[2024-01-24 13:40:43,824] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:43,830] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:43,830] [INFO] DQC Reference Directory: /var/lib/cwl/stg8374ccd7-6cf8-452b-bb18-f3e90dfdd2dd/dqc_reference
[2024-01-24 13:40:45,275] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:45,276] [INFO] Task started: Prodigal
[2024-01-24 13:40:45,277] [INFO] Running command: gunzip -c /var/lib/cwl/stgcfd406b1-a832-4833-875a-3da44fd4b925/GCF_016925675.1_ASM1692567v1_genomic.fna.gz | prodigal -d GCF_016925675.1_ASM1692567v1_genomic.fna/cds.fna -a GCF_016925675.1_ASM1692567v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:08,249] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:08,249] [INFO] Task started: HMMsearch
[2024-01-24 13:41:08,250] [INFO] Running command: hmmsearch --tblout GCF_016925675.1_ASM1692567v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8374ccd7-6cf8-452b-bb18-f3e90dfdd2dd/dqc_reference/reference_markers.hmm GCF_016925675.1_ASM1692567v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:08,631] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:08,632] [INFO] Found 6/6 markers.
[2024-01-24 13:41:08,683] [INFO] Query marker FASTA was written to GCF_016925675.1_ASM1692567v1_genomic.fna/markers.fasta
[2024-01-24 13:41:08,683] [INFO] Task started: Blastn
[2024-01-24 13:41:08,683] [INFO] Running command: blastn -query GCF_016925675.1_ASM1692567v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8374ccd7-6cf8-452b-bb18-f3e90dfdd2dd/dqc_reference/reference_markers.fasta -out GCF_016925675.1_ASM1692567v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:09,666] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:09,669] [INFO] Selected 13 target genomes.
[2024-01-24 13:41:09,669] [INFO] Target genome list was writen to GCF_016925675.1_ASM1692567v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:09,681] [INFO] Task started: fastANI
[2024-01-24 13:41:09,682] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfd406b1-a832-4833-875a-3da44fd4b925/GCF_016925675.1_ASM1692567v1_genomic.fna.gz --refList GCF_016925675.1_ASM1692567v1_genomic.fna/target_genomes.txt --output GCF_016925675.1_ASM1692567v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:33,002] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:33,002] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8374ccd7-6cf8-452b-bb18-f3e90dfdd2dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:33,003] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8374ccd7-6cf8-452b-bb18-f3e90dfdd2dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:33,014] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:33,014] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:33,014] [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 proteolytica	strain=CCUG 51515T	GCA_008692865.1	219574	219574	type	True	95.0208	1706	2095	95	conclusive
Pseudomonas proteolytica	strain=DSM 15321	GCA_007858275.1	219574	219574	type	True	94.9912	1712	2095	95	below_threshold
Pseudomonas gessardii		GCA_900625085.1	78544	78544	type	True	91.844	1596	2095	95	below_threshold
Pseudomonas gessardii	strain=DSM 17152	GCA_001983165.1	78544	78544	type	True	91.826	1587	2095	95	below_threshold
Pseudomonas brenneri	strain=JCM 13307	GCA_014646715.1	129817	129817	type	True	91.8217	1612	2095	95	below_threshold
Pseudomonas gessardii	strain=DSM 17152	GCA_009671285.1	78544	78544	type	True	91.8111	1589	2095	95	below_threshold
Pseudomonas brenneri	strain=DSM 15294	GCA_007858285.1	129817	129817	type	True	91.8012	1610	2095	95	below_threshold
Pseudomonas marginalis	strain=DSM 13124	GCA_007858155.1	298	298	suspected-type	True	86.5709	1419	2095	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	86.3607	1420	2095	95	below_threshold
Pseudomonas spelaei	strain=CCM 7893	GCA_009724245.1	1055469	1055469	type	True	86.2219	1450	2095	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	86.1578	1436	2095	95	below_threshold
Pseudomonas fluorescens	strain=NCTC10038	GCA_900475215.1	294	294	suspected-type	True	85.8892	1437	2095	95	below_threshold
Pseudomonas karstica	strain=CCM 7891	GCA_009707515.1	1055468	1055468	type	True	85.6623	1292	2095	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:33,018] [INFO] DFAST Taxonomy check result was written to GCF_016925675.1_ASM1692567v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:33,019] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:33,019] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:33,019] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8374ccd7-6cf8-452b-bb18-f3e90dfdd2dd/dqc_reference/checkm_data
[2024-01-24 13:41:33,020] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:33,084] [INFO] Task started: CheckM
[2024-01-24 13:41:33,084] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016925675.1_ASM1692567v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016925675.1_ASM1692567v1_genomic.fna/checkm_input GCF_016925675.1_ASM1692567v1_genomic.fna/checkm_result
[2024-01-24 13:42:38,803] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:38,804] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.75%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:38,835] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:38,836] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:38,836] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016925675.1_ASM1692567v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:38,836] [INFO] Task started: Blastn
[2024-01-24 13:42:38,837] [INFO] Running command: blastn -query GCF_016925675.1_ASM1692567v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8374ccd7-6cf8-452b-bb18-f3e90dfdd2dd/dqc_reference/reference_markers_gtdb.fasta -out GCF_016925675.1_ASM1692567v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:40,593] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:40,597] [INFO] Selected 8 target genomes.
[2024-01-24 13:42:40,598] [INFO] Target genome list was writen to GCF_016925675.1_ASM1692567v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:40,622] [INFO] Task started: fastANI
[2024-01-24 13:42:40,623] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfd406b1-a832-4833-875a-3da44fd4b925/GCF_016925675.1_ASM1692567v1_genomic.fna.gz --refList GCF_016925675.1_ASM1692567v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016925675.1_ASM1692567v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:56,808] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:56,823] [INFO] Found 8 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 13:42:56,824] [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_016925675.1	s__Pseudomonas_E sp012985665	100.0	2095	2095	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.30	97.44	0.92	0.88	4	inconclusive
GCF_007858275.1	s__Pseudomonas_E proteolytica	95.0033	1711	2095	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.69	98.38	0.90	0.86	19	inconclusive
GCF_012985465.1	s__Pseudomonas_E sp012985465	92.5161	1673	2095	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.03	98.94	0.91	0.90	5	-
GCF_003626995.1	s__Pseudomonas_E fluorescens_BA	91.9903	1677	2095	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.95	98.57	0.93	0.88	19	-
GCF_001983165.1	s__Pseudomonas_E gessardii	91.8145	1589	2095	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.96	98.08	0.94	0.88	9	-
GCF_007858285.1	s__Pseudomonas_E brenneri	91.8084	1609	2095	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.23	97.33	0.94	0.88	10	-
GCF_000730425.1	s__Pseudomonas_E fluorescens_X	91.727	1609	2095	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.75	99.75	0.93	0.93	2	-
GCF_900105325.1	s__Pseudomonas_E marginalis	86.5219	1445	2095	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.53	96.47	0.90	0.85	19	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:56,828] [INFO] GTDB search result was written to GCF_016925675.1_ASM1692567v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:56,828] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:56,831] [INFO] DFAST_QC result json was written to GCF_016925675.1_ASM1692567v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:56,831] [INFO] DFAST_QC completed!
[2024-01-24 13:42:56,832] [INFO] Total running time: 0h2m13s