[2024-01-24 13:58:25,701] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:25,703] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:25,703] [INFO] DQC Reference Directory: /var/lib/cwl/stg85157958-1b38-466e-b083-96d6543c5da6/dqc_reference
[2024-01-24 13:58:27,023] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:27,024] [INFO] Task started: Prodigal
[2024-01-24 13:58:27,024] [INFO] Running command: gunzip -c /var/lib/cwl/stg6e0484d3-0d8b-4644-8fb2-b04ee76c5267/GCF_900156285.1_IMG-taxon_2681812893_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900156285.1_IMG-taxon_2681812893_annotated_assembly_genomic.fna/cds.fna -a GCF_900156285.1_IMG-taxon_2681812893_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:32,224] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:32,224] [INFO] Task started: HMMsearch
[2024-01-24 13:58:32,224] [INFO] Running command: hmmsearch --tblout GCF_900156285.1_IMG-taxon_2681812893_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg85157958-1b38-466e-b083-96d6543c5da6/dqc_reference/reference_markers.hmm GCF_900156285.1_IMG-taxon_2681812893_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:32,550] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:32,552] [INFO] Found 6/6 markers.
[2024-01-24 13:58:32,584] [INFO] Query marker FASTA was written to GCF_900156285.1_IMG-taxon_2681812893_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:58:32,584] [INFO] Task started: Blastn
[2024-01-24 13:58:32,585] [INFO] Running command: blastn -query GCF_900156285.1_IMG-taxon_2681812893_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg85157958-1b38-466e-b083-96d6543c5da6/dqc_reference/reference_markers.fasta -out GCF_900156285.1_IMG-taxon_2681812893_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:33,195] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:33,198] [INFO] Selected 16 target genomes.
[2024-01-24 13:58:33,198] [INFO] Target genome list was writen to GCF_900156285.1_IMG-taxon_2681812893_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:58:33,207] [INFO] Task started: fastANI
[2024-01-24 13:58:33,207] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e0484d3-0d8b-4644-8fb2-b04ee76c5267/GCF_900156285.1_IMG-taxon_2681812893_annotated_assembly_genomic.fna.gz --refList GCF_900156285.1_IMG-taxon_2681812893_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900156285.1_IMG-taxon_2681812893_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:41,240] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:41,240] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg85157958-1b38-466e-b083-96d6543c5da6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:41,241] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg85157958-1b38-466e-b083-96d6543c5da6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:41,248] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:41,248] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:41,248] [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
Halanaerobium kushneri	strain=ATCC 700103	GCA_900156285.1	56779	56779	type	True	100.0	1047	1047	95	conclusive
Halanaerobium congolense	strain=DSMZ 11287	GCA_004366375.1	54121	54121	type	True	81.2189	483	1047	95	below_threshold
Halanaerobium saccharolyticum subsp. saccharolyticum	strain=type strain:DSM 6643	GCA_000350165.1	267736	43595	type	True	80.4998	486	1047	95	below_threshold
Halanaerobium praevalens	strain=DSM 2228	GCA_000165465.1	2331	2331	type	True	79.5599	365	1047	95	below_threshold
Halanaerobium salsuginis	strain=ATCC 51327	GCA_900114545.1	29563	29563	type	True	78.9194	335	1047	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:41,249] [INFO] DFAST Taxonomy check result was written to GCF_900156285.1_IMG-taxon_2681812893_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:58:41,250] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:41,250] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:41,250] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg85157958-1b38-466e-b083-96d6543c5da6/dqc_reference/checkm_data
[2024-01-24 13:58:41,251] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:41,305] [INFO] Task started: CheckM
[2024-01-24 13:58:41,305] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900156285.1_IMG-taxon_2681812893_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900156285.1_IMG-taxon_2681812893_annotated_assembly_genomic.fna/checkm_input GCF_900156285.1_IMG-taxon_2681812893_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:59:04,957] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:04,959] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:04,981] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:04,981] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:04,982] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900156285.1_IMG-taxon_2681812893_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:59:04,982] [INFO] Task started: Blastn
[2024-01-24 13:59:04,982] [INFO] Running command: blastn -query GCF_900156285.1_IMG-taxon_2681812893_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg85157958-1b38-466e-b083-96d6543c5da6/dqc_reference/reference_markers_gtdb.fasta -out GCF_900156285.1_IMG-taxon_2681812893_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:05,755] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:05,759] [INFO] Selected 9 target genomes.
[2024-01-24 13:59:05,759] [INFO] Target genome list was writen to GCF_900156285.1_IMG-taxon_2681812893_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:05,768] [INFO] Task started: fastANI
[2024-01-24 13:59:05,768] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e0484d3-0d8b-4644-8fb2-b04ee76c5267/GCF_900156285.1_IMG-taxon_2681812893_annotated_assembly_genomic.fna.gz --refList GCF_900156285.1_IMG-taxon_2681812893_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900156285.1_IMG-taxon_2681812893_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:11,320] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:11,332] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:11,332] [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_900156285.1	s__Halanaerobium kushneri	100.0	1047	1047	d__Bacteria;p__Firmicutes_F;c__Halanaerobiia;o__Halanaerobiales;f__Halanaerobiaceae;g__Halanaerobium	95.0	97.73	97.73	0.83	0.83	2	conclusive
GCA_003070825.1	s__Halanaerobium sp003070825	84.6888	470	1047	d__Bacteria;p__Firmicutes_F;c__Halanaerobiia;o__Halanaerobiales;f__Halanaerobiaceae;g__Halanaerobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053565.1	s__Halanaerobium saccharolyticum_B	84.114	710	1047	d__Bacteria;p__Firmicutes_F;c__Halanaerobiia;o__Halanaerobiales;f__Halanaerobiaceae;g__Halanaerobium	95.0	96.03	96.03	0.86	0.86	2	-
GCF_003259895.1	s__Halanaerobium saccharolyticum_A	81.8056	643	1047	d__Bacteria;p__Firmicutes_F;c__Halanaerobiia;o__Halanaerobiales;f__Halanaerobiaceae;g__Halanaerobium	95.0	100.00	99.99	0.99	0.99	3	-
GCF_004362045.1	s__Halanaerobium saccharolyticum_C	81.7044	661	1047	d__Bacteria;p__Firmicutes_F;c__Halanaerobiia;o__Halanaerobiales;f__Halanaerobiaceae;g__Halanaerobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004366375.1	s__Halanaerobium congolense	81.2334	481	1047	d__Bacteria;p__Firmicutes_F;c__Halanaerobiia;o__Halanaerobiales;f__Halanaerobiaceae;g__Halanaerobium	95.0	97.80	95.58	0.84	0.73	19	-
GCF_000350165.1	s__Halanaerobium saccharolyticum	80.5017	485	1047	d__Bacteria;p__Firmicutes_F;c__Halanaerobiia;o__Halanaerobiales;f__Halanaerobiaceae;g__Halanaerobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000165465.1	s__Halanaerobium praevalens	79.5618	364	1047	d__Bacteria;p__Firmicutes_F;c__Halanaerobiia;o__Halanaerobiales;f__Halanaerobiaceae;g__Halanaerobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:11,334] [INFO] GTDB search result was written to GCF_900156285.1_IMG-taxon_2681812893_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:11,334] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:11,337] [INFO] DFAST_QC result json was written to GCF_900156285.1_IMG-taxon_2681812893_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:59:11,337] [INFO] DFAST_QC completed!
[2024-01-24 13:59:11,337] [INFO] Total running time: 0h0m46s