33,332] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e5c0e4b-6df8-47c4-9504-092f4309ee1a/GCF_024448505.1_ASM2444850v1_genomic.fna.gz --refList GCF_024448505.1_ASM2444850v1_genomic.fna/target_genomes.txt --output GCF_024448505.1_ASM2444850v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:42,979] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:42,979] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg536d29ff-af09-4b4b-bc52-76f1d371c097/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:42,980] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg536d29ff-af09-4b4b-bc52-76f1d371c097/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:42,989] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:20:42,989] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:20:42,989] [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 degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	100.0	1321	1323	95	conclusive
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	99.9989	1323	1323	95	conclusive
Stutzerimonas degradans	strain=DSM 50238	GCA_002891015.1	2968968	2968968	type	True	99.9985	1323	1323	95	conclusive
Stutzerimonas stutzeri	strain=CGMCC 1.1803	GCA_000219605.1	316	316	type	True	85.2529	1018	1323	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	85.2283	993	1323	95	below_threshold
Stutzerimonas stutzeri	strain=FDAARGOS_875	GCA_016028655.1	316	316	type	True	85.204	1014	1323	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	85.1581	1021	1323	95	below_threshold
Pseudomonas nitrititolerans	strain=GL14	GCA_003696285.1	2482751	2482751	type	True	83.4448	915	1323	95	below_threshold
Azotobacter beijerinckii	strain=DSM 378	GCA_900110885.1	170623	170623	type	True	81.5982	640	1323	95	below_threshold
Pseudomonas thermotolerans	strain=DSM 14292	GCA_000364625.1	157784	157784	type	True	81.4619	665	1323	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:42,991] [INFO] DFAST Taxonomy check result was written to GCF_024448505.1_ASM2444850v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:42,992] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:42,992] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:42,992] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg536d29ff-af09-4b4b-bc52-76f1d371c097/dqc_reference/checkm_data
[2024-01-24 11:20:42,993] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:43,036] [INFO] Task started: CheckM
[2024-01-24 11:20:43,036] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024448505.1_ASM2444850v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024448505.1_ASM2444850v1_genomic.fna/checkm_input GCF_024448505.1_ASM2444850v1_genomic.fna/checkm_result
[2024-01-24 11:21:20,158] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:20,160] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:20,183] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:20,183] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:20,183] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024448505.1_ASM2444850v1_genomic.fna/markers.fasta)
[2024-01-24 11:21:20,184] [INFO] Task started: Blastn
[2024-01-24 11:21:20,184] [INFO] Running command: blastn -query GCF_024448505.1_ASM2444850v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg536d29ff-af09-4b4b-bc52-76f1d371c097/dqc_reference/reference_markers_gtdb.fasta -out GCF_024448505.1_ASM2444850v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:22,218] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:22,222] [INFO] Selected 7 target genomes.
[2024-01-24 11:21:22,222] [INFO] Target genome list was writen to GCF_024448505.1_ASM2444850v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:22,227] [INFO] Task started: fastANI
[2024-01-24 11:21:22,227] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e5c0e4b-6df8-47c4-9504-092f4309ee1a/GCF_024448505.1_ASM2444850v1_genomic.fna.gz --refList GCF_024448505.1_ASM2444850v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024448505.1_ASM2444850v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:29,844] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:29,851] [INFO] Found 7 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 11:21:29,852] [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_907163115.1	s__Pseudomonas_A stutzeri_AL	96.5173	1216	1323	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.05	96.55	0.94	0.91	6	inconclusive
GCF_005844005.1	s__Pseudomonas_A sp000765155	95.9866	1187	1323	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.19	98.01	0.92	0.89	5	inconclusive
GCF_000263395.1	s__Pseudomonas_A stutzeri_C	93.0523	1098	1323	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002890915.1	s__Pseudomonas_A stutzeri_AF	85.9787	1038	1323	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.35	98.08	0.91	0.89	3	-
GCF_000219605.1	s__Pseudomonas_A stutzeri	85.2529	1018	1323	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.69	96.98	0.90	0.83	156	-
GCF_003205815.1	s__Pseudomonas_A sp003205815	85.2275	1003	1323	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.18	96.58	0.91	0.87	27	-
GCF_015070855.1	s__Pseudomonas_A lopnurensis	85.1349	964	1323	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.76	98.41	0.83	0.83	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:21:29,853] [INFO] GTDB search result was written to GCF_024448505.1_ASM2444850v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:29,854] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:29,857] [INFO] DFAST_QC result json was written to GCF_024448505.1_ASM2444850v1_genomic.fna/dqc_result.json
[2024-01-24 11:21:29,857] [INFO] DFAST_QC completed!
[2024-01-24 11:21:29,857] [INFO] Total running time: 0h1m11s