[2024-01-24 13:47:10,395] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:47:10,397] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:47:10,397] [INFO] DQC Reference Directory: /var/lib/cwl/stg984bea67-40cd-4980-90ce-a674dd9e242b/dqc_reference
[2024-01-24 13:47:11,723] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:47:11,724] [INFO] Task started: Prodigal
[2024-01-24 13:47:11,724] [INFO] Running command: gunzip -c /var/lib/cwl/stg1716f7ac-8fff-4b96-8c64-1736ab120518/GCF_013200955.2_ASM1320095v2_genomic.fna.gz | prodigal -d GCF_013200955.2_ASM1320095v2_genomic.fna/cds.fna -a GCF_013200955.2_ASM1320095v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:47:26,216] [INFO] Task succeeded: Prodigal
[2024-01-24 13:47:26,216] [INFO] Task started: HMMsearch
[2024-01-24 13:47:26,217] [INFO] Running command: hmmsearch --tblout GCF_013200955.2_ASM1320095v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg984bea67-40cd-4980-90ce-a674dd9e242b/dqc_reference/reference_markers.hmm GCF_013200955.2_ASM1320095v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:47:26,517] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:47:26,519] [INFO] Found 6/6 markers.
[2024-01-24 13:47:26,561] [INFO] Query marker FASTA was written to GCF_013200955.2_ASM1320095v2_genomic.fna/markers.fasta
[2024-01-24 13:47:26,562] [INFO] Task started: Blastn
[2024-01-24 13:47:26,562] [INFO] Running command: blastn -query GCF_013200955.2_ASM1320095v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg984bea67-40cd-4980-90ce-a674dd9e242b/dqc_reference/reference_markers.fasta -out GCF_013200955.2_ASM1320095v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:27,617] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:27,621] [INFO] Selected 14 target genomes.
[2024-01-24 13:47:27,621] [INFO] Target genome list was writen to GCF_013200955.2_ASM1320095v2_genomic.fna/target_genomes.txt
[2024-01-24 13:47:27,634] [INFO] Task started: fastANI
[2024-01-24 13:47:27,634] [INFO] Running command: fastANI --query /var/lib/cwl/stg1716f7ac-8fff-4b96-8c64-1736ab120518/GCF_013200955.2_ASM1320095v2_genomic.fna.gz --refList GCF_013200955.2_ASM1320095v2_genomic.fna/target_genomes.txt --output GCF_013200955.2_ASM1320095v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:44,844] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:44,845] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg984bea67-40cd-4980-90ce-a674dd9e242b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:44,845] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg984bea67-40cd-4980-90ce-a674dd9e242b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:44,860] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:47:44,860] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:44,861] [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 campi	strain=S1-A32-2	GCA_013200955.2	2731681	2731681	type	True	100.0	1476	1478	95	conclusive
Pseudomonas guryensis	strain=SR9	GCA_014164785.1	2759165	2759165	type	True	93.1522	1268	1478	95	below_threshold
Pseudomonas ullengensis	strain=UL070	GCA_014174475.1	2759166	2759166	type	True	86.7264	1096	1478	95	below_threshold
Pseudomonas alcaligenes	strain=NCTC10367	GCA_900455475.1	43263	43263	type	True	86.1608	1104	1478	95	below_threshold
Pseudomonas alcaligenes	strain=NBRC 14159	GCA_000467105.1	43263	43263	type	True	86.1502	1076	1478	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	83.9459	873	1478	95	below_threshold
Pseudomonas benzenivorans	strain=DSM 8628	GCA_900100495.1	556533	556533	type	True	83.8818	968	1478	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	83.5623	921	1478	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	83.5539	936	1478	95	below_threshold
Pseudomonas carbonaria	strain=CIP 111764	GCA_904061905.1	2762745	2762745	type	True	83.4697	906	1478	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	83.4032	916	1478	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	83.3679	924	1478	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	82.719	681	1478	95	below_threshold
Pseudomonas kuykendallii	strain=NRRL B-59562	GCA_900106975.1	1007099	1007099	type	True	82.2077	814	1478	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:44,862] [INFO] DFAST Taxonomy check result was written to GCF_013200955.2_ASM1320095v2_genomic.fna/tc_result.tsv
[2024-01-24 13:47:44,863] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:44,863] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:44,863] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg984bea67-40cd-4980-90ce-a674dd9e242b/dqc_reference/checkm_data
[2024-01-24 13:47:44,864] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:44,907] [INFO] Task started: CheckM
[2024-01-24 13:47:44,907] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013200955.2_ASM1320095v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013200955.2_ASM1320095v2_genomic.fna/checkm_input GCF_013200955.2_ASM1320095v2_genomic.fna/checkm_result
[2024-01-24 13:48:28,539] [INFO] Task succeeded: CheckM
[2024-01-24 13:48:28,541] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:48:28,561] [INFO] ===== Completeness check finished =====
[2024-01-24 13:48:28,561] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:48:28,562] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013200955.2_ASM1320095v2_genomic.fna/markers.fasta)
[2024-01-24 13:48:28,562] [INFO] Task started: Blastn
[2024-01-24 13:48:28,562] [INFO] Running command: blastn -query GCF_013200955.2_ASM1320095v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg984bea67-40cd-4980-90ce-a674dd9e242b/dqc_reference/reference_markers_gtdb.fasta -out GCF_013200955.2_ASM1320095v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:30,532] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:30,536] [INFO] Selected 9 target genomes.
[2024-01-24 13:48:30,536] [INFO] Target genome list was writen to GCF_013200955.2_ASM1320095v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:48:30,554] [INFO] Task started: fastANI
[2024-01-24 13:48:30,554] [INFO] Running command: fastANI --query /var/lib/cwl/stg1716f7ac-8fff-4b96-8c64-1736ab120518/GCF_013200955.2_ASM1320095v2_genomic.fna.gz --refList GCF_013200955.2_ASM1320095v2_genomic.fna/target_genomes_gtdb.txt --output GCF_013200955.2_ASM1320095v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:42,827] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:42,838] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:48:42,838] [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_013200955.2	s__Pseudomonas_E campi	100.0	1476	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014164785.1	s__Pseudomonas_E sp014164785	93.1496	1269	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009799925.1	s__Pseudomonas_E sp009799925	89.7889	1096	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506505.1	s__Pseudomonas_E sp902506505	89.7239	1085	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.45	95.45	0.88	0.88	2	-
GCF_014174475.1	s__Pseudomonas_E sp014174475	86.7234	1096	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003205495.1	s__Pseudomonas_E alcaligenes_B	86.4933	1040	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014851905.1	s__Pseudomonas_E sp014851905	85.8103	1028	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156545.1	s__Pseudomonas_E alcaligenes_A	85.6028	1079	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.95	95.95	0.92	0.92	2	-
GCF_900106975.1	s__Pseudomonas_O kuykendallii	82.188	818	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_O	95.0	96.83	96.68	0.93	0.91	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:48:42,840] [INFO] GTDB search result was written to GCF_013200955.2_ASM1320095v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:42,841] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:42,844] [INFO] DFAST_QC result json was written to GCF_013200955.2_ASM1320095v2_genomic.fna/dqc_result.json
[2024-01-24 13:48:42,844] [INFO] DFAST_QC completed!
[2024-01-24 13:48:42,844] [INFO] Total running time: 0h1m32s