[2024-01-25 18:41:05,898] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:41:05,901] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:41:05,901] [INFO] DQC Reference Directory: /var/lib/cwl/stg3a7c8d17-d794-4d46-afdc-646f96c26173/dqc_reference
[2024-01-25 18:41:07,031] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:41:07,032] [INFO] Task started: Prodigal
[2024-01-25 18:41:07,032] [INFO] Running command: gunzip -c /var/lib/cwl/stg1bcf6512-9300-4299-873f-ff56785a16a7/GCF_002607855.1_ASM260785v1_genomic.fna.gz | prodigal -d GCF_002607855.1_ASM260785v1_genomic.fna/cds.fna -a GCF_002607855.1_ASM260785v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:41:14,825] [INFO] Task succeeded: Prodigal
[2024-01-25 18:41:14,826] [INFO] Task started: HMMsearch
[2024-01-25 18:41:14,826] [INFO] Running command: hmmsearch --tblout GCF_002607855.1_ASM260785v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3a7c8d17-d794-4d46-afdc-646f96c26173/dqc_reference/reference_markers.hmm GCF_002607855.1_ASM260785v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:41:15,127] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:41:15,128] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1bcf6512-9300-4299-873f-ff56785a16a7/GCF_002607855.1_ASM260785v1_genomic.fna.gz]
[2024-01-25 18:41:15,163] [INFO] Query marker FASTA was written to GCF_002607855.1_ASM260785v1_genomic.fna/markers.fasta
[2024-01-25 18:41:15,164] [INFO] Task started: Blastn
[2024-01-25 18:41:15,164] [INFO] Running command: blastn -query GCF_002607855.1_ASM260785v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a7c8d17-d794-4d46-afdc-646f96c26173/dqc_reference/reference_markers.fasta -out GCF_002607855.1_ASM260785v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:41:15,730] [INFO] Task succeeded: Blastn
[2024-01-25 18:41:15,733] [INFO] Selected 8 target genomes.
[2024-01-25 18:41:15,733] [INFO] Target genome list was writen to GCF_002607855.1_ASM260785v1_genomic.fna/target_genomes.txt
[2024-01-25 18:41:15,737] [INFO] Task started: fastANI
[2024-01-25 18:41:15,737] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bcf6512-9300-4299-873f-ff56785a16a7/GCF_002607855.1_ASM260785v1_genomic.fna.gz --refList GCF_002607855.1_ASM260785v1_genomic.fna/target_genomes.txt --output GCF_002607855.1_ASM260785v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:41:20,991] [INFO] Task succeeded: fastANI
[2024-01-25 18:41:20,992] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3a7c8d17-d794-4d46-afdc-646f96c26173/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:41:20,992] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3a7c8d17-d794-4d46-afdc-646f96c26173/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:41:20,998] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:41:20,998] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:41:20,998] [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
Desulforamulus profundi	strain=Bs107	GCA_002607855.1	1383067	1383067	type	True	100.0	1092	1096	95	conclusive
Desulforamulus putei	strain=DSM 12395	GCA_900129195.1	74701	74701	type	True	86.6255	720	1096	95	below_threshold
Desulfotomaculum nigrificans	strain=DSM 574	GCA_000189755.3	1565	1565	type	True	80.1112	299	1096	95	below_threshold
Desulforamulus hydrothermalis	strain=Lam5	GCA_000315365.1	412895	412895	type	True	79.8932	415	1096	95	below_threshold
Desulforamulus hydrothermalis	strain=DSM 18033	GCA_900129895.1	412895	412895	type	True	79.6716	395	1096	95	below_threshold
Desulforamulus ruminis	strain=DSM 2154	GCA_000215085.1	1564	1564	type	True	78.4678	265	1096	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:41:20,999] [INFO] DFAST Taxonomy check result was written to GCF_002607855.1_ASM260785v1_genomic.fna/tc_result.tsv
[2024-01-25 18:41:21,000] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:41:21,000] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:41:21,000] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3a7c8d17-d794-4d46-afdc-646f96c26173/dqc_reference/checkm_data
[2024-01-25 18:41:21,001] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:41:21,035] [INFO] Task started: CheckM
