[2024-01-24 15:19:52,415] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:19:52,417] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:19:52,417] [INFO] DQC Reference Directory: /var/lib/cwl/stg74cd3ded-225d-48af-92e5-14b4434a32c7/dqc_reference
[2024-01-24 15:19:53,686] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:19:53,687] [INFO] Task started: Prodigal
[2024-01-24 15:19:53,687] [INFO] Running command: gunzip -c /var/lib/cwl/stgf94258b6-8a72-4e81-923f-a567ea201446/GCF_013184545.1_ASM1318454v1_genomic.fna.gz | prodigal -d GCF_013184545.1_ASM1318454v1_genomic.fna/cds.fna -a GCF_013184545.1_ASM1318454v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:20:10,607] [INFO] Task succeeded: Prodigal
[2024-01-24 15:20:10,607] [INFO] Task started: HMMsearch
[2024-01-24 15:20:10,607] [INFO] Running command: hmmsearch --tblout GCF_013184545.1_ASM1318454v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg74cd3ded-225d-48af-92e5-14b4434a32c7/dqc_reference/reference_markers.hmm GCF_013184545.1_ASM1318454v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:20:10,984] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:20:10,985] [INFO] Found 6/6 markers.
[2024-01-24 15:20:11,041] [INFO] Query marker FASTA was written to GCF_013184545.1_ASM1318454v1_genomic.fna/markers.fasta
[2024-01-24 15:20:11,041] [INFO] Task started: Blastn
[2024-01-24 15:20:11,042] [INFO] Running command: blastn -query GCF_013184545.1_ASM1318454v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74cd3ded-225d-48af-92e5-14b4434a32c7/dqc_reference/reference_markers.fasta -out GCF_013184545.1_ASM1318454v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:12,137] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:12,144] [INFO] Selected 13 target genomes.
[2024-01-24 15:20:12,145] [INFO] Target genome list was writen to GCF_013184545.1_ASM1318454v1_genomic.fna/target_genomes.txt
[2024-01-24 15:20:12,155] [INFO] Task started: fastANI
[2024-01-24 15:20:12,156] [INFO] Running command: fastANI --query /var/lib/cwl/stgf94258b6-8a72-4e81-923f-a567ea201446/GCF_013184545.1_ASM1318454v1_genomic.fna.gz --refList GCF_013184545.1_ASM1318454v1_genomic.fna/target_genomes.txt --output GCF_013184545.1_ASM1318454v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:20:28,141] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:28,142] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg74cd3ded-225d-48af-92e5-14b4434a32c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:20:28,142] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg74cd3ded-225d-48af-92e5-14b4434a32c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:20:28,157] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:20:28,158] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:20:28,158] [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 tumuqii	strain=LAMW06	GCA_013184545.1	2715755	2715755	type	True	100.0	1802	1807	95	conclusive
Pseudomonas borbori	strain=DSM 17834	GCA_900115555.1	289003	289003	type	True	91.5756	1331	1807	95	below_threshold
Pseudomonas benzenivorans	strain=DSM 8628	GCA_900100495.1	556533	556533	type	True	87.0758	1378	1807	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	85.0687	1099	1807	95	below_threshold
Pseudomonas taeanensis	strain=MS-3	GCA_000498575.2	574962	574962	type	True	83.7149	1117	1807	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	83.1246	1035	1807	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	82.9247	978	1807	95	below_threshold
Pseudomonas peli	strain=DSM 17833	GCA_900099645.1	592361	592361	type	True	82.6631	955	1807	95	below_threshold
Pseudomonas peli	strain=DSM 17833	GCA_012986145.1	592361	592361	type	True	82.6514	949	1807	95	below_threshold
Pseudomonas ullengensis	strain=UL070	GCA_014174475.1	2759166	2759166	type	True	82.5379	904	1807	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	82.3846	902	1807	95	below_threshold
Pseudomonas argentinensis	strain=CCUG 50743	GCA_008801645.1	289370	289370	type	True	81.922	865	1807	95	below_threshold
Pseudomonas argentinensis	strain=LMG 22563	GCA_900113905.1	289370	289370	type	True	81.9216	860	1807	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:20:28,160] [INFO] DFAST Taxonomy check result was written to GCF_013184545.1_ASM1318454v1_genomic.fna/tc_result.tsv
[2024-01-24 15:20:28,161] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:20:28,161] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:20:28,161] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg74cd3ded-225d-48af-92e5-14b4434a32c7/dqc_reference/checkm_data
[2024-01-24 15:20:28,163] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:20:28,215] [INFO] Task started: CheckM
[2024-01-24 15:20:28,215] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013184545.1_ASM1318454v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013184545.1_ASM1318454v1_genomic.fna/checkm_input GCF_013184545.1_ASM1318454v1_genomic.fna/checkm_result
[2024-01-24 15:21:17,309] [INFO] Task succeeded: CheckM
[2024-01-24 15:21:17,311] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:21:17,334] [INFO] ===== Completeness check finished =====
[2024-01-24 15:21:17,335] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:21:17,335] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013184545.1_ASM1318454v1_genomic.fna/markers.fasta)
[2024-01-24 15:21:17,336] [INFO] Task started: Blastn
[2024-01-24 15:21:17,336] [INFO] Running command: blastn -query GCF_013184545.1_ASM1318454v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74cd3ded-225d-48af-92e5-14b4434a32c7/dqc_reference/reference_markers_gtdb.fasta -out GCF_013184545.1_ASM1318454v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:21:19,267] [INFO] Task succeeded: Blastn
[2024-01-24 15:21:19,270] [INFO] Selected 11 target genomes.
[2024-01-24 15:21:19,270] [INFO] Target genome list was writen to GCF_013184545.1_ASM1318454v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:21:19,279] [INFO] Task started: fastANI
[2024-01-24 15:21:19,280] [INFO] Running command: fastANI --query /var/lib/cwl/stgf94258b6-8a72-4e81-923f-a567ea201446/GCF_013184545.1_ASM1318454v1_genomic.fna.gz --refList GCF_013184545.1_ASM1318454v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013184545.1_ASM1318454v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:21:32,925] [INFO] Task succeeded: fastANI
[2024-01-24 15:21:32,937] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:21:32,938] [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_013184545.1	s__Pseudomonas_E sp013184545	100.0	1802	1807	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_900115555.1	s__Pseudomonas_E borbori	91.5715	1332	1807	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_002025205.1	s__Pseudomonas_E sp002025205	90.221	1289	1807	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_900100495.1	s__Pseudomonas_E benzenivorans	87.0401	1383	1807	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_002354655.1	s__Pseudomonas_E sp002354655	84.9092	1081	1807	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_007993865.1	s__Pseudomonas_E sp007993865	84.4224	1111	1807	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_000498575.2	s__Pseudomonas_E taeanensis	83.6917	1120	1807	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_002840155.1	s__Pseudomonas_E sp002840155	83.4116	1004	1807	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	82.4103	926	1807	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_018827205.1	s__Pseudomonas_E sp018827205	82.2527	854	1807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.54	99.51	0.89	0.88	4	-
GCA_001830395.1	s__Pseudomonas_E sp001830395	80.8857	505	1807	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 15:21:32,939] [INFO] GTDB search result was written to GCF_013184545.1_ASM1318454v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:21:32,940] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:21:32,943] [INFO] DFAST_QC result json was written to GCF_013184545.1_ASM1318454v1_genomic.fna/dqc_result.json
[2024-01-24 15:21:32,943] [INFO] DFAST_QC completed!
[2024-01-24 15:21:32,943] [INFO] Total running time: 0h1m41s