[2024-01-24 12:06:33,445] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:33,448] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:33,448] [INFO] DQC Reference Directory: /var/lib/cwl/stge899a5c7-d5f5-494c-957c-590dde712725/dqc_reference
[2024-01-24 12:06:34,736] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:34,737] [INFO] Task started: Prodigal
[2024-01-24 12:06:34,738] [INFO] Running command: gunzip -c /var/lib/cwl/stg194d592b-2a7e-4133-b996-a822a69eb0b8/GCF_004369225.1_ASM436922v1_genomic.fna.gz | prodigal -d GCF_004369225.1_ASM436922v1_genomic.fna/cds.fna -a GCF_004369225.1_ASM436922v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:43,942] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:43,942] [INFO] Task started: HMMsearch
[2024-01-24 12:06:43,942] [INFO] Running command: hmmsearch --tblout GCF_004369225.1_ASM436922v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge899a5c7-d5f5-494c-957c-590dde712725/dqc_reference/reference_markers.hmm GCF_004369225.1_ASM436922v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:44,197] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:44,198] [INFO] Found 6/6 markers.
[2024-01-24 12:06:44,230] [INFO] Query marker FASTA was written to GCF_004369225.1_ASM436922v1_genomic.fna/markers.fasta
[2024-01-24 12:06:44,230] [INFO] Task started: Blastn
[2024-01-24 12:06:44,230] [INFO] Running command: blastn -query GCF_004369225.1_ASM436922v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge899a5c7-d5f5-494c-957c-590dde712725/dqc_reference/reference_markers.fasta -out GCF_004369225.1_ASM436922v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:44,813] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:44,817] [INFO] Selected 18 target genomes.
[2024-01-24 12:06:44,818] [INFO] Target genome list was writen to GCF_004369225.1_ASM436922v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:44,825] [INFO] Task started: fastANI
[2024-01-24 12:06:44,826] [INFO] Running command: fastANI --query /var/lib/cwl/stg194d592b-2a7e-4133-b996-a822a69eb0b8/GCF_004369225.1_ASM436922v1_genomic.fna.gz --refList GCF_004369225.1_ASM436922v1_genomic.fna/target_genomes.txt --output GCF_004369225.1_ASM436922v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:54,735] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:54,735] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge899a5c7-d5f5-494c-957c-590dde712725/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:54,736] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge899a5c7-d5f5-494c-957c-590dde712725/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:54,742] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:54,743] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:54,743] [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 propionicicum	strain=MGP	GCA_004369225.1	258475	258475	type	True	100.0	1234	1234	95	conclusive
Pelotomaculum terephthalicicum	strain=JT	GCA_022410535.1	206393	206393	type	True	77.8689	115	1234	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:54,745] [INFO] DFAST Taxonomy check result was written to GCF_004369225.1_ASM436922v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:54,746] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:54,746] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:54,747] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge899a5c7-d5f5-494c-957c-590dde712725/dqc_reference/checkm_data
[2024-01-24 12:06:54,748] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:54,794] [INFO] Task started: CheckM
[2024-01-24 12:06:54,794] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004369225.1_ASM436922v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004369225.1_ASM436922v1_genomic.fna/checkm_input GCF_004369225.1_ASM436922v1_genomic.fna/checkm_result
[2024-01-24 12:07:26,362] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:26,363] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:26,393] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:26,394] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:26,394] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004369225.1_ASM436922v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:26,394] [INFO] Task started: Blastn
[2024-01-24 12:07:26,395] [INFO] Running command: blastn -query GCF_004369225.1_ASM436922v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge899a5c7-d5f5-494c-957c-590dde712725/dqc_reference/reference_markers_gtdb.fasta -out GCF_004369225.1_ASM436922v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:27,284] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:27,288] [INFO] Selected 17 target genomes.
[2024-01-24 12:07:27,289] [INFO] Target genome list was writen to GCF_004369225.1_ASM436922v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:27,367] [INFO] Task started: fastANI
[2024-01-24 12:07:27,367] [INFO] Running command: fastANI --query /var/lib/cwl/stg194d592b-2a7e-4133-b996-a822a69eb0b8/GCF_004369225.1_ASM436922v1_genomic.fna.gz --refList GCF_004369225.1_ASM436922v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004369225.1_ASM436922v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:35,763] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:35,779] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:35,779] [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_004369225.1	s__Pelotomaculum_B propionicicum	100.0	1234	1234	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Pelotomaculaceae;g__Pelotomaculum_B	95.0	99.42	99.42	0.93	0.93	2	conclusive
GCA_018435055.1	s__Syntrophopropionicum sp018435055	78.9371	272	1234	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Pelotomaculaceae;g__Syntrophopropionicum	95.0	98.89	98.89	0.95	0.95	2	-
GCA_002365855.1	s__UBA3103 sp002365855	78.6628	137	1234	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_002402945.1	s__Syntrophopropionicum sp002402945	78.2056	163	1234	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Pelotomaculaceae;g__Syntrophopropionicum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000010565.1	s__Pelotomaculum thermopropionicum	77.641	178	1234	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_002067965.1	s__MVRN01 sp002067965	77.3911	72	1234	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Pelotomaculaceae;g__MVRN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002365865.1	s__UBA3102 sp002365865	76.8883	65	1234	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_001512635.1	s__DTU098 sp001512635	76.7882	120	1234	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Pelotomaculaceae;g__DTU098	95.0	99.71	99.66	0.92	0.92	3	-
GCF_009428905.1	s__Desulfofundulus_A thermobenzoicus	76.0274	60	1234	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfovirgulaceae;g__Desulfofundulus_A	95.0	96.96	95.37	0.88	0.86	3	-
GCF_001655685.1	s__Desulfotomaculum_G copahuensis	75.8812	64	1234	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfovirgulaceae;g__Desulfotomaculum_G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000214705.1	s__Desulfofundulus kuznetsovii	75.7847	54	1234	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfovirgulaceae;g__Desulfofundulus	95.0	97.21	97.21	0.77	0.77	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:35,789] [INFO] GTDB search result was written to GCF_004369225.1_ASM436922v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:35,790] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:35,794] [INFO] DFAST_QC result json was written to GCF_004369225.1_ASM436922v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:35,794] [INFO] DFAST_QC completed!
[2024-01-24 12:07:35,794] [INFO] Total running time: 0h1m2s