[2024-01-24 12:06:50,758] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:50,759] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:50,760] [INFO] DQC Reference Directory: /var/lib/cwl/stgb01ef07b-03f9-4402-bd63-2448d5c70ba4/dqc_reference
[2024-01-24 12:06:52,007] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:52,008] [INFO] Task started: Prodigal
[2024-01-24 12:06:52,008] [INFO] Running command: gunzip -c /var/lib/cwl/stg47980173-5186-4572-aff4-6ec250faecfa/GCF_015070855.1_ASM1507085v1_genomic.fna.gz | prodigal -d GCF_015070855.1_ASM1507085v1_genomic.fna/cds.fna -a GCF_015070855.1_ASM1507085v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:07:06,393] [INFO] Task succeeded: Prodigal
[2024-01-24 12:07:06,394] [INFO] Task started: HMMsearch
[2024-01-24 12:07:06,394] [INFO] Running command: hmmsearch --tblout GCF_015070855.1_ASM1507085v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb01ef07b-03f9-4402-bd63-2448d5c70ba4/dqc_reference/reference_markers.hmm GCF_015070855.1_ASM1507085v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:07:06,683] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:07:06,685] [INFO] Found 6/6 markers.
[2024-01-24 12:07:06,728] [INFO] Query marker FASTA was written to GCF_015070855.1_ASM1507085v1_genomic.fna/markers.fasta
[2024-01-24 12:07:06,729] [INFO] Task started: Blastn
[2024-01-24 12:07:06,729] [INFO] Running command: blastn -query GCF_015070855.1_ASM1507085v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb01ef07b-03f9-4402-bd63-2448d5c70ba4/dqc_reference/reference_markers.fasta -out GCF_015070855.1_ASM1507085v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:07,861] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:07,864] [INFO] Selected 15 target genomes.
[2024-01-24 12:07:07,864] [INFO] Target genome list was writen to GCF_015070855.1_ASM1507085v1_genomic.fna/target_genomes.txt
[2024-01-24 12:07:07,870] [INFO] Task started: fastANI
[2024-01-24 12:07:07,870] [INFO] Running command: fastANI --query /var/lib/cwl/stg47980173-5186-4572-aff4-6ec250faecfa/GCF_015070855.1_ASM1507085v1_genomic.fna.gz --refList GCF_015070855.1_ASM1507085v1_genomic.fna/target_genomes.txt --output GCF_015070855.1_ASM1507085v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:22,165] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:22,166] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb01ef07b-03f9-4402-bd63-2448d5c70ba4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:22,167] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb01ef07b-03f9-4402-bd63-2448d5c70ba4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:22,181] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:07:22,182] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:07:22,182] [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 stutzeri	strain=CGMCC 1.1803	GCA_000219605.1	316	316	type	True	86.0025	1081	1585	95	below_threshold
Stutzerimonas stutzeri	strain=FDAARGOS_875	GCA_016028655.1	316	316	type	True	85.9778	1094	1585	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	85.7513	1083	1585	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_024448335.1	2968969	2968969	type	True	85.734	1066	1585	95	below_threshold
Pseudomonas songnenensis	strain=DSM 27560T	GCA_024448495.1	1176259	1176259	type	True	85.7239	1031	1585	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	85.6972	1095	1585	95	below_threshold
Pseudomonas songnenensis	strain=NEAU-ST5-5	GCA_003696315.1	1176259	1176259	type	True	85.6471	1045	1585	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_002891015.1	2968968	2968968	type	True	84.9258	976	1585	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	84.8971	976	1585	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	84.8886	961	1585	95	below_threshold
Pseudomonas nitrititolerans	strain=GL14	GCA_003696285.1	2482751	2482751	type	True	83.9206	956	1585	95	below_threshold
Stutzerimonas balearica	strain=DSM6083 (=SP1402)	GCA_000818015.1	74829	74829	type	True	83.4725	982	1585	95	below_threshold
[Pseudomonas] nosocomialis	strain=A31/70	GCA_005876855.1	1056496	1056496	type	True	83.266	925	1585	95	below_threshold
