[2024-01-24 13:33:41,353] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:33:41,354] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:33:41,354] [INFO] DQC Reference Directory: /var/lib/cwl/stg4743b57c-66e1-45b4-ae9d-368c91f29d0f/dqc_reference
[2024-01-24 13:33:42,663] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:33:42,664] [INFO] Task started: Prodigal
[2024-01-24 13:33:42,664] [INFO] Running command: gunzip -c /var/lib/cwl/stg98bfa072-702f-4dae-bc06-cf566f1ee336/GCF_900104455.1_IMG-taxon_2622736508_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900104455.1_IMG-taxon_2622736508_annotated_assembly_genomic.fna/cds.fna -a GCF_900104455.1_IMG-taxon_2622736508_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:33:55,360] [INFO] Task succeeded: Prodigal
[2024-01-24 13:33:55,361] [INFO] Task started: HMMsearch
[2024-01-24 13:33:55,361] [INFO] Running command: hmmsearch --tblout GCF_900104455.1_IMG-taxon_2622736508_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4743b57c-66e1-45b4-ae9d-368c91f29d0f/dqc_reference/reference_markers.hmm GCF_900104455.1_IMG-taxon_2622736508_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:33:55,660] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:33:55,661] [INFO] Found 6/6 markers.
[2024-01-24 13:33:55,700] [INFO] Query marker FASTA was written to GCF_900104455.1_IMG-taxon_2622736508_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:33:55,700] [INFO] Task started: Blastn
[2024-01-24 13:33:55,700] [INFO] Running command: blastn -query GCF_900104455.1_IMG-taxon_2622736508_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg4743b57c-66e1-45b4-ae9d-368c91f29d0f/dqc_reference/reference_markers.fasta -out GCF_900104455.1_IMG-taxon_2622736508_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:56,274] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:56,278] [INFO] Selected 19 target genomes.
[2024-01-24 13:33:56,278] [INFO] Target genome list was writen to GCF_900104455.1_IMG-taxon_2622736508_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:33:56,287] [INFO] Task started: fastANI
[2024-01-24 13:33:56,287] [INFO] Running command: fastANI --query /var/lib/cwl/stg98bfa072-702f-4dae-bc06-cf566f1ee336/GCF_900104455.1_IMG-taxon_2622736508_annotated_assembly_genomic.fna.gz --refList GCF_900104455.1_IMG-taxon_2622736508_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900104455.1_IMG-taxon_2622736508_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:34:10,070] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:10,071] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4743b57c-66e1-45b4-ae9d-368c91f29d0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:34:10,071] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4743b57c-66e1-45b4-ae9d-368c91f29d0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:34:10,076] [INFO] Found 3 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:34:10,076] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:34:10,076] [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
Dendrosporobacter quercicolus	strain=DSM 1736	GCA_900104455.1	146817	146817	type	True	100.0	1359	1362	95	conclusive
Dendrosporobacter quercicolus	strain=DSM 1736	GCA_013303165.1	146817	146817	type	True	99.9927	1354	1362	95	conclusive
Sporomusa sphaeroides	strain=DSM 2875	GCA_023660125.1	47679	47679	type	True	77.2524	114	1362	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:34:10,078] [INFO] DFAST Taxonomy check result was written to GCF_900104455.1_IMG-taxon_2622736508_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:34:10,078] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:34:10,078] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:34:10,079] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4743b57c-66e1-45b4-ae9d-368c91f29d0f/dqc_reference/checkm_data
[2024-01-24 13:34:10,080] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:34:10,120] [INFO] Task started: CheckM
[2024-01-24 13:34:10,120] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900104455.1_IMG-taxon_2622736508_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900104455.1_IMG-taxon_2622736508_annotated_assembly_genomic.fna/checkm_input GCF_900104455.1_IMG-taxon_2622736508_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:34:49,518] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:49,519] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:49,536] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:49,537] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:49,537] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900104455.1_IMG-taxon_2622736508_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:34:49,537] [INFO] Task started: Blastn
[2024-01-24 13:34:49,538] [INFO] Running command: blastn -query GCF_900104455.1_IMG-taxon_2622736508_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg4743b57c-66e1-45b4-ae9d-368c91f29d0f/dqc_reference/reference_markers_gtdb.fasta -out GCF_900104455.1_IMG-taxon_2622736508_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:50,257] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:50,261] [INFO] Selected 21 target genomes.
[2024-01-24 13:34:50,261] [INFO] Target genome list was writen to GCF_900104455.1_IMG-taxon_2622736508_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:50,325] [INFO] Task started: fastANI
[2024-01-24 13:34:50,325] [INFO] Running command: fastANI --query /var/lib/cwl/stg98bfa072-702f-4dae-bc06-cf566f1ee336/GCF_900104455.1_IMG-taxon_2622736508_annotated_assembly_genomic.fna.gz --refList GCF_900104455.1_IMG-taxon_2622736508_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900104455.1_IMG-taxon_2622736508_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:35:00,950] [INFO] Task succeeded: fastANI
[2024-01-24 13:35:00,961] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:35:00,961] [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_900104455.1	s__Dendrosporobacter quercicolus	100.0	1359	1362	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__DSM-1736;f__Dendrosporobacteraceae;g__Dendrosporobacter	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCA_003990955.1	s__Dendrosporobacter sp003990955	77.8691	286	1362	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__DSM-1736;f__Dendrosporobacteraceae;g__Dendrosporobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_012523975.1	s__JAAYSF01 sp012523975	76.8583	63	1362	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__JAAYSF01;f__JAAYSF01;g__JAAYSF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900476375.1	s__Lucifera butyrica	76.3487	91	1362	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__UPPP01;g__Lucifera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900542835.1	s__Anaerosporomusa sp900542835	76.3201	74	1362	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales_A;f__Acetonemaceae;g__Anaerosporomusa	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:35:00,963] [INFO] GTDB search result was written to GCF_900104455.1_IMG-taxon_2622736508_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:35:00,964] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:35:00,966] [INFO] DFAST_QC result json was written to GCF_900104455.1_IMG-taxon_2622736508_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:35:00,966] [INFO] DFAST_QC completed!
[2024-01-24 13:35:00,966] [INFO] Total running time: 0h1m20s