[2024-01-24 13:32:41,148] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:41,149] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:41,150] [INFO] DQC Reference Directory: /var/lib/cwl/stg2cb06030-e0ec-4e8e-9ef3-730e07837d35/dqc_reference
[2024-01-24 13:32:42,438] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:42,439] [INFO] Task started: Prodigal
[2024-01-24 13:32:42,439] [INFO] Running command: gunzip -c /var/lib/cwl/stg4552005c-efce-4b24-9ca6-382655b04c23/GCF_007570825.1_ASM757082v1_genomic.fna.gz | prodigal -d GCF_007570825.1_ASM757082v1_genomic.fna/cds.fna -a GCF_007570825.1_ASM757082v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:52,457] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:52,457] [INFO] Task started: HMMsearch
[2024-01-24 13:32:52,457] [INFO] Running command: hmmsearch --tblout GCF_007570825.1_ASM757082v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2cb06030-e0ec-4e8e-9ef3-730e07837d35/dqc_reference/reference_markers.hmm GCF_007570825.1_ASM757082v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:52,815] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:52,816] [INFO] Found 6/6 markers.
[2024-01-24 13:32:52,858] [INFO] Query marker FASTA was written to GCF_007570825.1_ASM757082v1_genomic.fna/markers.fasta
[2024-01-24 13:32:52,859] [INFO] Task started: Blastn
[2024-01-24 13:32:52,859] [INFO] Running command: blastn -query GCF_007570825.1_ASM757082v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2cb06030-e0ec-4e8e-9ef3-730e07837d35/dqc_reference/reference_markers.fasta -out GCF_007570825.1_ASM757082v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:53,507] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:53,509] [INFO] Selected 27 target genomes.
[2024-01-24 13:32:53,510] [INFO] Target genome list was writen to GCF_007570825.1_ASM757082v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:53,517] [INFO] Task started: fastANI
[2024-01-24 13:32:53,517] [INFO] Running command: fastANI --query /var/lib/cwl/stg4552005c-efce-4b24-9ca6-382655b04c23/GCF_007570825.1_ASM757082v1_genomic.fna.gz --refList GCF_007570825.1_ASM757082v1_genomic.fna/target_genomes.txt --output GCF_007570825.1_ASM757082v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:10,579] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:10,579] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2cb06030-e0ec-4e8e-9ef3-730e07837d35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:10,580] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2cb06030-e0ec-4e8e-9ef3-730e07837d35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:10,586] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:33:10,586] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:10,586] [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
Pleionea sediminis	strain=S1-5-21	GCA_007570825.1	2569479	2569479	type	True	100.0	1716	1717	95	conclusive
Pleionea mediterranea	strain=DSM 25350	GCA_003148745.1	523701	523701	type	True	77.7622	159	1717	95	below_threshold
Aliikangiella coralliicola	strain=M105	GCA_007004725.1	2592383	2592383	type	True	76.3157	52	1717	95	below_threshold
Aliikangiella marina	strain=GYP-15	GCA_007004765.1	1712262	1712262	type	True	76.127	53	1717	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:10,587] [INFO] DFAST Taxonomy check result was written to GCF_007570825.1_ASM757082v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:10,587] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:10,588] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:10,588] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2cb06030-e0ec-4e8e-9ef3-730e07837d35/dqc_reference/checkm_data
[2024-01-24 13:33:10,588] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:10,636] [INFO] Task started: CheckM
[2024-01-24 13:33:10,636] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007570825.1_ASM757082v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007570825.1_ASM757082v1_genomic.fna/checkm_input GCF_007570825.1_ASM757082v1_genomic.fna/checkm_result
[2024-01-24 13:33:43,693] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:43,694] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:43,709] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:43,709] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:43,710] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007570825.1_ASM757082v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:43,710] [INFO] Task started: Blastn
[2024-01-24 13:33:43,710] [INFO] Running command: blastn -query GCF_007570825.1_ASM757082v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2cb06030-e0ec-4e8e-9ef3-730e07837d35/dqc_reference/reference_markers_gtdb.fasta -out GCF_007570825.1_ASM757082v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:44,697] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:44,700] [INFO] Selected 25 target genomes.
[2024-01-24 13:33:44,700] [INFO] Target genome list was writen to GCF_007570825.1_ASM757082v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:44,777] [INFO] Task started: fastANI
[2024-01-24 13:33:44,777] [INFO] Running command: fastANI --query /var/lib/cwl/stg4552005c-efce-4b24-9ca6-382655b04c23/GCF_007570825.1_ASM757082v1_genomic.fna.gz --refList GCF_007570825.1_ASM757082v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007570825.1_ASM757082v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:00,383] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:00,388] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:00,389] [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_007570825.1	s__Pleionea sediminis	100.0	1716	1717	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Pleionea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003148745.1	s__Pleionea mediterranea	77.7559	160	1717	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Pleionea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373545.1	s__Pleionea sp013373545	76.9421	119	1717	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Pleionea	95.0	99.33	99.33	0.92	0.92	2	-
GCA_013373375.1	s__Pleionea sp013373375	76.6177	120	1717	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Pleionea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007004725.1	s__Aliikangiella coralliicola	76.1625	50	1717	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Aliikangiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007004765.1	s__Aliikangiella marina	76.0663	50	1717	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Aliikangiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:00,391] [INFO] GTDB search result was written to GCF_007570825.1_ASM757082v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:00,391] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:00,394] [INFO] DFAST_QC result json was written to GCF_007570825.1_ASM757082v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:00,394] [INFO] DFAST_QC completed!
[2024-01-24 13:34:00,394] [INFO] Total running time: 0h1m19s