[2024-01-25 18:41:21,035] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002607855.1_ASM260785v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002607855.1_ASM260785v1_genomic.fna/checkm_input GCF_002607855.1_ASM260785v1_genomic.fna/checkm_result
[2024-01-25 18:41:47,073] [INFO] Task succeeded: CheckM
[2024-01-25 18:41:47,074] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:41:47,093] [INFO] ===== Completeness check finished =====
[2024-01-25 18:41:47,093] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:41:47,094] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002607855.1_ASM260785v1_genomic.fna/markers.fasta)
[2024-01-25 18:41:47,094] [INFO] Task started: Blastn
[2024-01-25 18:41:47,094] [INFO] Running command: blastn -query GCF_002607855.1_ASM260785v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a7c8d17-d794-4d46-afdc-646f96c26173/dqc_reference/reference_markers_gtdb.fasta -out GCF_002607855.1_ASM260785v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:41:47,891] [INFO] Task succeeded: Blastn
[2024-01-25 18:41:47,896] [INFO] Selected 13 target genomes.
[2024-01-25 18:41:47,896] [INFO] Target genome list was writen to GCF_002607855.1_ASM260785v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:41:47,903] [INFO] Task started: fastANI
[2024-01-25 18:41:47,903] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bcf6512-9300-4299-873f-ff56785a16a7/GCF_002607855.1_ASM260785v1_genomic.fna.gz --refList GCF_002607855.1_ASM260785v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002607855.1_ASM260785v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:41:56,306] [INFO] Task succeeded: fastANI
[2024-01-25 18:41:56,314] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:41:56,314] [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_002607855.1	s__Desulfotomaculum profundi	100.0	1092	1096	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfotomaculaceae;g__Desulfotomaculum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900129195.1	s__Desulfotomaculum putei	86.6271	721	1096	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfotomaculaceae;g__Desulfotomaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000189755.2	s__Desulfotomaculum nigrificans	80.1369	300	1096	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfotomaculaceae;g__Desulfotomaculum	95.0	98.87	98.87	0.87	0.87	2	-
GCF_000315365.1	s__Desulfotomaculum hydrothermale	79.8932	415	1096	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfotomaculaceae;g__Desulfotomaculum	95.0	99.95	99.95	1.00	1.00	2	-
GCF_002005145.1	s__Desulfotomaculum ferrireducens	78.648	259	1096	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfotomaculaceae;g__Desulfotomaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000215085.1	s__Desulfotomaculum ruminis	78.4869	265	1096	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfotomaculaceae;g__Desulfotomaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142375.1	s__Desulfotomaculum aeronauticum	78.1464	235	1096	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfotomaculaceae;g__Desulfotomaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000961585.1	s__BRHc4a sp000961585	77.9809	51	1096	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfocucumaceae;g__BRHc4a	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000010565.1	s__Pelotomaculum thermopropionicum	77.3614	58	1096	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Pelotomaculaceae;g__Pelotomaculum	95.0	98.96	98.96	0.94	0.94	2	-
GCF_003627965.1	s__Desulfofundulus salinum	77.073	62	1096	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfovirgulaceae;g__Desulfofundulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001655685.1	s__Desulfotomaculum_G copahuensis	76.6862	58	1096	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	-
--------------------------------------------------------------------------------
[2024-01-25 18:41:56,315] [INFO] GTDB search result was written to GCF_002607855.1_ASM260785v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:41:56,316] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:41:56,318] [INFO] DFAST_QC result json was written to GCF_002607855.1_ASM260785v1_genomic.fna/dqc_result.json
[2024-01-25 18:41:56,318] [INFO] DFAST_QC completed!
[2024-01-25 18:41:56,318] [INFO] Total running time: 0h0m50s