[2024-01-25 19:43:50,354] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:43:50,355] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:43:50,355] [INFO] DQC Reference Directory: /var/lib/cwl/stg008bcbde-3c91-4d1d-9cf9-1560f7bb599d/dqc_reference
[2024-01-25 19:43:51,531] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:43:51,531] [INFO] Task started: Prodigal
[2024-01-25 19:43:51,532] [INFO] Running command: gunzip -c /var/lib/cwl/stg87ccb5a9-5c85-49b5-aaff-dd1921a2db89/GCF_030159895.1_ASM3015989v1_genomic.fna.gz | prodigal -d GCF_030159895.1_ASM3015989v1_genomic.fna/cds.fna -a GCF_030159895.1_ASM3015989v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:44:01,429] [INFO] Task succeeded: Prodigal
[2024-01-25 19:44:01,429] [INFO] Task started: HMMsearch
[2024-01-25 19:44:01,429] [INFO] Running command: hmmsearch --tblout GCF_030159895.1_ASM3015989v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg008bcbde-3c91-4d1d-9cf9-1560f7bb599d/dqc_reference/reference_markers.hmm GCF_030159895.1_ASM3015989v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:44:01,656] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:44:01,658] [INFO] Found 6/6 markers.
[2024-01-25 19:44:01,684] [INFO] Query marker FASTA was written to GCF_030159895.1_ASM3015989v1_genomic.fna/markers.fasta
[2024-01-25 19:44:01,684] [INFO] Task started: Blastn
[2024-01-25 19:44:01,684] [INFO] Running command: blastn -query GCF_030159895.1_ASM3015989v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg008bcbde-3c91-4d1d-9cf9-1560f7bb599d/dqc_reference/reference_markers.fasta -out GCF_030159895.1_ASM3015989v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:44:02,310] [INFO] Task succeeded: Blastn
[2024-01-25 19:44:02,313] [INFO] Selected 25 target genomes.
[2024-01-25 19:44:02,313] [INFO] Target genome list was writen to GCF_030159895.1_ASM3015989v1_genomic.fna/target_genomes.txt
[2024-01-25 19:44:02,363] [INFO] Task started: fastANI
[2024-01-25 19:44:02,364] [INFO] Running command: fastANI --query /var/lib/cwl/stg87ccb5a9-5c85-49b5-aaff-dd1921a2db89/GCF_030159895.1_ASM3015989v1_genomic.fna.gz --refList GCF_030159895.1_ASM3015989v1_genomic.fna/target_genomes.txt --output GCF_030159895.1_ASM3015989v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:44:18,759] [INFO] Task succeeded: fastANI
[2024-01-25 19:44:18,760] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg008bcbde-3c91-4d1d-9cf9-1560f7bb599d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:44:18,760] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg008bcbde-3c91-4d1d-9cf9-1560f7bb599d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:44:18,764] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:44:18,764] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:44:18,764] [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
Maritalea mobilis	strain=CGMCC 1.7002	GCA_004363175.1	483324	483324	type	True	77.7201	260	1113	95	below_threshold
Maritalea myrionectae	strain=DSM 19524	GCA_000423365.1	454601	454601	type	True	77.623	240	1113	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:44:18,771] [INFO] DFAST Taxonomy check result was written to GCF_030159895.1_ASM3015989v1_genomic.fna/tc_result.tsv
[2024-01-25 19:44:18,772] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:44:18,772] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:44:18,772] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg008bcbde-3c91-4d1d-9cf9-1560f7bb599d/dqc_reference/checkm_data
[2024-01-25 19:44:18,773] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:44:18,828] [INFO] Task started: CheckM
[2024-01-25 19:44:18,829] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030159895.1_ASM3015989v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030159895.1_ASM3015989v1_genomic.fna/checkm_input GCF_030159895.1_ASM3015989v1_genomic.fna/checkm_result
[2024-01-25 19:44:51,200] [INFO] Task succeeded: CheckM
[2024-01-25 19:44:51,201] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:44:51,229] [INFO] ===== Completeness check finished =====
[2024-01-25 19:44:51,229] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:44:51,230] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030159895.1_ASM3015989v1_genomic.fna/markers.fasta)
[2024-01-25 19:44:51,230] [INFO] Task started: Blastn
[2024-01-25 19:44:51,230] [INFO] Running command: blastn -query GCF_030159895.1_ASM3015989v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg008bcbde-3c91-4d1d-9cf9-1560f7bb599d/dqc_reference/reference_markers_gtdb.fasta -out GCF_030159895.1_ASM3015989v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:44:52,343] [INFO] Task succeeded: Blastn
[2024-01-25 19:44:52,347] [INFO] Selected 31 target genomes.
[2024-01-25 19:44:52,347] [INFO] Target genome list was writen to GCF_030159895.1_ASM3015989v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:44:52,389] [INFO] Task started: fastANI
[2024-01-25 19:44:52,389] [INFO] Running command: fastANI --query /var/lib/cwl/stg87ccb5a9-5c85-49b5-aaff-dd1921a2db89/GCF_030159895.1_ASM3015989v1_genomic.fna.gz --refList GCF_030159895.1_ASM3015989v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030159895.1_ASM3015989v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:45:12,222] [INFO] Task succeeded: fastANI
[2024-01-25 19:45:12,225] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:45:12,225] [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_004363175.1	s__Maritalea mobilis	77.7201	260	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Maritalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423365.1	s__Maritalea myrionectae	77.623	240	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Maritalea	95.0	97.03	97.03	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:45:12,227] [INFO] GTDB search result was written to GCF_030159895.1_ASM3015989v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:45:12,227] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:45:12,229] [INFO] DFAST_QC result json was written to GCF_030159895.1_ASM3015989v1_genomic.fna/dqc_result.json
[2024-01-25 19:45:12,229] [INFO] DFAST_QC completed!
[2024-01-25 19:45:12,229] [INFO] Total running time: 0h1m22s