[2024-01-24 12:39:41,712] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:39:41,713] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:39:41,714] [INFO] DQC Reference Directory: /var/lib/cwl/stg45e65d64-d25f-46c9-8717-ae87a0953a18/dqc_reference
[2024-01-24 12:39:43,217] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:39:43,218] [INFO] Task started: Prodigal
[2024-01-24 12:39:43,218] [INFO] Running command: gunzip -c /var/lib/cwl/stg03bc128d-cd16-4565-b6e5-cbf7e3c057b3/GCF_001267435.1_ASM126743v1_genomic.fna.gz | prodigal -d GCF_001267435.1_ASM126743v1_genomic.fna/cds.fna -a GCF_001267435.1_ASM126743v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:39:49,947] [INFO] Task succeeded: Prodigal
[2024-01-24 12:39:49,948] [INFO] Task started: HMMsearch
[2024-01-24 12:39:49,948] [INFO] Running command: hmmsearch --tblout GCF_001267435.1_ASM126743v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg45e65d64-d25f-46c9-8717-ae87a0953a18/dqc_reference/reference_markers.hmm GCF_001267435.1_ASM126743v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:39:50,205] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:39:50,206] [INFO] Found 6/6 markers.
[2024-01-24 12:39:50,242] [INFO] Query marker FASTA was written to GCF_001267435.1_ASM126743v1_genomic.fna/markers.fasta
[2024-01-24 12:39:50,242] [INFO] Task started: Blastn
[2024-01-24 12:39:50,243] [INFO] Running command: blastn -query GCF_001267435.1_ASM126743v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45e65d64-d25f-46c9-8717-ae87a0953a18/dqc_reference/reference_markers.fasta -out GCF_001267435.1_ASM126743v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:50,831] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:50,835] [INFO] Selected 10 target genomes.
[2024-01-24 12:39:50,836] [INFO] Target genome list was writen to GCF_001267435.1_ASM126743v1_genomic.fna/target_genomes.txt
[2024-01-24 12:39:50,840] [INFO] Task started: fastANI
[2024-01-24 12:39:50,840] [INFO] Running command: fastANI --query /var/lib/cwl/stg03bc128d-cd16-4565-b6e5-cbf7e3c057b3/GCF_001267435.1_ASM126743v1_genomic.fna.gz --refList GCF_001267435.1_ASM126743v1_genomic.fna/target_genomes.txt --output GCF_001267435.1_ASM126743v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:39:56,324] [INFO] Task succeeded: fastANI
[2024-01-24 12:39:56,324] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg45e65d64-d25f-46c9-8717-ae87a0953a18/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:39:56,325] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg45e65d64-d25f-46c9-8717-ae87a0953a18/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:39:56,332] [INFO] Found 7 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:39:56,332] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:39:56,333] [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
Moorella thermoacetica	strain=DSM 2955	GCA_001267435.1	1525	1525	type	True	100.0	873	874	95	conclusive
Moorella thermoacetica	strain=ATCC 35608	GCA_008121885.1	1525	1525	type	True	99.9783	858	874	95	conclusive
Moorella thermoacetica	strain=DSM 521	GCA_001267405.1	1525	1525	type	True	99.9254	840	874	95	conclusive
Moorella mulderi	strain=DSM 14980	GCA_001594015.1	202604	202604	type	True	81.7438	510	874	95	below_threshold
Moorella stamsii	strain=DSM 26217	GCA_002995805.1	1266720	1266720	type	True	81.124	481	874	95	below_threshold
Moorella glycerini	strain=DSM 11254	GCA_009735625.1	55779	55779	type	True	81.0894	519	874	95	below_threshold
Moorella humiferrea	strain=DSM 23265	GCA_002995755.1	676965	676965	type	True	80.1695	329	874	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:39:56,334] [INFO] DFAST Taxonomy check result was written to GCF_001267435.1_ASM126743v1_genomic.fna/tc_result.tsv
[2024-01-24 12:39:56,335] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:39:56,335] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:39:56,335] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg45e65d64-d25f-46c9-8717-ae87a0953a18/dqc_reference/checkm_data
[2024-01-24 12:39:56,336] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:39:56,366] [INFO] Task started: CheckM
[2024-01-24 12:39:56,366] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001267435.1_ASM126743v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001267435.1_ASM126743v1_genomic.fna/checkm_input GCF_001267435.1_ASM126743v1_genomic.fna/checkm_result
[2024-01-24 12:40:21,790] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:21,792] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:21,814] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:21,815] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:21,815] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001267435.1_ASM126743v1_genomic.fna/markers.fasta)
[2024-01-24 12:40:21,816] [INFO] Task started: Blastn
[2024-01-24 12:40:21,816] [INFO] Running command: blastn -query GCF_001267435.1_ASM126743v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45e65d64-d25f-46c9-8717-ae87a0953a18/dqc_reference/reference_markers_gtdb.fasta -out GCF_001267435.1_ASM126743v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:22,610] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:22,614] [INFO] Selected 12 target genomes.
[2024-01-24 12:40:22,614] [INFO] Target genome list was writen to GCF_001267435.1_ASM126743v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:40:23,220] [INFO] Task started: fastANI
[2024-01-24 12:40:23,221] [INFO] Running command: fastANI --query /var/lib/cwl/stg03bc128d-cd16-4565-b6e5-cbf7e3c057b3/GCF_001267435.1_ASM126743v1_genomic.fna.gz --refList GCF_001267435.1_ASM126743v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001267435.1_ASM126743v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:40:30,532] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:30,550] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:40:30,551] [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_001267405.1	s__Moorella thermoacetica	99.9254	840	874	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__Moorellales;f__Moorellaceae;g__Moorella	95.0	99.27	98.11	0.95	0.88	17	conclusive
GCF_001875325.1	s__Moorella thermoacetica_A	92.9336	653	874	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__Moorellales;f__Moorellaceae;g__Moorella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003116935.1	s__Moorella sp003116935	83.1586	618	874	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__Moorellales;f__Moorellaceae;g__Moorella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001594015.1	s__Moorella mulderi	81.7307	512	874	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__Moorellales;f__Moorellaceae;g__Moorella	95.265	N/A	N/A	N/A	N/A	1	-
GCF_006538365.1	s__Moorella sp006538365	81.6187	484	874	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__Moorellales;f__Moorellaceae;g__Moorella	95.0	99.18	99.18	0.87	0.87	2	-
GCF_002995805.1	s__Moorella stamsii	81.113	481	874	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__Moorellales;f__Moorellaceae;g__Moorella	95.265	99.99	99.99	0.99	0.99	2	-
GCF_009735625.1	s__Moorella glycerini	81.095	517	874	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__Moorellales;f__Moorellaceae;g__Moorella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002995755.1	s__Moorella humiferrea	80.1873	329	874	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__Moorellales;f__Moorellaceae;g__Moorella	95.0	97.49	97.49	0.85	0.85	2	-
GCA_002383405.1	s__Moorella sp002383405	78.7553	235	874	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__Moorellales;f__Moorellaceae;g__Moorella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012727745.1	s__JAAYGJ01 sp012727745	76.7469	59	874	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__Moorellales;f__Moorellaceae;g__JAAYGJ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:40:30,553] [INFO] GTDB search result was written to GCF_001267435.1_ASM126743v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:40:30,553] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:40:30,559] [INFO] DFAST_QC result json was written to GCF_001267435.1_ASM126743v1_genomic.fna/dqc_result.json
[2024-01-24 12:40:30,559] [INFO] DFAST_QC completed!
[2024-01-24 12:40:30,559] [INFO] Total running time: 0h0m49s