[2024-01-25 17:39:50,426] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:39:50,428] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:39:50,428] [INFO] DQC Reference Directory: /var/lib/cwl/stg98455d33-cf6e-417d-be2d-b9fe4a73ac6f/dqc_reference
[2024-01-25 17:39:51,521] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:39:51,521] [INFO] Task started: Prodigal
[2024-01-25 17:39:51,522] [INFO] Running command: gunzip -c /var/lib/cwl/stg1ef2579b-3496-45cb-8979-844ecc7e26c7/GCF_018128545.1_ASM1812854v1_genomic.fna.gz | prodigal -d GCF_018128545.1_ASM1812854v1_genomic.fna/cds.fna -a GCF_018128545.1_ASM1812854v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:40:01,413] [INFO] Task succeeded: Prodigal
[2024-01-25 17:40:01,414] [INFO] Task started: HMMsearch
[2024-01-25 17:40:01,414] [INFO] Running command: hmmsearch --tblout GCF_018128545.1_ASM1812854v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg98455d33-cf6e-417d-be2d-b9fe4a73ac6f/dqc_reference/reference_markers.hmm GCF_018128545.1_ASM1812854v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:40:01,668] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:40:01,669] [INFO] Found 6/6 markers.
[2024-01-25 17:40:01,706] [INFO] Query marker FASTA was written to GCF_018128545.1_ASM1812854v1_genomic.fna/markers.fasta
[2024-01-25 17:40:01,707] [INFO] Task started: Blastn
[2024-01-25 17:40:01,707] [INFO] Running command: blastn -query GCF_018128545.1_ASM1812854v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg98455d33-cf6e-417d-be2d-b9fe4a73ac6f/dqc_reference/reference_markers.fasta -out GCF_018128545.1_ASM1812854v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:02,244] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:02,247] [INFO] Selected 17 target genomes.
[2024-01-25 17:40:02,248] [INFO] Target genome list was writen to GCF_018128545.1_ASM1812854v1_genomic.fna/target_genomes.txt
[2024-01-25 17:40:02,256] [INFO] Task started: fastANI
[2024-01-25 17:40:02,256] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ef2579b-3496-45cb-8979-844ecc7e26c7/GCF_018128545.1_ASM1812854v1_genomic.fna.gz --refList GCF_018128545.1_ASM1812854v1_genomic.fna/target_genomes.txt --output GCF_018128545.1_ASM1812854v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:40:11,654] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:11,654] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg98455d33-cf6e-417d-be2d-b9fe4a73ac6f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:40:11,654] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg98455d33-cf6e-417d-be2d-b9fe4a73ac6f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:40:11,659] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:40:11,659] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:40:11,659] [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
Sinanaerobacter chloroacetimidivorans	strain=BAD-6	GCA_018128545.1	2818044	2818044	type	True	100.0	1562	1565	95	conclusive
Aminipila luticellarii	strain=JN-18	GCA_004103735.1	2507160	2507160	type	True	78.7447	72	1565	95	below_threshold
Anaerovorax odorimutans	strain=DSM 5092	GCA_000426305.1	109327	109327	type	True	77.3763	78	1565	95	below_threshold
Zhenpiania hominis	strain=BX12	GCA_014333425.1	2763644	2763644	type	True	76.1427	50	1565	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:40:11,661] [INFO] DFAST Taxonomy check result was written to GCF_018128545.1_ASM1812854v1_genomic.fna/tc_result.tsv
[2024-01-25 17:40:11,661] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:40:11,661] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:40:11,661] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg98455d33-cf6e-417d-be2d-b9fe4a73ac6f/dqc_reference/checkm_data
[2024-01-25 17:40:11,662] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:40:11,707] [INFO] Task started: CheckM
[2024-01-25 17:40:11,707] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018128545.1_ASM1812854v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018128545.1_ASM1812854v1_genomic.fna/checkm_input GCF_018128545.1_ASM1812854v1_genomic.fna/checkm_result
[2024-01-25 17:40:44,080] [INFO] Task succeeded: CheckM
[2024-01-25 17:40:44,081] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:40:44,099] [INFO] ===== Completeness check finished =====
[2024-01-25 17:40:44,099] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:40:44,100] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018128545.1_ASM1812854v1_genomic.fna/markers.fasta)
[2024-01-25 17:40:44,100] [INFO] Task started: Blastn
[2024-01-25 17:40:44,100] [INFO] Running command: blastn -query GCF_018128545.1_ASM1812854v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg98455d33-cf6e-417d-be2d-b9fe4a73ac6f/dqc_reference/reference_markers_gtdb.fasta -out GCF_018128545.1_ASM1812854v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:44,977] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:44,979] [INFO] Selected 19 target genomes.
[2024-01-25 17:40:44,979] [INFO] Target genome list was writen to GCF_018128545.1_ASM1812854v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:40:45,000] [INFO] Task started: fastANI
[2024-01-25 17:40:45,000] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ef2579b-3496-45cb-8979-844ecc7e26c7/GCF_018128545.1_ASM1812854v1_genomic.fna.gz --refList GCF_018128545.1_ASM1812854v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018128545.1_ASM1812854v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:40:55,309] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:55,314] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:40:55,314] [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_018128545.1	s__BAD-6 sp018128545	100.0	1562	1565	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__BAD-6	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_015243575.1	s__MT110 sp015243575	78.1842	210	1565	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__MT110	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017168145.1	s__IOR16 sp017168145	77.4578	64	1565	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__IOR16	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426305.1	s__Anaerovorax odorimutans	77.3763	78	1565	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Anaerovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012838265.1	s__DUPP01 sp012838265	76.9439	69	1565	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__DUPP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014333425.1	s__BX12 sp014333425	76.1427	50	1565	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__BX12	95.0	98.83	98.83	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:40:55,315] [INFO] GTDB search result was written to GCF_018128545.1_ASM1812854v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:40:55,316] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:40:55,318] [INFO] DFAST_QC result json was written to GCF_018128545.1_ASM1812854v1_genomic.fna/dqc_result.json
[2024-01-25 17:40:55,318] [INFO] DFAST_QC completed!
[2024-01-25 17:40:55,318] [INFO] Total running time: 0h1m5s