Pseudomonas carbonaria	strain=CIP 111764	GCA_904061905.1	2762745	2762745	type	True	82.8301	839	1585	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	82.5767	700	1585	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:22,183] [INFO] DFAST Taxonomy check result was written to GCF_015070855.1_ASM1507085v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:22,184] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:22,184] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:22,184] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb01ef07b-03f9-4402-bd63-2448d5c70ba4/dqc_reference/checkm_data
[2024-01-24 12:07:22,185] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:22,236] [INFO] Task started: CheckM
[2024-01-24 12:07:22,236] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015070855.1_ASM1507085v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015070855.1_ASM1507085v1_genomic.fna/checkm_input GCF_015070855.1_ASM1507085v1_genomic.fna/checkm_result
[2024-01-24 12:08:05,204] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:05,205] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:05,229] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:05,229] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:05,229] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015070855.1_ASM1507085v1_genomic.fna/markers.fasta)
[2024-01-24 12:08:05,230] [INFO] Task started: Blastn
[2024-01-24 12:08:05,230] [INFO] Running command: blastn -query GCF_015070855.1_ASM1507085v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb01ef07b-03f9-4402-bd63-2448d5c70ba4/dqc_reference/reference_markers_gtdb.fasta -out GCF_015070855.1_ASM1507085v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:07,427] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:07,431] [INFO] Selected 13 target genomes.
[2024-01-24 12:08:07,431] [INFO] Target genome list was writen to GCF_015070855.1_ASM1507085v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:07,441] [INFO] Task started: fastANI
[2024-01-24 12:08:07,441] [INFO] Running command: fastANI --query /var/lib/cwl/stg47980173-5186-4572-aff4-6ec250faecfa/GCF_015070855.1_ASM1507085v1_genomic.fna.gz --refList GCF_015070855.1_ASM1507085v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015070855.1_ASM1507085v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:22,536] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:22,554] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:22,554] [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_015070855.1	s__Pseudomonas_A lopnurensis	100.0	1581	1585	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.76	98.41	0.83	0.83	4	conclusive
GCF_002890915.1	s__Pseudomonas_A stutzeri_AF	90.6102	1219	1585	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_000307775.2	s__Pseudomonas_A stutzeri_B	86.6039	1107	1585	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.65	98.65	0.90	0.90	2	-
GCF_000219605.1	s__Pseudomonas_A stutzeri	86.0079	1081	1585	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_000341615.1	s__Pseudomonas_A stutzeri_G	85.9881	1095	1585	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.57	97.27	0.90	0.83	4	-
GCF_003205815.1	s__Pseudomonas_A sp003205815	85.7442	1107	1585	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_003696315.1	s__Pseudomonas_A songnenensis	85.6366	1046	1585	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.36	98.32	0.94	0.90	4	-
GCF_000263395.1	s__Pseudomonas_A stutzeri_C	85.5873	959	1585	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_000327065.1	s__Pseudomonas_A stutzeri_AE	85.4267	1071	1585	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.70	97.56	0.93	0.91	3	-
GCF_907163115.1	s__Pseudomonas_A stutzeri_AL	85.0822	977	1585	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.05	96.55	0.94	0.91	6	-
GCF_005844005.1	s__Pseudomonas_A sp000765155	84.8003	984	1585	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.19	98.01	0.92	0.89	5	-
GCF_003696285.1	s__Pseudomonas_A nitrititolerans	83.9137	957	1585	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.45	96.83	0.90	0.83	53	-
GCF_904061905.1	s__Pseudomonas_E carbonaria	82.841	837	1585	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:22,556] [INFO] GTDB search result was written to GCF_015070855.1_ASM1507085v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:22,556] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:22,560] [INFO] DFAST_QC result json was written to GCF_015070855.1_ASM1507085v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:22,560] [INFO] DFAST_QC completed!
[2024-01-24 12:08:22,560] [INFO] Total running time: 0h1m32s