[2024-01-24 13:28:29,151] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:29,153] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:29,153] [INFO] DQC Reference Directory: /var/lib/cwl/stg7da80ae1-8cfa-4b30-a5b5-1ea9867e47fd/dqc_reference
[2024-01-24 13:28:30,391] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:30,392] [INFO] Task started: Prodigal
[2024-01-24 13:28:30,392] [INFO] Running command: gunzip -c /var/lib/cwl/stg917d4aa3-cb25-4040-8b29-0f1c8d91b1f8/GCF_004369205.1_ASM436920v1_genomic.fna.gz | prodigal -d GCF_004369205.1_ASM436920v1_genomic.fna/cds.fna -a GCF_004369205.1_ASM436920v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:41,516] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:41,517] [INFO] Task started: HMMsearch
[2024-01-24 13:28:41,517] [INFO] Running command: hmmsearch --tblout GCF_004369205.1_ASM436920v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7da80ae1-8cfa-4b30-a5b5-1ea9867e47fd/dqc_reference/reference_markers.hmm GCF_004369205.1_ASM436920v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:41,806] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:41,808] [INFO] Found 6/6 markers.
[2024-01-24 13:28:41,848] [INFO] Query marker FASTA was written to GCF_004369205.1_ASM436920v1_genomic.fna/markers.fasta
[2024-01-24 13:28:41,849] [INFO] Task started: Blastn
[2024-01-24 13:28:41,849] [INFO] Running command: blastn -query GCF_004369205.1_ASM436920v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7da80ae1-8cfa-4b30-a5b5-1ea9867e47fd/dqc_reference/reference_markers.fasta -out GCF_004369205.1_ASM436920v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:42,434] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:42,437] [INFO] Selected 18 target genomes.
[2024-01-24 13:28:42,437] [INFO] Target genome list was writen to GCF_004369205.1_ASM436920v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:42,447] [INFO] Task started: fastANI
[2024-01-24 13:28:42,447] [INFO] Running command: fastANI --query /var/lib/cwl/stg917d4aa3-cb25-4040-8b29-0f1c8d91b1f8/GCF_004369205.1_ASM436920v1_genomic.fna.gz --refList GCF_004369205.1_ASM436920v1_genomic.fna/target_genomes.txt --output GCF_004369205.1_ASM436920v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:54,028] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:54,029] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7da80ae1-8cfa-4b30-a5b5-1ea9867e47fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:54,029] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7da80ae1-8cfa-4b30-a5b5-1ea9867e47fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:54,032] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:54,032] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:54,033] [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
Pelotomaculum schinkii	strain=HH	GCA_004369205.1	78350	78350	type	True	100.0	1475	1475	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:28:54,034] [INFO] DFAST Taxonomy check result was written to GCF_004369205.1_ASM436920v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:54,035] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:54,035] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:54,035] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7da80ae1-8cfa-4b30-a5b5-1ea9867e47fd/dqc_reference/checkm_data
[2024-01-24 13:28:54,036] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:54,086] [INFO] Task started: CheckM
[2024-01-24 13:28:54,086] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004369205.1_ASM436920v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004369205.1_ASM436920v1_genomic.fna/checkm_input GCF_004369205.1_ASM436920v1_genomic.fna/checkm_result
[2024-01-24 13:29:30,853] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:30,855] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:30,874] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:30,874] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:30,875] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004369205.1_ASM436920v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:30,875] [INFO] Task started: Blastn
[2024-01-24 13:29:30,875] [INFO] Running command: blastn -query GCF_004369205.1_ASM436920v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7da80ae1-8cfa-4b30-a5b5-1ea9867e47fd/dqc_reference/reference_markers_gtdb.fasta -out GCF_004369205.1_ASM436920v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:31,763] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:31,766] [INFO] Selected 20 target genomes.
[2024-01-24 13:29:31,766] [INFO] Target genome list was writen to GCF_004369205.1_ASM436920v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:31,909] [INFO] Task started: fastANI
[2024-01-24 13:29:31,909] [INFO] Running command: fastANI --query /var/lib/cwl/stg917d4aa3-cb25-4040-8b29-0f1c8d91b1f8/GCF_004369205.1_ASM436920v1_genomic.fna.gz --refList GCF_004369205.1_ASM436920v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004369205.1_ASM436920v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:41,863] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:41,872] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:41,872] [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_004369205.1	s__Pelotomaculum_C schinkii	100.0	1474	1475	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Pelotomaculaceae;g__Pelotomaculum_C	95.0	97.26	97.26	0.80	0.80	2	conclusive
GCA_002408725.1	s__DTU098 sp002408725	77.743	138	1475	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Pelotomaculaceae;g__DTU098	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002365855.1	s__UBA3103 sp002365855	77.4827	91	1475	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Pelotomaculaceae;g__UBA3103	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001512635.1	s__DTU098 sp001512635	77.4488	130	1475	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Pelotomaculaceae;g__DTU098	95.0	99.71	99.66	0.92	0.92	3	-
GCA_002365865.1	s__UBA3102 sp002365865	77.4071	60	1475	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Pelotomaculaceae;g__UBA3102	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000010565.1	s__Pelotomaculum thermopropionicum	77.3629	132	1475	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Pelotomaculaceae;g__Pelotomaculum	95.0	98.96	98.96	0.94	0.94	2	-
GCA_002067515.1	s__MVQK01 sp002067515	77.0698	66	1475	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Pelotomaculaceae;g__MVQK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002305915.1	s__DTU098 sp002305915	77.068	119	1475	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Pelotomaculaceae;g__DTU098	95.0	99.38	99.38	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:41,874] [INFO] GTDB search result was written to GCF_004369205.1_ASM436920v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:41,874] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:41,878] [INFO] DFAST_QC result json was written to GCF_004369205.1_ASM436920v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:41,879] [INFO] DFAST_QC completed!
[2024-01-24 13:29:41,879] [INFO] Total running time: 0h1m13s