[2024-01-24 11:34:38,200] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:38,203] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:38,203] [INFO] DQC Reference Directory: /var/lib/cwl/stgfc953c9d-0370-47c2-a61a-c1cc443c8f37/dqc_reference
[2024-01-24 11:34:39,640] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:39,642] [INFO] Task started: Prodigal
[2024-01-24 11:34:39,642] [INFO] Running command: gunzip -c /var/lib/cwl/stgebe91ed4-4157-4015-b579-6b6a7e6b471c/GCF_012986145.1_ASM1298614v1_genomic.fna.gz | prodigal -d GCF_012986145.1_ASM1298614v1_genomic.fna/cds.fna -a GCF_012986145.1_ASM1298614v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:53,482] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:53,482] [INFO] Task started: HMMsearch
[2024-01-24 11:34:53,483] [INFO] Running command: hmmsearch --tblout GCF_012986145.1_ASM1298614v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfc953c9d-0370-47c2-a61a-c1cc443c8f37/dqc_reference/reference_markers.hmm GCF_012986145.1_ASM1298614v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:53,749] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:53,751] [INFO] Found 6/6 markers.
[2024-01-24 11:34:53,792] [INFO] Query marker FASTA was written to GCF_012986145.1_ASM1298614v1_genomic.fna/markers.fasta
[2024-01-24 11:34:53,792] [INFO] Task started: Blastn
[2024-01-24 11:34:53,792] [INFO] Running command: blastn -query GCF_012986145.1_ASM1298614v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc953c9d-0370-47c2-a61a-c1cc443c8f37/dqc_reference/reference_markers.fasta -out GCF_012986145.1_ASM1298614v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:34:54,804] [INFO] Task succeeded: Blastn
[2024-01-24 11:34:54,808] [INFO] Selected 14 target genomes.
[2024-01-24 11:34:54,809] [INFO] Target genome list was writen to GCF_012986145.1_ASM1298614v1_genomic.fna/target_genomes.txt
[2024-01-24 11:34:54,815] [INFO] Task started: fastANI
[2024-01-24 11:34:54,815] [INFO] Running command: fastANI --query /var/lib/cwl/stgebe91ed4-4157-4015-b579-6b6a7e6b471c/GCF_012986145.1_ASM1298614v1_genomic.fna.gz --refList GCF_012986145.1_ASM1298614v1_genomic.fna/target_genomes.txt --output GCF_012986145.1_ASM1298614v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:10,860] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:10,861] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfc953c9d-0370-47c2-a61a-c1cc443c8f37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:10,861] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfc953c9d-0370-47c2-a61a-c1cc443c8f37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:10,873] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:35:10,873] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:10,874] [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 peli	strain=DSM 17833	GCA_012986145.1	592361	592361	type	True	100.0	1493	1498	95	conclusive
Pseudomonas peli	strain=DSM 17833	GCA_900099645.1	592361	592361	type	True	99.9932	1483	1498	95	conclusive
Pseudomonas guineae	strain=LMG 24016	GCA_900113745.1	425504	425504	type	True	84.5051	1019	1498	95	below_threshold
Pseudomonas tumuqii	strain=LAMW06	GCA_013184545.1	2715755	2715755	type	True	82.7032	948	1498	95	below_threshold
Pseudomonas borbori	strain=DSM 17834	GCA_900115555.1	289003	289003	type	True	82.6929	908	1498	95	below_threshold
Pseudomonas benzenivorans	strain=DSM 8628	GCA_900100495.1	556533	556533	type	True	82.4896	975	1498	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	82.0297	872	1498	95	below_threshold
Pseudomonas guryensis	strain=SR9	GCA_014164785.1	2759165	2759165	type	True	81.9753	839	1498	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	81.8086	926	1498	95	below_threshold
Pseudomonas ullengensis	strain=UL070	GCA_014174475.1	2759166	2759166	type	True	81.7604	830	1498	95	below_threshold
Pseudomonas taeanensis	strain=MS-3	GCA_000498575.2	574962	574962	type	True	81.4637	906	1498	95	below_threshold
Pseudomonas toyotomiensis	strain=JCM 15604	GCA_900115695.1	554344	554344	type	True	81.4309	925	1498	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	81.2694	784	1498	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	81.0377	762	1498	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:10,875] [INFO] DFAST Taxonomy check result was written to GCF_012986145.1_ASM1298614v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:10,876] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:10,876] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:10,876] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfc953c9d-0370-47c2-a61a-c1cc443c8f37/dqc_reference/checkm_data
