[2024-01-25 19:39:50,578] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:39:50,581] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:39:50,582] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d7480a5-47c1-484d-9d5a-a7835e7667c0/dqc_reference
[2024-01-25 19:39:51,742] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:39:51,745] [INFO] Task started: Prodigal
[2024-01-25 19:39:51,745] [INFO] Running command: gunzip -c /var/lib/cwl/stgf7066c7f-dca4-432d-a5b2-39dca87f9ddf/GCF_025567485.1_ASM2556748v1_genomic.fna.gz | prodigal -d GCF_025567485.1_ASM2556748v1_genomic.fna/cds.fna -a GCF_025567485.1_ASM2556748v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:39:56,354] [INFO] Task succeeded: Prodigal
[2024-01-25 19:39:56,355] [INFO] Task started: HMMsearch
[2024-01-25 19:39:56,355] [INFO] Running command: hmmsearch --tblout GCF_025567485.1_ASM2556748v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d7480a5-47c1-484d-9d5a-a7835e7667c0/dqc_reference/reference_markers.hmm GCF_025567485.1_ASM2556748v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:39:56,588] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:39:56,589] [INFO] Found 6/6 markers.
[2024-01-25 19:39:56,615] [INFO] Query marker FASTA was written to GCF_025567485.1_ASM2556748v1_genomic.fna/markers.fasta
[2024-01-25 19:39:56,615] [INFO] Task started: Blastn
[2024-01-25 19:39:56,615] [INFO] Running command: blastn -query GCF_025567485.1_ASM2556748v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d7480a5-47c1-484d-9d5a-a7835e7667c0/dqc_reference/reference_markers.fasta -out GCF_025567485.1_ASM2556748v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:39:57,193] [INFO] Task succeeded: Blastn
[2024-01-25 19:39:57,197] [INFO] Selected 14 target genomes.
[2024-01-25 19:39:57,197] [INFO] Target genome list was writen to GCF_025567485.1_ASM2556748v1_genomic.fna/target_genomes.txt
[2024-01-25 19:39:57,208] [INFO] Task started: fastANI
[2024-01-25 19:39:57,208] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7066c7f-dca4-432d-a5b2-39dca87f9ddf/GCF_025567485.1_ASM2556748v1_genomic.fna.gz --refList GCF_025567485.1_ASM2556748v1_genomic.fna/target_genomes.txt --output GCF_025567485.1_ASM2556748v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:40:02,884] [INFO] Task succeeded: fastANI
[2024-01-25 19:40:02,884] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d7480a5-47c1-484d-9d5a-a7835e7667c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:40:02,885] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d7480a5-47c1-484d-9d5a-a7835e7667c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:40:02,886] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:40:02,886] [INFO] The taxonomy check result is classified as 'no_hit'.
[2024-01-25 19:40:02,886] [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
--------------------------------------------------------------------------------
[2024-01-25 19:40:02,887] [INFO] DFAST Taxonomy check result was written to GCF_025567485.1_ASM2556748v1_genomic.fna/tc_result.tsv
[2024-01-25 19:40:02,888] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:40:02,888] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:40:02,888] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d7480a5-47c1-484d-9d5a-a7835e7667c0/dqc_reference/checkm_data
[2024-01-25 19:40:02,890] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:40:02,918] [INFO] Task started: CheckM
[2024-01-25 19:40:02,919] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025567485.1_ASM2556748v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025567485.1_ASM2556748v1_genomic.fna/checkm_input GCF_025567485.1_ASM2556748v1_genomic.fna/checkm_result
[2024-01-25 19:40:22,513] [INFO] Task succeeded: CheckM
[2024-01-25 19:40:22,514] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:40:22,529] [INFO] ===== Completeness check finished =====
[2024-01-25 19:40:22,529] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:40:22,530] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025567485.1_ASM2556748v1_genomic.fna/markers.fasta)
[2024-01-25 19:40:22,530] [INFO] Task started: Blastn
[2024-01-25 19:40:22,530] [INFO] Running command: blastn -query GCF_025567485.1_ASM2556748v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d7480a5-47c1-484d-9d5a-a7835e7667c0/dqc_reference/reference_markers_gtdb.fasta -out GCF_025567485.1_ASM2556748v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:40:23,491] [INFO] Task succeeded: Blastn
[2024-01-25 19:40:23,494] [INFO] Selected 18 target genomes.
[2024-01-25 19:40:23,494] [INFO] Target genome list was writen to GCF_025567485.1_ASM2556748v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:40:23,523] [INFO] Task started: fastANI
[2024-01-25 19:40:23,524] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7066c7f-dca4-432d-a5b2-39dca87f9ddf/GCF_025567485.1_ASM2556748v1_genomic.fna.gz --refList GCF_025567485.1_ASM2556748v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025567485.1_ASM2556748v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:40:30,702] [INFO] Task succeeded: fastANI
[2024-01-25 19:40:30,709] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:40:30,710] [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
GCA_902362965.1	s__UBA1394 sp900066845	100.0	838	839	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UBA1394	95.0	98.61	98.18	0.90	0.86	6	conclusive
GCA_900554975.1	s__UBA1394 sp900554975	78.9293	142	839	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UBA1394	95.0	98.07	98.05	0.85	0.82	3	-
GCA_002305725.1	s__UBA1394 sp002305725	78.7772	190	839	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UBA1394	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588145.1	s__UBA1394 sp910588145	78.4539	211	839	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UBA1394	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015066715.1	s__UBA1394 sp015066715	78.1338	168	839	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UBA1394	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002438605.1	s__Ruminococcus sp002438605	77.7765	98	839	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	98.60	98.45	0.90	0.84	7	-
GCA_017416665.1	s__UBA1394 sp017416665	77.7344	80	839	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UBA1394	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905199285.1	s__Ruminococcus sp905199285	77.4131	74	839	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902796865.1	s__UBA1394 sp902796865	76.9031	93	839	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UBA1394	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902783235.1	s__UBA1394 sp902783235	76.0529	56	839	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UBA1394	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:40:30,711] [INFO] GTDB search result was written to GCF_025567485.1_ASM2556748v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:40:30,711] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:40:30,713] [INFO] DFAST_QC result json was written to GCF_025567485.1_ASM2556748v1_genomic.fna/dqc_result.json
[2024-01-25 19:40:30,713] [INFO] DFAST_QC completed!
[2024-01-25 19:40:30,713] [INFO] Total running time: 0h0m40s