[2024-01-24 12:29:51,371] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:51,373] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:51,373] [INFO] DQC Reference Directory: /var/lib/cwl/stg834deead-0ec7-40a6-b2a0-481d6102638f/dqc_reference
[2024-01-24 12:29:52,586] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:52,587] [INFO] Task started: Prodigal
[2024-01-24 12:29:52,588] [INFO] Running command: gunzip -c /var/lib/cwl/stgce47fd52-9584-4469-bf77-6aacc0e29ccd/GCF_004364155.1_ASM436415v1_genomic.fna.gz | prodigal -d GCF_004364155.1_ASM436415v1_genomic.fna/cds.fna -a GCF_004364155.1_ASM436415v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:58,351] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:58,352] [INFO] Task started: HMMsearch
[2024-01-24 12:29:58,352] [INFO] Running command: hmmsearch --tblout GCF_004364155.1_ASM436415v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg834deead-0ec7-40a6-b2a0-481d6102638f/dqc_reference/reference_markers.hmm GCF_004364155.1_ASM436415v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:58,585] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:58,586] [INFO] Found 6/6 markers.
[2024-01-24 12:29:58,613] [INFO] Query marker FASTA was written to GCF_004364155.1_ASM436415v1_genomic.fna/markers.fasta
[2024-01-24 12:29:58,613] [INFO] Task started: Blastn
[2024-01-24 12:29:58,613] [INFO] Running command: blastn -query GCF_004364155.1_ASM436415v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg834deead-0ec7-40a6-b2a0-481d6102638f/dqc_reference/reference_markers.fasta -out GCF_004364155.1_ASM436415v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:59,182] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:59,186] [INFO] Selected 14 target genomes.
[2024-01-24 12:29:59,186] [INFO] Target genome list was writen to GCF_004364155.1_ASM436415v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:59,208] [INFO] Task started: fastANI
[2024-01-24 12:29:59,208] [INFO] Running command: fastANI --query /var/lib/cwl/stgce47fd52-9584-4469-bf77-6aacc0e29ccd/GCF_004364155.1_ASM436415v1_genomic.fna.gz --refList GCF_004364155.1_ASM436415v1_genomic.fna/target_genomes.txt --output GCF_004364155.1_ASM436415v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:07,778] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:07,779] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg834deead-0ec7-40a6-b2a0-481d6102638f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:07,779] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg834deead-0ec7-40a6-b2a0-481d6102638f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:07,785] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:30:07,785] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:07,785] [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
Fonticella tunisiensis	strain=DSM 24455	GCA_004364155.1	1096341	1096341	type	True	100.0	997	1001	95	conclusive
Clostridium prolinivorans	strain=PYR-10	GCA_004011155.1	2769420	2769420	type	True	79.2874	53	1001	95	below_threshold
Caloramator australicus	strain=RC3	GCA_000297115.1	515264	515264	type	True	77.0036	70	1001	95	below_threshold
Caloramator mitchellensis	strain=VF08	GCA_001440545.1	908809	908809	type	True	76.905	69	1001	95	below_threshold
Caloramator fervidus	strain=DSM 5463	GCA_900108045.1	29344	29344	type	True	76.7174	59	1001	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:07,787] [INFO] DFAST Taxonomy check result was written to GCF_004364155.1_ASM436415v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:07,788] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:07,788] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:07,788] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg834deead-0ec7-40a6-b2a0-481d6102638f/dqc_reference/checkm_data
[2024-01-24 12:30:07,789] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:07,823] [INFO] Task started: CheckM
[2024-01-24 12:30:07,823] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004364155.1_ASM436415v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004364155.1_ASM436415v1_genomic.fna/checkm_input GCF_004364155.1_ASM436415v1_genomic.fna/checkm_result
[2024-01-24 12:30:32,634] [INFO] Task succeeded: CheckM
[2024-01-24 12:30:32,635] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:30:32,664] [INFO] ===== Completeness check finished =====
[2024-01-24 12:30:32,664] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:30:32,665] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004364155.1_ASM436415v1_genomic.fna/markers.fasta)
[2024-01-24 12:30:32,665] [INFO] Task started: Blastn
[2024-01-24 12:30:32,665] [INFO] Running command: blastn -query GCF_004364155.1_ASM436415v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg834deead-0ec7-40a6-b2a0-481d6102638f/dqc_reference/reference_markers_gtdb.fasta -out GCF_004364155.1_ASM436415v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:33,465] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:33,469] [INFO] Selected 19 target genomes.
[2024-01-24 12:30:33,469] [INFO] Target genome list was writen to GCF_004364155.1_ASM436415v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:30:33,555] [INFO] Task started: fastANI
[2024-01-24 12:30:33,555] [INFO] Running command: fastANI --query /var/lib/cwl/stgce47fd52-9584-4469-bf77-6aacc0e29ccd/GCF_004364155.1_ASM436415v1_genomic.fna.gz --refList GCF_004364155.1_ASM436415v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004364155.1_ASM436415v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:30:43,532] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:43,540] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:30:43,540] [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_004364155.1	s__Fonticella tunisiensis	100.0	997	1001	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__Fonticella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900167505.1	s__F0540 sp900167505	78.6515	53	1001	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__F0540	95.0	98.87	98.87	0.90	0.90	2	-
GCF_900167605.1	s__Caloramator_B quimbayensis	77.4609	104	1001	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__Caloramator_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129265.1	s__Caloramator_A proteoclasticus	77.3112	84	1001	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__Caloramator_A	95.0	98.54	98.54	0.90	0.90	2	-
GCF_000297115.1	s__Caloramator australicus	77.1054	70	1001	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__Caloramator	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001440545.1	s__Caloramator mitchellensis	76.905	69	1001	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__Caloramator	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108045.1	s__Caloramator fervidus	76.6781	60	1001	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__Caloramator	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016765585.1	s__F0540 sp016765585	75.5503	57	1001	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__F0540	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000466585.1	s__F0540 sp000466585	75.5338	51	1001	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__F0540	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:30:43,543] [INFO] GTDB search result was written to GCF_004364155.1_ASM436415v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:30:43,543] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:30:43,546] [INFO] DFAST_QC result json was written to GCF_004364155.1_ASM436415v1_genomic.fna/dqc_result.json
[2024-01-24 12:30:43,546] [INFO] DFAST_QC completed!
[2024-01-24 12:30:43,547] [INFO] Total running time: 0h0m52s