[2024-01-24 12:31:32,822] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:32,824] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:32,824] [INFO] DQC Reference Directory: /var/lib/cwl/stg9fdac43c-035a-41b4-b6c6-b642ec091fd2/dqc_reference
[2024-01-24 12:31:33,945] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:33,946] [INFO] Task started: Prodigal
[2024-01-24 12:31:33,946] [INFO] Running command: gunzip -c /var/lib/cwl/stg01ece3d3-0012-40ca-aad5-b8bf641d00c5/GCF_004339095.1_ASM433909v1_genomic.fna.gz | prodigal -d GCF_004339095.1_ASM433909v1_genomic.fna/cds.fna -a GCF_004339095.1_ASM433909v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:38,843] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:38,843] [INFO] Task started: HMMsearch
[2024-01-24 12:31:38,843] [INFO] Running command: hmmsearch --tblout GCF_004339095.1_ASM433909v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9fdac43c-035a-41b4-b6c6-b642ec091fd2/dqc_reference/reference_markers.hmm GCF_004339095.1_ASM433909v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:39,062] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:39,063] [INFO] Found 6/6 markers.
[2024-01-24 12:31:39,087] [INFO] Query marker FASTA was written to GCF_004339095.1_ASM433909v1_genomic.fna/markers.fasta
[2024-01-24 12:31:39,087] [INFO] Task started: Blastn
[2024-01-24 12:31:39,088] [INFO] Running command: blastn -query GCF_004339095.1_ASM433909v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9fdac43c-035a-41b4-b6c6-b642ec091fd2/dqc_reference/reference_markers.fasta -out GCF_004339095.1_ASM433909v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:39,623] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:39,626] [INFO] Selected 23 target genomes.
[2024-01-24 12:31:39,626] [INFO] Target genome list was writen to GCF_004339095.1_ASM433909v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:39,632] [INFO] Task started: fastANI
[2024-01-24 12:31:39,633] [INFO] Running command: fastANI --query /var/lib/cwl/stg01ece3d3-0012-40ca-aad5-b8bf641d00c5/GCF_004339095.1_ASM433909v1_genomic.fna.gz --refList GCF_004339095.1_ASM433909v1_genomic.fna/target_genomes.txt --output GCF_004339095.1_ASM433909v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:52,555] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:52,555] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9fdac43c-035a-41b4-b6c6-b642ec091fd2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:52,555] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9fdac43c-035a-41b4-b6c6-b642ec091fd2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:52,561] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:52,561] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:52,561] [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 hydrolytica	strain=DSM 24176	GCA_004339095.1	680378	680378	type	True	100.0	983	984	95	conclusive
Natranaerovirga pectinivora	strain=DSM 24629	GCA_004342165.1	682400	682400	type	True	78.032	267	984	95	below_threshold
Vallitalea pronyensis	strain=FatNI3	GCA_018141445.1	1348613	1348613	type	True	76.7046	52	984	95	below_threshold
Vallitalea guaymasensis	strain=Ra1766G1	GCA_018141425.1	1185412	1185412	type	True	76.447	68	984	95	below_threshold
Senegalia massiliensis	strain=SIT17	GCA_900626135.1	1720316	1720316	type	True	75.3245	50	984	95	below_threshold
Clostridium weizhouense	strain=YB-6	GCA_019431045.1	2859781	2859781	type	True	75.0094	55	984	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:52,562] [INFO] DFAST Taxonomy check result was written to GCF_004339095.1_ASM433909v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:52,563] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:52,563] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:52,564] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9fdac43c-035a-41b4-b6c6-b642ec091fd2/dqc_reference/checkm_data
[2024-01-24 12:31:52,564] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:52,594] [INFO] Task started: CheckM
[2024-01-24 12:31:52,594] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004339095.1_ASM433909v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004339095.1_ASM433909v1_genomic.fna/checkm_input GCF_004339095.1_ASM433909v1_genomic.fna/checkm_result
[2024-01-24 12:32:12,202] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:12,203] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:12,219] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:12,219] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:12,219] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004339095.1_ASM433909v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:12,219] [INFO] Task started: Blastn
[2024-01-24 12:32:12,219] [INFO] Running command: blastn -query GCF_004339095.1_ASM433909v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9fdac43c-035a-41b4-b6c6-b642ec091fd2/dqc_reference/reference_markers_gtdb.fasta -out GCF_004339095.1_ASM433909v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:12,929] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:12,932] [INFO] Selected 25 target genomes.
[2024-01-24 12:32:12,932] [INFO] Target genome list was writen to GCF_004339095.1_ASM433909v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:12,944] [INFO] Task started: fastANI
[2024-01-24 12:32:12,944] [INFO] Running command: fastANI --query /var/lib/cwl/stg01ece3d3-0012-40ca-aad5-b8bf641d00c5/GCF_004339095.1_ASM433909v1_genomic.fna.gz --refList GCF_004339095.1_ASM433909v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004339095.1_ASM433909v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:26,513] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:26,517] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:26,517] [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_004339095.1	s__Natranaerovirga hydrolytica	100.0	983	984	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_004342165.1	s__Natranaerovirga pectinivora	78.019	268	984	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_018141445.1	s__Vallitalea pronyensis	76.7046	52	984	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Vallitaleaceae;g__Vallitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018141425.1	s__Vallitalea guaymasensis	76.447	68	984	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Vallitaleaceae;g__Vallitalea	95.0	97.34	97.34	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:26,518] [INFO] GTDB search result was written to GCF_004339095.1_ASM433909v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:26,519] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:26,521] [INFO] DFAST_QC result json was written to GCF_004339095.1_ASM433909v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:26,521] [INFO] DFAST_QC completed!
[2024-01-24 12:32:26,521] [INFO] Total running time: 0h0m54s