[2023-06-05 02:54:13,126] [INFO] DFAST_QC pipeline started.
[2023-06-05 02:54:13,128] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 02:54:13,128] [INFO] DQC Reference Directory: /var/lib/cwl/stg6185f5fd-8df7-4848-adc2-1b59d41f6c9d/dqc_reference
[2023-06-05 02:54:14,406] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 02:54:14,407] [INFO] Task started: Prodigal
[2023-06-05 02:54:14,408] [INFO] Running command: gunzip -c /var/lib/cwl/stg8019d1f0-08ce-4b13-80f9-1a0d8c39d0be/GCA_001604005.1_ASM160400v1_genomic.fna.gz | prodigal -d GCA_001604005.1_ASM160400v1_genomic.fna/cds.fna -a GCA_001604005.1_ASM160400v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 02:54:19,393] [INFO] Task succeeded: Prodigal
[2023-06-05 02:54:19,394] [INFO] Task started: HMMsearch
[2023-06-05 02:54:19,394] [INFO] Running command: hmmsearch --tblout GCA_001604005.1_ASM160400v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6185f5fd-8df7-4848-adc2-1b59d41f6c9d/dqc_reference/reference_markers.hmm GCA_001604005.1_ASM160400v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 02:54:19,625] [INFO] Task succeeded: HMMsearch
[2023-06-05 02:54:19,626] [INFO] Found 6/6 markers.
[2023-06-05 02:54:19,651] [INFO] Query marker FASTA was written to GCA_001604005.1_ASM160400v1_genomic.fna/markers.fasta
[2023-06-05 02:54:19,651] [INFO] Task started: Blastn
[2023-06-05 02:54:19,651] [INFO] Running command: blastn -query GCA_001604005.1_ASM160400v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6185f5fd-8df7-4848-adc2-1b59d41f6c9d/dqc_reference/reference_markers.fasta -out GCA_001604005.1_ASM160400v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:54:20,235] [INFO] Task succeeded: Blastn
[2023-06-05 02:54:20,240] [INFO] Selected 16 target genomes.
[2023-06-05 02:54:20,240] [INFO] Target genome list was writen to GCA_001604005.1_ASM160400v1_genomic.fna/target_genomes.txt
[2023-06-05 02:54:20,289] [INFO] Task started: fastANI
[2023-06-05 02:54:20,290] [INFO] Running command: fastANI --query /var/lib/cwl/stg8019d1f0-08ce-4b13-80f9-1a0d8c39d0be/GCA_001604005.1_ASM160400v1_genomic.fna.gz --refList GCA_001604005.1_ASM160400v1_genomic.fna/target_genomes.txt --output GCA_001604005.1_ASM160400v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 02:54:32,044] [INFO] Task succeeded: fastANI
[2023-06-05 02:54:32,045] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6185f5fd-8df7-4848-adc2-1b59d41f6c9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 02:54:32,045] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6185f5fd-8df7-4848-adc2-1b59d41f6c9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 02:54:32,047] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 02:54:32,047] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 02:54:32,047] [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
--------------------------------------------------------------------------------
[2023-06-05 02:54:32,049] [INFO] DFAST Taxonomy check result was written to GCA_001604005.1_ASM160400v1_genomic.fna/tc_result.tsv
[2023-06-05 02:54:32,049] [INFO] ===== Taxonomy check completed =====
[2023-06-05 02:54:32,050] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 02:54:32,050] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6185f5fd-8df7-4848-adc2-1b59d41f6c9d/dqc_reference/checkm_data
[2023-06-05 02:54:32,053] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 02:54:32,076] [INFO] Task started: CheckM
[2023-06-05 02:54:32,076] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_001604005.1_ASM160400v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_001604005.1_ASM160400v1_genomic.fna/checkm_input GCA_001604005.1_ASM160400v1_genomic.fna/checkm_result
[2023-06-05 02:54:52,775] [INFO] Task succeeded: CheckM
[2023-06-05 02:54:52,777] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 02:54:52,794] [INFO] ===== Completeness check finished =====
[2023-06-05 02:54:52,794] [INFO] ===== Start GTDB Search =====
[2023-06-05 02:54:52,795] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_001604005.1_ASM160400v1_genomic.fna/markers.fasta)
[2023-06-05 02:54:52,795] [INFO] Task started: Blastn
[2023-06-05 02:54:52,795] [INFO] Running command: blastn -query GCA_001604005.1_ASM160400v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6185f5fd-8df7-4848-adc2-1b59d41f6c9d/dqc_reference/reference_markers_gtdb.fasta -out GCA_001604005.1_ASM160400v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:54:53,631] [INFO] Task succeeded: Blastn
[2023-06-05 02:54:53,636] [INFO] Selected 21 target genomes.
[2023-06-05 02:54:53,636] [INFO] Target genome list was writen to GCA_001604005.1_ASM160400v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 02:54:53,697] [INFO] Task started: fastANI
[2023-06-05 02:54:53,698] [INFO] Running command: fastANI --query /var/lib/cwl/stg8019d1f0-08ce-4b13-80f9-1a0d8c39d0be/GCA_001604005.1_ASM160400v1_genomic.fna.gz --refList GCA_001604005.1_ASM160400v1_genomic.fna/target_genomes_gtdb.txt --output GCA_001604005.1_ASM160400v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 02:55:00,378] [INFO] Task succeeded: fastANI
[2023-06-05 02:55:00,391] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 02:55:00,392] [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_001604005.1	s__Firm-07 sp001604005	100.0	515	517	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__Firm-07	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017415805.1	s__Firm-07 sp017415805	77.2321	75	517	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__Firm-07	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900548735.1	s__Firm-07 sp900548735	76.9994	83	517	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__Firm-07	95.0	97.86	97.81	0.89	0.83	3	-
GCA_900770145.1	s__Firm-07 sp900770145	76.9277	67	517	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__Firm-07	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015064185.1	s__Firm-07 sp015064185	76.662	53	517	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__Firm-07	95.0	98.12	98.04	0.91	0.88	3	-
GCA_015064005.1	s__Firm-07 sp015064005	76.6229	58	517	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__Firm-07	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017453325.1	s__Firm-07 sp017453325	76.6169	72	517	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__Firm-07	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017462615.1	s__Firm-07 sp017462615	76.4955	57	517	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__Firm-07	95.0	97.86	97.86	0.90	0.90	2	-
GCA_015065135.1	s__Firm-07 sp015065135	76.4496	68	517	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__Firm-07	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015064415.1	s__Firm-07 sp015064415	76.3641	72	517	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__Firm-07	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 02:55:00,394] [INFO] GTDB search result was written to GCA_001604005.1_ASM160400v1_genomic.fna/result_gtdb.tsv
[2023-06-05 02:55:00,394] [INFO] ===== GTDB Search completed =====
[2023-06-05 02:55:00,397] [INFO] DFAST_QC result json was written to GCA_001604005.1_ASM160400v1_genomic.fna/dqc_result.json
[2023-06-05 02:55:00,397] [INFO] DFAST_QC completed!
[2023-06-05 02:55:00,397] [INFO] Total running time: 0h0m47s