[2024-01-24 15:02:03,503] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:03,505] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:03,505] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d2cf282-0d69-485b-a103-739a69d63d66/dqc_reference
[2024-01-24 15:02:06,130] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:06,131] [INFO] Task started: Prodigal
[2024-01-24 15:02:06,131] [INFO] Running command: gunzip -c /var/lib/cwl/stg11b1f3d6-c677-488e-bf60-31656bb95434/GCF_003020045.1_ASM302004v1_genomic.fna.gz | prodigal -d GCF_003020045.1_ASM302004v1_genomic.fna/cds.fna -a GCF_003020045.1_ASM302004v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:15,851] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:15,851] [INFO] Task started: HMMsearch
[2024-01-24 15:02:15,851] [INFO] Running command: hmmsearch --tblout GCF_003020045.1_ASM302004v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d2cf282-0d69-485b-a103-739a69d63d66/dqc_reference/reference_markers.hmm GCF_003020045.1_ASM302004v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:16,120] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:16,122] [INFO] Found 6/6 markers.
[2024-01-24 15:02:16,151] [INFO] Query marker FASTA was written to GCF_003020045.1_ASM302004v1_genomic.fna/markers.fasta
[2024-01-24 15:02:16,152] [INFO] Task started: Blastn
[2024-01-24 15:02:16,152] [INFO] Running command: blastn -query GCF_003020045.1_ASM302004v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d2cf282-0d69-485b-a103-739a69d63d66/dqc_reference/reference_markers.fasta -out GCF_003020045.1_ASM302004v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:16,904] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:16,911] [INFO] Selected 20 target genomes.
[2024-01-24 15:02:16,912] [INFO] Target genome list was writen to GCF_003020045.1_ASM302004v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:16,937] [INFO] Task started: fastANI
[2024-01-24 15:02:16,937] [INFO] Running command: fastANI --query /var/lib/cwl/stg11b1f3d6-c677-488e-bf60-31656bb95434/GCF_003020045.1_ASM302004v1_genomic.fna.gz --refList GCF_003020045.1_ASM302004v1_genomic.fna/target_genomes.txt --output GCF_003020045.1_ASM302004v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:27,775] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:27,776] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d2cf282-0d69-485b-a103-739a69d63d66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:27,776] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d2cf282-0d69-485b-a103-739a69d63d66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:27,781] [INFO] Found 4 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:02:27,781] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:02:27,781] [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_003020045.1	253239	253239	type	True	100.0	1003	1003	95	conclusive
Ethanoligenens harbinense	strain=YUAN-3	GCA_000178115.2	253239	253239	type	True	99.9969	1001	1003	95	conclusive
Anaerotruncus massiliensis	strain=AT3	GCA_900199635.1	1673720	1673720	type	True	77.3177	68	1003	95	below_threshold
Ligaoa zhengdingensis	strain=NSJ-31	GCA_014384885.1	2763658	2763658	type	True	76.8812	60	1003	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:27,783] [INFO] DFAST Taxonomy check result was written to GCF_003020045.1_ASM302004v1_genomic.fna/tc_result.tsv
[2024-01-24 15:02:27,784] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:27,784] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:27,784] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d2cf282-0d69-485b-a103-739a69d63d66/dqc_reference/checkm_data
[2024-01-24 15:02:27,785] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:27,814] [INFO] Task started: CheckM
[2024-01-24 15:02:27,815] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003020045.1_ASM302004v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003020045.1_ASM302004v1_genomic.fna/checkm_input GCF_003020045.1_ASM302004v1_genomic.fna/checkm_result
[2024-01-24 15:03:01,477] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:01,478] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:01,497] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:01,497] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:01,498] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003020045.1_ASM302004v1_genomic.fna/markers.fasta)
[2024-01-24 15:03:01,498] [INFO] Task started: Blastn
[2024-01-24 15:03:01,498] [INFO] Running command: blastn -query GCF_003020045.1_ASM302004v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d2cf282-0d69-485b-a103-739a69d63d66/dqc_reference/reference_markers_gtdb.fasta -out GCF_003020045.1_ASM302004v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:02,786] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:02,790] [INFO] Selected 29 target genomes.
[2024-01-24 15:03:02,790] [INFO] Target genome list was writen to GCF_003020045.1_ASM302004v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:02,811] [INFO] Task started: fastANI
[2024-01-24 15:03:02,812] [INFO] Running command: fastANI --query /var/lib/cwl/stg11b1f3d6-c677-488e-bf60-31656bb95434/GCF_003020045.1_ASM302004v1_genomic.fna.gz --refList GCF_003020045.1_ASM302004v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003020045.1_ASM302004v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:03:14,552] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:14,557] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:03:14,557] [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	99.9969	1001	1003	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	77.3237	68	1003	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	76.8227	61	1003	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Hydrogenoanaerobacterium	95.0	98.59	98.59	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:03:14,559] [INFO] GTDB search result was written to GCF_003020045.1_ASM302004v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:03:14,560] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:03:14,563] [INFO] DFAST_QC result json was written to GCF_003020045.1_ASM302004v1_genomic.fna/dqc_result.json
[2024-01-24 15:03:14,563] [INFO] DFAST_QC completed!
[2024-01-24 15:03:14,563] [INFO] Total running time: 0h1m11s