[2024-01-25 18:54:20,633] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:54:20,635] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:54:20,635] [INFO] DQC Reference Directory: /var/lib/cwl/stg5cfa8dae-f429-414d-8ebb-06acab8eccdd/dqc_reference
[2024-01-25 18:54:21,795] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:54:21,796] [INFO] Task started: Prodigal
[2024-01-25 18:54:21,796] [INFO] Running command: gunzip -c /var/lib/cwl/stg17b7ca1e-4a0e-4eec-8e54-5bba3d7ad64d/GCF_000178115.2_ASM17811v2_genomic.fna.gz | prodigal -d GCF_000178115.2_ASM17811v2_genomic.fna/cds.fna -a GCF_000178115.2_ASM17811v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:54:30,355] [INFO] Task succeeded: Prodigal
[2024-01-25 18:54:30,356] [INFO] Task started: HMMsearch
[2024-01-25 18:54:30,356] [INFO] Running command: hmmsearch --tblout GCF_000178115.2_ASM17811v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5cfa8dae-f429-414d-8ebb-06acab8eccdd/dqc_reference/reference_markers.hmm GCF_000178115.2_ASM17811v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:54:30,561] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:54:30,562] [INFO] Found 6/6 markers.
[2024-01-25 18:54:30,590] [INFO] Query marker FASTA was written to GCF_000178115.2_ASM17811v2_genomic.fna/markers.fasta
[2024-01-25 18:54:30,591] [INFO] Task started: Blastn
[2024-01-25 18:54:30,591] [INFO] Running command: blastn -query GCF_000178115.2_ASM17811v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg5cfa8dae-f429-414d-8ebb-06acab8eccdd/dqc_reference/reference_markers.fasta -out GCF_000178115.2_ASM17811v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:54:31,265] [INFO] Task succeeded: Blastn
[2024-01-25 18:54:31,268] [INFO] Selected 20 target genomes.
[2024-01-25 18:54:31,268] [INFO] Target genome list was writen to GCF_000178115.2_ASM17811v2_genomic.fna/target_genomes.txt
[2024-01-25 18:54:31,298] [INFO] Task started: fastANI
[2024-01-25 18:54:31,298] [INFO] Running command: fastANI --query /var/lib/cwl/stg17b7ca1e-4a0e-4eec-8e54-5bba3d7ad64d/GCF_000178115.2_ASM17811v2_genomic.fna.gz --refList GCF_000178115.2_ASM17811v2_genomic.fna/target_genomes.txt --output GCF_000178115.2_ASM17811v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:54:42,699] [INFO] Task succeeded: fastANI
[2024-01-25 18:54:42,699] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5cfa8dae-f429-414d-8ebb-06acab8eccdd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:54:42,700] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5cfa8dae-f429-414d-8ebb-06acab8eccdd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:54:42,704] [INFO] Found 4 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:54:42,704] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:54:42,704] [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
Ethanoligenens harbinense	strain=YUAN-3	GCA_000178115.2	253239	253239	type	True	100.0	1002	1002	95	conclusive
Ethanoligenens harbinense	strain=YUAN-3	GCA_003020045.1	253239	253239	type	True	99.9972	998	1002	95	conclusive
Anaerotruncus massiliensis	strain=AT3	GCA_900199635.1	1673720	1673720	type	True	77.2409	69	1002	95	below_threshold
Ligaoa zhengdingensis	strain=NSJ-31	GCA_014384885.1	2763658	2763658	type	True	76.6576	66	1002	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:54:42,705] [INFO] DFAST Taxonomy check result was written to GCF_000178115.2_ASM17811v2_genomic.fna/tc_result.tsv
[2024-01-25 18:54:42,706] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:54:42,706] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:54:42,706] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5cfa8dae-f429-414d-8ebb-06acab8eccdd/dqc_reference/checkm_data
[2024-01-25 18:54:42,707] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:54:42,739] [INFO] Task started: CheckM
[2024-01-25 18:54:42,739] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000178115.2_ASM17811v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000178115.2_ASM17811v2_genomic.fna/checkm_input GCF_000178115.2_ASM17811v2_genomic.fna/checkm_result
[2024-01-25 18:55:10,694] [INFO] Task succeeded: CheckM
[2024-01-25 18:55:10,695] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:55:10,709] [INFO] ===== Completeness check finished =====
[2024-01-25 18:55:10,709] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:55:10,710] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000178115.2_ASM17811v2_genomic.fna/markers.fasta)
[2024-01-25 18:55:10,710] [INFO] Task started: Blastn
[2024-01-25 18:55:10,710] [INFO] Running command: blastn -query GCF_000178115.2_ASM17811v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg5cfa8dae-f429-414d-8ebb-06acab8eccdd/dqc_reference/reference_markers_gtdb.fasta -out GCF_000178115.2_ASM17811v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:55:11,888] [INFO] Task succeeded: Blastn
[2024-01-25 18:55:11,891] [INFO] Selected 29 target genomes.
[2024-01-25 18:55:11,891] [INFO] Target genome list was writen to GCF_000178115.2_ASM17811v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:55:11,928] [INFO] Task started: fastANI
[2024-01-25 18:55:11,928] [INFO] Running command: fastANI --query /var/lib/cwl/stg17b7ca1e-4a0e-4eec-8e54-5bba3d7ad64d/GCF_000178115.2_ASM17811v2_genomic.fna.gz --refList GCF_000178115.2_ASM17811v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000178115.2_ASM17811v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:55:23,652] [INFO] Task succeeded: fastANI
[2024-01-25 18:55:23,656] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:55:23,656] [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_000178115.2	s__Ethanoligenens harbinense	100.0	1001	1002	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ethanoligenenaceae;g__Ethanoligenens	95.0	99.99	99.99	1.00	1.00	5	conclusive
GCF_900199635.1	s__Anaerotruncus massiliensis	77.0007	68	1002	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	98.56	98.01	0.95	0.93	6	-
GCA_014384885.1	s__Hydrogenoanaerobacterium sp014384885	76.709	65	1002	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Hydrogenoanaerobacterium	95.0	98.59	98.59	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:55:23,658] [INFO] GTDB search result was written to GCF_000178115.2_ASM17811v2_genomic.fna/result_gtdb.tsv
[2024-01-25 18:55:23,658] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:55:23,660] [INFO] DFAST_QC result json was written to GCF_000178115.2_ASM17811v2_genomic.fna/dqc_result.json
[2024-01-25 18:55:23,660] [INFO] DFAST_QC completed!
[2024-01-25 18:55:23,660] [INFO] Total running time: 0h1m3s