[2024-01-24 14:06:30,874] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:30,876] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:30,876] [INFO] DQC Reference Directory: /var/lib/cwl/stg6334ad25-baa0-41b6-af16-e869f5b81cfc/dqc_reference
[2024-01-24 14:06:32,235] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:32,236] [INFO] Task started: Prodigal
[2024-01-24 14:06:32,237] [INFO] Running command: gunzip -c /var/lib/cwl/stg38145fd2-e2c6-4cba-9e6f-fac7ea9095a6/GCF_902498845.1_Genoma_RA15_genomic.fna.gz | prodigal -d GCF_902498845.1_Genoma_RA15_genomic.fna/cds.fna -a GCF_902498845.1_Genoma_RA15_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:43,853] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:43,853] [INFO] Task started: HMMsearch
[2024-01-24 14:06:43,853] [INFO] Running command: hmmsearch --tblout GCF_902498845.1_Genoma_RA15_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6334ad25-baa0-41b6-af16-e869f5b81cfc/dqc_reference/reference_markers.hmm GCF_902498845.1_Genoma_RA15_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:44,229] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:44,230] [INFO] Found 6/6 markers.
[2024-01-24 14:06:44,282] [INFO] Query marker FASTA was written to GCF_902498845.1_Genoma_RA15_genomic.fna/markers.fasta
[2024-01-24 14:06:44,283] [INFO] Task started: Blastn
[2024-01-24 14:06:44,283] [INFO] Running command: blastn -query GCF_902498845.1_Genoma_RA15_genomic.fna/markers.fasta -db /var/lib/cwl/stg6334ad25-baa0-41b6-af16-e869f5b81cfc/dqc_reference/reference_markers.fasta -out GCF_902498845.1_Genoma_RA15_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:45,049] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:45,052] [INFO] Selected 9 target genomes.
[2024-01-24 14:06:45,052] [INFO] Target genome list was writen to GCF_902498845.1_Genoma_RA15_genomic.fna/target_genomes.txt
[2024-01-24 14:06:45,095] [INFO] Task started: fastANI
[2024-01-24 14:06:45,095] [INFO] Running command: fastANI --query /var/lib/cwl/stg38145fd2-e2c6-4cba-9e6f-fac7ea9095a6/GCF_902498845.1_Genoma_RA15_genomic.fna.gz --refList GCF_902498845.1_Genoma_RA15_genomic.fna/target_genomes.txt --output GCF_902498845.1_Genoma_RA15_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:55,717] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:55,718] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6334ad25-baa0-41b6-af16-e869f5b81cfc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:55,718] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6334ad25-baa0-41b6-af16-e869f5b81cfc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:55,727] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:55,727] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:55,728] [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
Pseudoalteromonas rhizosphaerae	strain=RA15	GCA_902498845.1	2518973	2518973	type	True	100.0	1727	1728	95	conclusive
Pseudoalteromonas ostreae	strain=hOe-66	GCA_018069805.1	2774154	2774154	type	True	93.9086	1242	1728	95	below_threshold
Pseudoalteromonas prydzensis	strain=DSM 14232	GCA_001661495.1	182141	182141	type	True	85.8549	1233	1728	95	below_threshold
Pseudoalteromonas prydzensis	strain=ACAM 620	GCA_014925355.1	182141	182141	type	True	85.846	1229	1728	95	below_threshold
Pseudoalteromonas neustonica	strain=PAMC 28425	GCA_001653135.1	1840331	1840331	type	True	83.0455	923	1728	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	80.2046	648	1728	95	below_threshold
Shewanella inventionis	strain=KCTC 42807	GCA_023283595.1	1738770	1738770	type	True	76.2665	72	1728	95	below_threshold
Shewanella psychromarinicola	strain=JCM 32090	GCA_023283865.1	2487742	2487742	type	True	75.9239	70	1728	95	below_threshold
Shewanella psychromarinicola	strain=M2	GCA_003855155.1	2487742	2487742	type	True	75.8631	73	1728	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:55,729] [INFO] DFAST Taxonomy check result was written to GCF_902498845.1_Genoma_RA15_genomic.fna/tc_result.tsv
[2024-01-24 14:06:55,730] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:55,730] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:55,731] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6334ad25-baa0-41b6-af16-e869f5b81cfc/dqc_reference/checkm_data
[2024-01-24 14:06:55,732] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:55,786] [INFO] Task started: CheckM
[2024-01-24 14:06:55,786] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902498845.1_Genoma_RA15_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902498845.1_Genoma_RA15_genomic.fna/checkm_input GCF_902498845.1_Genoma_RA15_genomic.fna/checkm_result
[2024-01-24 14:07:33,873] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:33,874] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:33,899] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:33,899] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:33,900] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902498845.1_Genoma_RA15_genomic.fna/markers.fasta)
[2024-01-24 14:07:33,900] [INFO] Task started: Blastn
[2024-01-24 14:07:33,901] [INFO] Running command: blastn -query GCF_902498845.1_Genoma_RA15_genomic.fna/markers.fasta -db /var/lib/cwl/stg6334ad25-baa0-41b6-af16-e869f5b81cfc/dqc_reference/reference_markers_gtdb.fasta -out GCF_902498845.1_Genoma_RA15_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:35,120] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:35,124] [INFO] Selected 6 target genomes.
[2024-01-24 14:07:35,124] [INFO] Target genome list was writen to GCF_902498845.1_Genoma_RA15_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:35,132] [INFO] Task started: fastANI
[2024-01-24 14:07:35,132] [INFO] Running command: fastANI --query /var/lib/cwl/stg38145fd2-e2c6-4cba-9e6f-fac7ea9095a6/GCF_902498845.1_Genoma_RA15_genomic.fna.gz --refList GCF_902498845.1_Genoma_RA15_genomic.fna/target_genomes_gtdb.txt --output GCF_902498845.1_Genoma_RA15_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:43,730] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:43,737] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:43,738] [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_902498845.1	s__Pseudoalteromonas rhizosphaerae	100.0	1727	1728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.81	97.24	0.86	0.81	17	conclusive
GCF_018069805.1	s__Pseudoalteromonas sp018069805	93.8933	1243	1728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927645.1	s__Pseudoalteromonas arctica_A	92.2472	1074	1728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011050055.1	s__Pseudoalteromonas prydzensis_A	87.7167	1179	1728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001661495.1	s__Pseudoalteromonas prydzensis	85.8499	1234	1728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.53	97.08	0.91	0.82	3	-
GCF_001653135.1	s__Pseudoalteromonas neustonica	83.0181	925	1728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.11	98.62	0.93	0.89	5	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:43,739] [INFO] GTDB search result was written to GCF_902498845.1_Genoma_RA15_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:43,740] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:43,750] [INFO] DFAST_QC result json was written to GCF_902498845.1_Genoma_RA15_genomic.fna/dqc_result.json
[2024-01-24 14:07:43,750] [INFO] DFAST_QC completed!
[2024-01-24 14:07:43,750] [INFO] Total running time: 0h1m13s