[2024-01-24 12:06:14,545] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:14,547] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:14,547] [INFO] DQC Reference Directory: /var/lib/cwl/stg05f08825-3fcb-44ff-a6d9-ad53c395dfc3/dqc_reference
[2024-01-24 12:06:15,977] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:15,978] [INFO] Task started: Prodigal
[2024-01-24 12:06:15,978] [INFO] Running command: gunzip -c /var/lib/cwl/stg3f92ecfc-57bd-4070-843b-7d4a5e872888/GCF_004342165.1_ASM434216v1_genomic.fna.gz | prodigal -d GCF_004342165.1_ASM434216v1_genomic.fna/cds.fna -a GCF_004342165.1_ASM434216v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:21,439] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:21,440] [INFO] Task started: HMMsearch
[2024-01-24 12:06:21,440] [INFO] Running command: hmmsearch --tblout GCF_004342165.1_ASM434216v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05f08825-3fcb-44ff-a6d9-ad53c395dfc3/dqc_reference/reference_markers.hmm GCF_004342165.1_ASM434216v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:21,836] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:21,837] [INFO] Found 6/6 markers.
[2024-01-24 12:06:21,870] [INFO] Query marker FASTA was written to GCF_004342165.1_ASM434216v1_genomic.fna/markers.fasta
[2024-01-24 12:06:21,870] [INFO] Task started: Blastn
[2024-01-24 12:06:21,870] [INFO] Running command: blastn -query GCF_004342165.1_ASM434216v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05f08825-3fcb-44ff-a6d9-ad53c395dfc3/dqc_reference/reference_markers.fasta -out GCF_004342165.1_ASM434216v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:22,455] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:22,459] [INFO] Selected 20 target genomes.
[2024-01-24 12:06:22,459] [INFO] Target genome list was writen to GCF_004342165.1_ASM434216v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:22,537] [INFO] Task started: fastANI
[2024-01-24 12:06:22,537] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f92ecfc-57bd-4070-843b-7d4a5e872888/GCF_004342165.1_ASM434216v1_genomic.fna.gz --refList GCF_004342165.1_ASM434216v1_genomic.fna/target_genomes.txt --output GCF_004342165.1_ASM434216v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:35,567] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:35,567] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05f08825-3fcb-44ff-a6d9-ad53c395dfc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:35,568] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05f08825-3fcb-44ff-a6d9-ad53c395dfc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:35,577] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:35,577] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:35,577] [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
Natranaerovirga pectinivora	strain=DSM 24629	GCA_004342165.1	682400	682400	type	True	100.0	1004	1005	95	conclusive
Natranaerovirga hydrolytica	strain=DSM 24176	GCA_004339095.1	680378	680378	type	True	78.0651	261	1005	95	below_threshold
Vallitalea guaymasensis	strain=Ra1766G1	GCA_018141425.1	1185412	1185412	type	True	76.1756	100	1005	95	below_threshold
Crassaminicella profunda	strain=Ra1766H	GCA_019884785.1	1286698	1286698	type	True	75.4965	51	1005	95	below_threshold
Tepidibacter formicigenes	strain=DSM 15518	GCA_900142235.1	227138	227138	type	True	75.1064	57	1005	95	below_threshold
Clostridium drakei	strain=SL1	GCA_003096175.1	332101	332101	type	True	75.0442	56	1005	95	below_threshold
Clostridium scatologenes	strain=ATCC 25775	GCA_000968375.1	1548	1548	type	True	75.0348	54	1005	95	below_threshold
Clostridium weizhouense	strain=YB-6	GCA_019431045.1	2859781	2859781	type	True	74.9494	58	1005	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:35,579] [INFO] DFAST Taxonomy check result was written to GCF_004342165.1_ASM434216v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:35,579] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:35,579] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:35,580] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05f08825-3fcb-44ff-a6d9-ad53c395dfc3/dqc_reference/checkm_data
[2024-01-24 12:06:35,581] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:35,614] [INFO] Task started: CheckM
[2024-01-24 12:06:35,614] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004342165.1_ASM434216v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004342165.1_ASM434216v1_genomic.fna/checkm_input GCF_004342165.1_ASM434216v1_genomic.fna/checkm_result
[2024-01-24 12:06:58,839] [INFO] Task succeeded: CheckM
[2024-01-24 12:06:58,840] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:06:58,859] [INFO] ===== Completeness check finished =====
[2024-01-24 12:06:58,860] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:06:58,860] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004342165.1_ASM434216v1_genomic.fna/markers.fasta)
[2024-01-24 12:06:58,860] [INFO] Task started: Blastn
[2024-01-24 12:06:58,861] [INFO] Running command: blastn -query GCF_004342165.1_ASM434216v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05f08825-3fcb-44ff-a6d9-ad53c395dfc3/dqc_reference/reference_markers_gtdb.fasta -out GCF_004342165.1_ASM434216v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:59,639] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:59,644] [INFO] Selected 21 target genomes.
[2024-01-24 12:06:59,644] [INFO] Target genome list was writen to GCF_004342165.1_ASM434216v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:06:59,706] [INFO] Task started: fastANI
[2024-01-24 12:06:59,707] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f92ecfc-57bd-4070-843b-7d4a5e872888/GCF_004342165.1_ASM434216v1_genomic.fna.gz --refList GCF_004342165.1_ASM434216v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004342165.1_ASM434216v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:10,794] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:10,802] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:10,802] [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_004342165.1	s__Natranaerovirga pectinivora	100.0	1004	1005	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__DSM-24629;g__Natranaerovirga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004339095.1	s__Natranaerovirga hydrolytica	78.051	262	1005	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__DSM-24629;g__Natranaerovirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018141425.1	s__Vallitalea guaymasensis	76.1756	100	1005	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Vallitaleaceae;g__Vallitalea	95.0	97.34	97.34	0.88	0.88	2	-
GCA_002841625.1	s__HGW-1 sp002841625	75.9874	58	1005	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Vallitaleaceae;g__HGW-1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002841375.1	s__HGW-1 sp002841375	75.7946	59	1005	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Vallitaleaceae;g__HGW-1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:10,804] [INFO] GTDB search result was written to GCF_004342165.1_ASM434216v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:10,804] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:10,807] [INFO] DFAST_QC result json was written to GCF_004342165.1_ASM434216v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:10,807] [INFO] DFAST_QC completed!
[2024-01-24 12:07:10,808] [INFO] Total running time: 0h0m56s