[2024-01-24 11:18:04,651] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:18:04,653] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:18:04,653] [INFO] DQC Reference Directory: /var/lib/cwl/stgc9836726-05f2-45cf-92ff-a37442f075eb/dqc_reference
[2024-01-24 11:18:05,831] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:18:05,832] [INFO] Task started: Prodigal
[2024-01-24 11:18:05,832] [INFO] Running command: gunzip -c /var/lib/cwl/stg479611d3-4a98-49e3-bbce-6656f9d5ccf5/GCF_017368455.1_ASM1736845v1_genomic.fna.gz | prodigal -d GCF_017368455.1_ASM1736845v1_genomic.fna/cds.fna -a GCF_017368455.1_ASM1736845v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:18:13,909] [INFO] Task succeeded: Prodigal
[2024-01-24 11:18:13,910] [INFO] Task started: HMMsearch
[2024-01-24 11:18:13,910] [INFO] Running command: hmmsearch --tblout GCF_017368455.1_ASM1736845v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc9836726-05f2-45cf-92ff-a37442f075eb/dqc_reference/reference_markers.hmm GCF_017368455.1_ASM1736845v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:18:14,198] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:18:14,199] [INFO] Found 6/6 markers.
[2024-01-24 11:18:14,230] [INFO] Query marker FASTA was written to GCF_017368455.1_ASM1736845v1_genomic.fna/markers.fasta
[2024-01-24 11:18:14,230] [INFO] Task started: Blastn
[2024-01-24 11:18:14,230] [INFO] Running command: blastn -query GCF_017368455.1_ASM1736845v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9836726-05f2-45cf-92ff-a37442f075eb/dqc_reference/reference_markers.fasta -out GCF_017368455.1_ASM1736845v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:18:15,070] [INFO] Task succeeded: Blastn
[2024-01-24 11:18:15,074] [INFO] Selected 21 target genomes.
[2024-01-24 11:18:15,074] [INFO] Target genome list was writen to GCF_017368455.1_ASM1736845v1_genomic.fna/target_genomes.txt
[2024-01-24 11:18:15,291] [INFO] Task started: fastANI
[2024-01-24 11:18:15,291] [INFO] Running command: fastANI --query /var/lib/cwl/stg479611d3-4a98-49e3-bbce-6656f9d5ccf5/GCF_017368455.1_ASM1736845v1_genomic.fna.gz --refList GCF_017368455.1_ASM1736845v1_genomic.fna/target_genomes.txt --output GCF_017368455.1_ASM1736845v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:18:26,968] [INFO] Task succeeded: fastANI
[2024-01-24 11:18:26,968] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc9836726-05f2-45cf-92ff-a37442f075eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:18:26,969] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc9836726-05f2-45cf-92ff-a37442f075eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:18:26,976] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:18:26,976] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:18:26,976] [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
Proteiniclasticum aestuarii	strain=SCR006	GCA_017368455.1	2817862	2817862	type	True	100.0	1045	1046	95	conclusive
Proteiniclasticum ruminis	strain=DSM 24773	GCA_000701905.1	398199	398199	type	True	78.7335	298	1046	95	below_threshold
Proteiniclasticum sediminis	strain=BAD-10	GCA_018128025.1	2804028	2804028	type	True	77.5143	189	1046	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:18:26,978] [INFO] DFAST Taxonomy check result was written to GCF_017368455.1_ASM1736845v1_genomic.fna/tc_result.tsv
[2024-01-24 11:18:26,978] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:18:26,978] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:18:26,979] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc9836726-05f2-45cf-92ff-a37442f075eb/dqc_reference/checkm_data
[2024-01-24 11:18:26,979] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:18:27,014] [INFO] Task started: CheckM
[2024-01-24 11:18:27,015] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017368455.1_ASM1736845v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017368455.1_ASM1736845v1_genomic.fna/checkm_input GCF_017368455.1_ASM1736845v1_genomic.fna/checkm_result
[2024-01-24 11:18:57,414] [INFO] Task succeeded: CheckM
[2024-01-24 11:18:57,417] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:18:57,439] [INFO] ===== Completeness check finished =====
[2024-01-24 11:18:57,439] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:18:57,440] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017368455.1_ASM1736845v1_genomic.fna/markers.fasta)
[2024-01-24 11:18:57,440] [INFO] Task started: Blastn
[2024-01-24 11:18:57,440] [INFO] Running command: blastn -query GCF_017368455.1_ASM1736845v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9836726-05f2-45cf-92ff-a37442f075eb/dqc_reference/reference_markers_gtdb.fasta -out GCF_017368455.1_ASM1736845v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:18:58,236] [INFO] Task succeeded: Blastn
[2024-01-24 11:18:58,240] [INFO] Selected 14 target genomes.
[2024-01-24 11:18:58,241] [INFO] Target genome list was writen to GCF_017368455.1_ASM1736845v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:18:58,269] [INFO] Task started: fastANI
[2024-01-24 11:18:58,269] [INFO] Running command: fastANI --query /var/lib/cwl/stg479611d3-4a98-49e3-bbce-6656f9d5ccf5/GCF_017368455.1_ASM1736845v1_genomic.fna.gz --refList GCF_017368455.1_ASM1736845v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017368455.1_ASM1736845v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:19:05,793] [INFO] Task succeeded: fastANI
[2024-01-24 11:19:05,806] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:19:05,807] [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_017368455.1	s__Proteiniclasticum sp017368455	100.0	1045	1046	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Proteiniclasticum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009930125.1	s__Proteiniclasticum sp009930125	93.1119	538	1046	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Proteiniclasticum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115135.1	s__Proteiniclasticum ruminis_A	78.7964	309	1046	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Proteiniclasticum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000701905.1	s__Proteiniclasticum ruminis	78.7335	298	1046	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Proteiniclasticum	95.0	97.65	96.61	0.91	0.86	5	-
GCA_003514505.1	s__Proteiniclasticum sp003514505	78.5654	253	1046	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Proteiniclasticum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018128025.1	s__Proteiniclasticum sp018128025	77.5143	189	1046	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Proteiniclasticum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003510765.1	s__Proteiniclasticum sp003510765	77.4187	82	1046	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Proteiniclasticum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:19:05,808] [INFO] GTDB search result was written to GCF_017368455.1_ASM1736845v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:19:05,809] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:19:05,811] [INFO] DFAST_QC result json was written to GCF_017368455.1_ASM1736845v1_genomic.fna/dqc_result.json
[2024-01-24 11:19:05,811] [INFO] DFAST_QC completed!
[2024-01-24 11:19:05,811] [INFO] Total running time: 0h1m1s