[2023-06-13 20:24:22,979] [INFO] DFAST_QC pipeline started.
[2023-06-13 20:24:22,981] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 20:24:22,981] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b594264-7d74-422c-9a85-6ffef99065a7/dqc_reference
[2023-06-13 20:24:24,143] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 20:24:24,144] [INFO] Task started: Prodigal
[2023-06-13 20:24:24,144] [INFO] Running command: gunzip -c /var/lib/cwl/stg39411993-8786-4601-97b3-70aee3334cf7/GCA_022792175.1_ASM2279217v1_genomic.fna.gz | prodigal -d GCA_022792175.1_ASM2279217v1_genomic.fna/cds.fna -a GCA_022792175.1_ASM2279217v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 20:24:31,639] [INFO] Task succeeded: Prodigal
[2023-06-13 20:24:31,640] [INFO] Task started: HMMsearch
[2023-06-13 20:24:31,640] [INFO] Running command: hmmsearch --tblout GCA_022792175.1_ASM2279217v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b594264-7d74-422c-9a85-6ffef99065a7/dqc_reference/reference_markers.hmm GCA_022792175.1_ASM2279217v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 20:24:31,859] [INFO] Task succeeded: HMMsearch
[2023-06-13 20:24:31,860] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg39411993-8786-4601-97b3-70aee3334cf7/GCA_022792175.1_ASM2279217v1_genomic.fna.gz]
[2023-06-13 20:24:31,889] [INFO] Query marker FASTA was written to GCA_022792175.1_ASM2279217v1_genomic.fna/markers.fasta
[2023-06-13 20:24:31,889] [INFO] Task started: Blastn
[2023-06-13 20:24:31,889] [INFO] Running command: blastn -query GCA_022792175.1_ASM2279217v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b594264-7d74-422c-9a85-6ffef99065a7/dqc_reference/reference_markers.fasta -out GCA_022792175.1_ASM2279217v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 20:24:32,500] [INFO] Task succeeded: Blastn
[2023-06-13 20:24:32,507] [INFO] Selected 19 target genomes.
[2023-06-13 20:24:32,508] [INFO] Target genome list was writen to GCA_022792175.1_ASM2279217v1_genomic.fna/target_genomes.txt
[2023-06-13 20:24:32,509] [INFO] Task started: fastANI
[2023-06-13 20:24:32,510] [INFO] Running command: fastANI --query /var/lib/cwl/stg39411993-8786-4601-97b3-70aee3334cf7/GCA_022792175.1_ASM2279217v1_genomic.fna.gz --refList GCA_022792175.1_ASM2279217v1_genomic.fna/target_genomes.txt --output GCA_022792175.1_ASM2279217v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 20:24:44,419] [INFO] Task succeeded: fastANI
[2023-06-13 20:24:44,420] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b594264-7d74-422c-9a85-6ffef99065a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 20:24:44,420] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b594264-7d74-422c-9a85-6ffef99065a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 20:24:44,425] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 20:24:44,425] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 20:24:44,425] [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
Provencibacterium massiliense	strain=Marseille-P2780	GCA_900169495.1	1841868	1841868	type	True	77.3067	174	994	95	below_threshold
Anaerotruncus massiliensis	strain=AT3	GCA_900199635.1	1673720	1673720	type	True	76.4443	81	994	95	below_threshold
Bittarella massiliensis	strain=GD6	GCA_001486165.1	1720313	1720313	type	True	76.2858	58	994	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 20:24:44,427] [INFO] DFAST Taxonomy check result was written to GCA_022792175.1_ASM2279217v1_genomic.fna/tc_result.tsv
[2023-06-13 20:24:44,427] [INFO] ===== Taxonomy check completed =====
[2023-06-13 20:24:44,428] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 20:24:44,428] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b594264-7d74-422c-9a85-6ffef99065a7/dqc_reference/checkm_data
[2023-06-13 20:24:44,429] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 20:24:44,460] [INFO] Task started: CheckM
[2023-06-13 20:24:44,460] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022792175.1_ASM2279217v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022792175.1_ASM2279217v1_genomic.fna/checkm_input GCA_022792175.1_ASM2279217v1_genomic.fna/checkm_result
[2023-06-13 20:25:10,672] [INFO] Task succeeded: CheckM
[2023-06-13 20:25:10,673] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 20:25:10,694] [INFO] ===== Completeness check finished =====
[2023-06-13 20:25:10,694] [INFO] ===== Start GTDB Search =====
[2023-06-13 20:25:10,695] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022792175.1_ASM2279217v1_genomic.fna/markers.fasta)
[2023-06-13 20:25:10,695] [INFO] Task started: Blastn
[2023-06-13 20:25:10,695] [INFO] Running command: blastn -query GCA_022792175.1_ASM2279217v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b594264-7d74-422c-9a85-6ffef99065a7/dqc_reference/reference_markers_gtdb.fasta -out GCA_022792175.1_ASM2279217v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 20:25:11,596] [INFO] Task succeeded: Blastn
[2023-06-13 20:25:11,605] [INFO] Selected 18 target genomes.
[2023-06-13 20:25:11,605] [INFO] Target genome list was writen to GCA_022792175.1_ASM2279217v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 20:25:11,608] [INFO] Task started: fastANI
[2023-06-13 20:25:11,608] [INFO] Running command: fastANI --query /var/lib/cwl/stg39411993-8786-4601-97b3-70aee3334cf7/GCA_022792175.1_ASM2279217v1_genomic.fna.gz --refList GCA_022792175.1_ASM2279217v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022792175.1_ASM2279217v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 20:25:18,680] [INFO] Task succeeded: fastANI
[2023-06-13 20:25:18,687] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 20:25:18,687] [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_004340125.1	s__Harryflintia acetispora	77.3627	162	994	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Harryflintia	95.0	98.73	98.54	0.92	0.90	6	-
GCF_904398325.1	s__Neoruminococcus faecicola	76.4742	76	994	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Neoruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900199635.1	s__Anaerotruncus massiliensis	76.4443	81	994	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	98.56	98.01	0.95	0.93	6	-
GCA_900547455.1	s__Negativibacillus faecipullorum	75.8906	57	994	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Negativibacillus	95.0	97.80	97.60	0.92	0.88	7	-
GCF_000820765.1	s__Soleaferrea massiliensis	75.8453	51	994	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Soleaferrea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000403395.2	s__Anaerotruncus sp000403395	75.8222	65	994	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	98.44	98.36	0.83	0.79	7	-
GCF_904420585.1	s__Howiella intestinavium	75.7806	52	994	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Howiella	95.0	98.63	98.63	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-06-13 20:25:18,689] [INFO] GTDB search result was written to GCA_022792175.1_ASM2279217v1_genomic.fna/result_gtdb.tsv
[2023-06-13 20:25:18,689] [INFO] ===== GTDB Search completed =====
[2023-06-13 20:25:18,692] [INFO] DFAST_QC result json was written to GCA_022792175.1_ASM2279217v1_genomic.fna/dqc_result.json
[2023-06-13 20:25:18,692] [INFO] DFAST_QC completed!
[2023-06-13 20:25:18,692] [INFO] Total running time: 0h0m56s