[2024-01-24 15:32:03,828] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:32:03,829] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:32:03,830] [INFO] DQC Reference Directory: /var/lib/cwl/stg69fdd80f-b577-4aa7-b4e8-615d8b350a87/dqc_reference
[2024-01-24 15:32:05,065] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:32:05,066] [INFO] Task started: Prodigal
[2024-01-24 15:32:05,067] [INFO] Running command: gunzip -c /var/lib/cwl/stgbe3d89c8-ed1b-4a74-a1a8-d2a867e5d218/GCF_002149925.1_ASM214992v1_genomic.fna.gz | prodigal -d GCF_002149925.1_ASM214992v1_genomic.fna/cds.fna -a GCF_002149925.1_ASM214992v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:32:14,842] [INFO] Task succeeded: Prodigal
[2024-01-24 15:32:14,843] [INFO] Task started: HMMsearch
[2024-01-24 15:32:14,843] [INFO] Running command: hmmsearch --tblout GCF_002149925.1_ASM214992v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69fdd80f-b577-4aa7-b4e8-615d8b350a87/dqc_reference/reference_markers.hmm GCF_002149925.1_ASM214992v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:32:15,096] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:32:15,098] [INFO] Found 6/6 markers.
[2024-01-24 15:32:15,156] [INFO] Query marker FASTA was written to GCF_002149925.1_ASM214992v1_genomic.fna/markers.fasta
[2024-01-24 15:32:15,156] [INFO] Task started: Blastn
[2024-01-24 15:32:15,157] [INFO] Running command: blastn -query GCF_002149925.1_ASM214992v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg69fdd80f-b577-4aa7-b4e8-615d8b350a87/dqc_reference/reference_markers.fasta -out GCF_002149925.1_ASM214992v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:32:15,807] [INFO] Task succeeded: Blastn
[2024-01-24 15:32:15,811] [INFO] Selected 29 target genomes.
[2024-01-24 15:32:15,811] [INFO] Target genome list was writen to GCF_002149925.1_ASM214992v1_genomic.fna/target_genomes.txt
[2024-01-24 15:32:15,825] [INFO] Task started: fastANI
[2024-01-24 15:32:15,825] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe3d89c8-ed1b-4a74-a1a8-d2a867e5d218/GCF_002149925.1_ASM214992v1_genomic.fna.gz --refList GCF_002149925.1_ASM214992v1_genomic.fna/target_genomes.txt --output GCF_002149925.1_ASM214992v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:32:36,225] [INFO] Task succeeded: fastANI
[2024-01-24 15:32:36,226] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69fdd80f-b577-4aa7-b4e8-615d8b350a87/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:32:36,226] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69fdd80f-b577-4aa7-b4e8-615d8b350a87/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:32:36,233] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:32:36,233] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:32:36,233] [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
Thioflexithrix psekupsensis	strain=D3	GCA_002149925.1	1570016	1570016	type	True	100.0	1309	1310	95	conclusive
Beggiatoa leptomitoformis	strain=D-402	GCA_001305575.3	288004	288004	neotype	True	76.6852	72	1310	95	below_threshold
Beggiatoa alba	strain=B18LD	GCA_000245015.1	1022	1022	suspected-type	True	76.2235	82	1310	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:32:36,235] [INFO] DFAST Taxonomy check result was written to GCF_002149925.1_ASM214992v1_genomic.fna/tc_result.tsv
[2024-01-24 15:32:36,235] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:32:36,236] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:32:36,236] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69fdd80f-b577-4aa7-b4e8-615d8b350a87/dqc_reference/checkm_data
[2024-01-24 15:32:36,237] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:32:36,278] [INFO] Task started: CheckM
[2024-01-24 15:32:36,278] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002149925.1_ASM214992v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002149925.1_ASM214992v1_genomic.fna/checkm_input GCF_002149925.1_ASM214992v1_genomic.fna/checkm_result
[2024-01-24 15:33:10,000] [INFO] Task succeeded: CheckM
[2024-01-24 15:33:10,001] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:33:10,024] [INFO] ===== Completeness check finished =====
[2024-01-24 15:33:10,024] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:33:10,024] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002149925.1_ASM214992v1_genomic.fna/markers.fasta)
[2024-01-24 15:33:10,025] [INFO] Task started: Blastn
[2024-01-24 15:33:10,025] [INFO] Running command: blastn -query GCF_002149925.1_ASM214992v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg69fdd80f-b577-4aa7-b4e8-615d8b350a87/dqc_reference/reference_markers_gtdb.fasta -out GCF_002149925.1_ASM214992v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:33:11,007] [INFO] Task succeeded: Blastn
[2024-01-24 15:33:11,012] [INFO] Selected 26 target genomes.
[2024-01-24 15:33:11,012] [INFO] Target genome list was writen to GCF_002149925.1_ASM214992v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:33:11,144] [INFO] Task started: fastANI
[2024-01-24 15:33:11,145] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe3d89c8-ed1b-4a74-a1a8-d2a867e5d218/GCF_002149925.1_ASM214992v1_genomic.fna.gz --refList GCF_002149925.1_ASM214992v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002149925.1_ASM214992v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:33:28,891] [INFO] Task succeeded: fastANI
[2024-01-24 15:33:28,903] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:33:28,903] [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_002149925.1	s__Thioflexothrix psekupsii	100.0	1308	1310	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Beggiatoales;f__Beggiatoaceae;g__Thioflexothrix	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001305575.3	s__Beggiatoa leptomitoformis	76.6799	72	1310	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Beggiatoales;f__Beggiatoaceae;g__Beggiatoa	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000245015.1	s__Beggiatoa alba	76.2813	78	1310	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Beggiatoales;f__Beggiatoaceae;g__Beggiatoa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003245895.1	s__SZUA-411 sp003245895	76.2214	155	1310	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Beggiatoales;f__Beggiatoaceae;g__SZUA-411	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012032555.1	s__Thioploca sp012032555	76.1242	52	1310	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Beggiatoales;f__Beggiatoaceae;g__Thioploca	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744725.1	s__BB20 sp016744725	75.7723	61	1310	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Beggiatoales;f__Beggiatoaceae;g__BB20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002085445.1	s__UBA10656 sp002085445	75.2805	54	1310	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Beggiatoales;f__Beggiatoaceae;g__UBA10656	95.0	99.66	99.66	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:33:28,905] [INFO] GTDB search result was written to GCF_002149925.1_ASM214992v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:33:28,906] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:33:28,908] [INFO] DFAST_QC result json was written to GCF_002149925.1_ASM214992v1_genomic.fna/dqc_result.json
[2024-01-24 15:33:28,908] [INFO] DFAST_QC completed!
[2024-01-24 15:33:28,908] [INFO] Total running time: 0h1m25s