[2024-01-24 14:06:30,877] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:30,880] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:30,880] [INFO] DQC Reference Directory: /var/lib/cwl/stg12b5fa57-e0a3-4f63-aced-973dc5addf65/dqc_reference
[2024-01-24 14:06:32,289] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:32,291] [INFO] Task started: Prodigal
[2024-01-24 14:06:32,291] [INFO] Running command: gunzip -c /var/lib/cwl/stg1062a1d6-e0d4-4304-af51-ac52d06feb3c/GCF_016028635.1_ASM1602863v1_genomic.fna.gz | prodigal -d GCF_016028635.1_ASM1602863v1_genomic.fna/cds.fna -a GCF_016028635.1_ASM1602863v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:44,842] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:44,842] [INFO] Task started: HMMsearch
[2024-01-24 14:06:44,843] [INFO] Running command: hmmsearch --tblout GCF_016028635.1_ASM1602863v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg12b5fa57-e0a3-4f63-aced-973dc5addf65/dqc_reference/reference_markers.hmm GCF_016028635.1_ASM1602863v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:45,160] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:45,161] [INFO] Found 6/6 markers.
[2024-01-24 14:06:45,205] [INFO] Query marker FASTA was written to GCF_016028635.1_ASM1602863v1_genomic.fna/markers.fasta
[2024-01-24 14:06:45,206] [INFO] Task started: Blastn
[2024-01-24 14:06:45,206] [INFO] Running command: blastn -query GCF_016028635.1_ASM1602863v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg12b5fa57-e0a3-4f63-aced-973dc5addf65/dqc_reference/reference_markers.fasta -out GCF_016028635.1_ASM1602863v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:46,426] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:46,429] [INFO] Selected 10 target genomes.
[2024-01-24 14:06:46,429] [INFO] Target genome list was writen to GCF_016028635.1_ASM1602863v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:46,458] [INFO] Task started: fastANI
[2024-01-24 14:06:46,459] [INFO] Running command: fastANI --query /var/lib/cwl/stg1062a1d6-e0d4-4304-af51-ac52d06feb3c/GCF_016028635.1_ASM1602863v1_genomic.fna.gz --refList GCF_016028635.1_ASM1602863v1_genomic.fna/target_genomes.txt --output GCF_016028635.1_ASM1602863v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:56,934] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:56,934] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg12b5fa57-e0a3-4f63-aced-973dc5addf65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:56,934] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg12b5fa57-e0a3-4f63-aced-973dc5addf65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:56,944] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:06:56,944] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:56,945] [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=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	100.0	1345	1347	95	conclusive
Stutzerimonas degradans	strain=DSM 50238	GCA_002891015.1	2968968	2968968	type	True	99.9922	1332	1347	95	conclusive
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	99.974	1321	1347	95	conclusive
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	85.314	1025	1347	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	85.2995	1025	1347	95	below_threshold
Stutzerimonas stutzeri	strain=FDAARGOS_875	GCA_016028655.1	316	316	type	True	85.2117	1046	1347	95	below_threshold
Stutzerimonas stutzeri	strain=CGMCC 1.1803	GCA_000219605.1	316	316	type	True	85.1468	1039	1347	95	below_threshold
Pseudomonas nitrititolerans	strain=GL14	GCA_003696285.1	2482751	2482751	type	True	83.4996	924	1347	95	below_threshold
Azotobacter beijerinckii	strain=DSM 378	GCA_900110885.1	170623	170623	type	True	81.4995	640	1347	95	below_threshold
Pseudomonas thermotolerans	strain=DSM 14292	GCA_000364625.1	157784	157784	type	True	81.4641	686	1347	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:56,946] [INFO] DFAST Taxonomy check result was written to GCF_016028635.1_ASM1602863v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:56,947] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:56,947] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:56,947] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg12b5fa57-e0a3-4f63-aced-973dc5addf65/dqc_reference/checkm_data
[2024-01-24 14:06:56,949] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:56,991] [INFO] Task started: CheckM
[2024-01-24 14:06:56,991] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016028635.1_ASM1602863v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016028635.1_ASM1602863v1_genomic.fna/checkm_input GCF_016028635.1_ASM1602863v1_genomic.fna/checkm_result
[2024-01-24 14:07:36,746] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:36,747] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:36,767] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:36,767] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:36,768] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016028635.1_ASM1602863v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:36,768] [INFO] Task started: Blastn
[2024-01-24 14:07:36,768] [INFO] Running command: blastn -query GCF_016028635.1_ASM1602863v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg12b5fa57-e0a3-4f63-aced-973dc5addf65/dqc_reference/reference_markers_gtdb.fasta -out GCF_016028635.1_ASM1602863v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:39,043] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:39,047] [INFO] Selected 7 target genomes.
[2024-01-24 14:07:39,047] [INFO] Target genome list was writen to GCF_016028635.1_ASM1602863v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:39,058] [INFO] Task started: fastANI
[2024-01-24 14:07:39,058] [INFO] Running command: fastANI --query /var/lib/cwl/stg1062a1d6-e0d4-4304-af51-ac52d06feb3c/GCF_016028635.1_ASM1602863v1_genomic.fna.gz --refList GCF_016028635.1_ASM1602863v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016028635.1_ASM1602863v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:47,155] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:47,163] [INFO] Found 7 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 14:07:47,163] [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	96.4571	1233	1347	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	95.9995	1201	1347	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	92.9917	1109	1347	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	86.0099	1056	1347	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_003205815.1	s__Pseudomonas_A sp003205815	85.2545	1021	1347	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_000219605.1	s__Pseudomonas_A stutzeri	85.1654	1038	1347	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_015070855.1	s__Pseudomonas_A lopnurensis	85.0264	979	1347	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 14:07:47,169] [INFO] GTDB search result was written to GCF_016028635.1_ASM1602863v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:47,170] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:47,175] [INFO] DFAST_QC result json was written to GCF_016028635.1_ASM1602863v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:47,176] [INFO] DFAST_QC completed!
[2024-01-24 14:07:47,176] [INFO] Total running time: 0h1m16s