[2023-06-19 09:28:40,425] [INFO] DFAST_QC pipeline started.
[2023-06-19 09:28:40,432] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 09:28:40,432] [INFO] DQC Reference Directory: /var/lib/cwl/stgc2f048c8-357d-4062-987c-05d17331645f/dqc_reference
[2023-06-19 09:28:41,700] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 09:28:41,701] [INFO] Task started: Prodigal
[2023-06-19 09:28:41,701] [INFO] Running command: gunzip -c /var/lib/cwl/stg3480bef7-8352-4c25-9b0d-757785eac49f/GCA_018378735.1_ASM1837873v1_genomic.fna.gz | prodigal -d GCA_018378735.1_ASM1837873v1_genomic.fna/cds.fna -a GCA_018378735.1_ASM1837873v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 09:28:50,448] [INFO] Task succeeded: Prodigal
[2023-06-19 09:28:50,448] [INFO] Task started: HMMsearch
[2023-06-19 09:28:50,449] [INFO] Running command: hmmsearch --tblout GCA_018378735.1_ASM1837873v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc2f048c8-357d-4062-987c-05d17331645f/dqc_reference/reference_markers.hmm GCA_018378735.1_ASM1837873v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 09:28:50,729] [INFO] Task succeeded: HMMsearch
[2023-06-19 09:28:50,731] [INFO] Found 6/6 markers.
[2023-06-19 09:28:50,767] [INFO] Query marker FASTA was written to GCA_018378735.1_ASM1837873v1_genomic.fna/markers.fasta
[2023-06-19 09:28:50,768] [INFO] Task started: Blastn
[2023-06-19 09:28:50,768] [INFO] Running command: blastn -query GCA_018378735.1_ASM1837873v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2f048c8-357d-4062-987c-05d17331645f/dqc_reference/reference_markers.fasta -out GCA_018378735.1_ASM1837873v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 09:28:51,481] [INFO] Task succeeded: Blastn
[2023-06-19 09:28:51,485] [INFO] Selected 23 target genomes.
[2023-06-19 09:28:51,486] [INFO] Target genome list was writen to GCA_018378735.1_ASM1837873v1_genomic.fna/target_genomes.txt
[2023-06-19 09:28:51,491] [INFO] Task started: fastANI
[2023-06-19 09:28:51,491] [INFO] Running command: fastANI --query /var/lib/cwl/stg3480bef7-8352-4c25-9b0d-757785eac49f/GCA_018378735.1_ASM1837873v1_genomic.fna.gz --refList GCA_018378735.1_ASM1837873v1_genomic.fna/target_genomes.txt --output GCA_018378735.1_ASM1837873v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 09:29:05,713] [INFO] Task succeeded: fastANI
[2023-06-19 09:29:05,714] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc2f048c8-357d-4062-987c-05d17331645f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 09:29:05,714] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc2f048c8-357d-4062-987c-05d17331645f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 09:29:05,717] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 09:29:05,717] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 09:29:05,717] [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
--------------------------------------------------------------------------------
[2023-06-19 09:29:05,719] [INFO] DFAST Taxonomy check result was written to GCA_018378735.1_ASM1837873v1_genomic.fna/tc_result.tsv
[2023-06-19 09:29:05,720] [INFO] ===== Taxonomy check completed =====
[2023-06-19 09:29:05,720] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 09:29:05,720] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc2f048c8-357d-4062-987c-05d17331645f/dqc_reference/checkm_data
[2023-06-19 09:29:05,723] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 09:29:05,761] [INFO] Task started: CheckM
[2023-06-19 09:29:05,761] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018378735.1_ASM1837873v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018378735.1_ASM1837873v1_genomic.fna/checkm_input GCA_018378735.1_ASM1837873v1_genomic.fna/checkm_result
[2023-06-19 09:29:37,192] [INFO] Task succeeded: CheckM
[2023-06-19 09:29:37,194] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 09:29:37,225] [INFO] ===== Completeness check finished =====
[2023-06-19 09:29:37,226] [INFO] ===== Start GTDB Search =====
[2023-06-19 09:29:37,226] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018378735.1_ASM1837873v1_genomic.fna/markers.fasta)
[2023-06-19 09:29:37,227] [INFO] Task started: Blastn
[2023-06-19 09:29:37,227] [INFO] Running command: blastn -query GCA_018378735.1_ASM1837873v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2f048c8-357d-4062-987c-05d17331645f/dqc_reference/reference_markers_gtdb.fasta -out GCA_018378735.1_ASM1837873v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 09:29:38,373] [INFO] Task succeeded: Blastn
[2023-06-19 09:29:38,379] [INFO] Selected 9 target genomes.
[2023-06-19 09:29:38,380] [INFO] Target genome list was writen to GCA_018378735.1_ASM1837873v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 09:29:38,383] [INFO] Task started: fastANI
[2023-06-19 09:29:38,384] [INFO] Running command: fastANI --query /var/lib/cwl/stg3480bef7-8352-4c25-9b0d-757785eac49f/GCA_018378735.1_ASM1837873v1_genomic.fna.gz --refList GCA_018378735.1_ASM1837873v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018378735.1_ASM1837873v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 09:29:42,808] [INFO] Task succeeded: fastANI
[2023-06-19 09:29:42,818] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 09:29:42,818] [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
GCA_900544715.1	s__Fimivicinus sp900544715	99.0289	818	995	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Fimivicinus	95.0	99.21	98.64	0.95	0.92	5	conclusive
GCA_900544375.1	s__Fimivicinus sp900544375	90.1523	669	995	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Fimivicinus	95.0	99.36	99.30	0.94	0.93	4	-
GCA_900549825.1	s__Fimivicinus sp900549825	84.5049	569	995	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Fimivicinus	95.0	100.00	100.00	0.99	0.99	2	-
GCA_002320555.1	s__Fimivicinus sp002320555	83.5699	482	995	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Fimivicinus	95.0	97.14	96.72	0.87	0.86	4	-
GCA_900552985.1	s__Fimivicinus intestinavium	79.3952	249	995	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Fimivicinus	95.0	98.94	98.94	0.95	0.95	2	-
GCA_018712345.1	s__Onthovicinus excrementipullorum	76.7488	90	995	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Onthovicinus	95.0	99.16	98.33	0.94	0.92	3	-
--------------------------------------------------------------------------------
[2023-06-19 09:29:42,820] [INFO] GTDB search result was written to GCA_018378735.1_ASM1837873v1_genomic.fna/result_gtdb.tsv
[2023-06-19 09:29:42,820] [INFO] ===== GTDB Search completed =====
[2023-06-19 09:29:42,823] [INFO] DFAST_QC result json was written to GCA_018378735.1_ASM1837873v1_genomic.fna/dqc_result.json
[2023-06-19 09:29:42,823] [INFO] DFAST_QC completed!
[2023-06-19 09:29:42,824] [INFO] Total running time: 0h1m2s