[2024-01-24 11:35:10,877] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:10,918] [INFO] Task started: CheckM
[2024-01-24 11:35:10,918] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012986145.1_ASM1298614v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012986145.1_ASM1298614v1_genomic.fna/checkm_input GCF_012986145.1_ASM1298614v1_genomic.fna/checkm_result
[2024-01-24 11:35:53,113] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:53,114] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:53,132] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:53,132] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:53,133] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012986145.1_ASM1298614v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:53,133] [INFO] Task started: Blastn
[2024-01-24 11:35:53,133] [INFO] Running command: blastn -query GCF_012986145.1_ASM1298614v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc953c9d-0370-47c2-a61a-c1cc443c8f37/dqc_reference/reference_markers_gtdb.fasta -out GCF_012986145.1_ASM1298614v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:54,869] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:54,872] [INFO] Selected 13 target genomes.
[2024-01-24 11:35:54,873] [INFO] Target genome list was writen to GCF_012986145.1_ASM1298614v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:54,882] [INFO] Task started: fastANI
[2024-01-24 11:35:54,882] [INFO] Running command: fastANI --query /var/lib/cwl/stgebe91ed4-4157-4015-b579-6b6a7e6b471c/GCF_012986145.1_ASM1298614v1_genomic.fna.gz --refList GCF_012986145.1_ASM1298614v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012986145.1_ASM1298614v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:08,404] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:08,419] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:08,420] [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_900099645.1	s__Pseudomonas_E peli	99.9932	1483	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.85	96.04	0.90	0.85	7	conclusive
GCA_002840155.1	s__Pseudomonas_E sp002840155	90.8179	1232	1498	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_900105355.1	s__Pseudomonas_E anguilliseptica	89.8343	1171	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.12	96.12	0.88	0.88	2	-
GCA_018827205.1	s__Pseudomonas_E sp018827205	88.6123	1077	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.54	99.51	0.89	0.88	4	-
GCF_003060885.1	s__Pseudomonas_E sp003060885	88.51	1126	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018816095.1	s__Pseudomonas_E sp018816095	85.9125	947	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.20	96.15	0.83	0.82	4	-
GCF_004920405.1	s__Pseudomonas_E leptonychotis	85.6038	1097	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001465025.1	s__Pseudomonas_E sp001465025	84.5683	959	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.96	95.96	0.61	0.61	2	-
GCA_002354655.1	s__Pseudomonas_E sp002354655	83.9565	1010	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.84	99.84	0.95	0.95	2	-
GCF_009763245.1	s__Pseudomonas_E sp009763245	83.4225	952	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018826895.1	s__Pseudomonas_E sp018826895	82.4	786	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.86	99.82	0.88	0.84	6	-
GCF_014851905.1	s__Pseudomonas_E sp014851905	81.546	823	1498	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_005508865.1	s__Pseudomonas_E sp005508865	81.3794	837	1498	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 11:36:08,421] [INFO] GTDB search result was written to GCF_012986145.1_ASM1298614v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:08,422] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:08,427] [INFO] DFAST_QC result json was written to GCF_012986145.1_ASM1298614v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:08,427] [INFO] DFAST_QC completed!
[2024-01-24 11:36:08,427] [INFO] Total running time: 0h1m30s