[2023-06-18 10:25:30,304] [INFO] DFAST_QC pipeline started.
[2023-06-18 10:25:30,307] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 10:25:30,307] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d6d91b4-44af-4c39-b83b-f56b087bc63f/dqc_reference
[2023-06-18 10:25:31,646] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 10:25:31,648] [INFO] Task started: Prodigal
[2023-06-18 10:25:31,649] [INFO] Running command: gunzip -c /var/lib/cwl/stg70e2e8e1-0271-4552-86fd-af355492244f/GCA_018654345.1_ASM1865434v1_genomic.fna.gz | prodigal -d GCA_018654345.1_ASM1865434v1_genomic.fna/cds.fna -a GCA_018654345.1_ASM1865434v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 10:25:34,884] [INFO] Task succeeded: Prodigal
[2023-06-18 10:25:34,884] [INFO] Task started: HMMsearch
[2023-06-18 10:25:34,885] [INFO] Running command: hmmsearch --tblout GCA_018654345.1_ASM1865434v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d6d91b4-44af-4c39-b83b-f56b087bc63f/dqc_reference/reference_markers.hmm GCA_018654345.1_ASM1865434v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 10:25:35,172] [INFO] Task succeeded: HMMsearch
[2023-06-18 10:25:35,175] [INFO] Found 6/6 markers.
[2023-06-18 10:25:35,199] [INFO] Query marker FASTA was written to GCA_018654345.1_ASM1865434v1_genomic.fna/markers.fasta
[2023-06-18 10:25:35,199] [INFO] Task started: Blastn
[2023-06-18 10:25:35,199] [INFO] Running command: blastn -query GCA_018654345.1_ASM1865434v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d6d91b4-44af-4c39-b83b-f56b087bc63f/dqc_reference/reference_markers.fasta -out GCA_018654345.1_ASM1865434v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 10:25:35,881] [INFO] Task succeeded: Blastn
[2023-06-18 10:25:35,888] [INFO] Selected 31 target genomes.
[2023-06-18 10:25:35,888] [INFO] Target genome list was writen to GCA_018654345.1_ASM1865434v1_genomic.fna/target_genomes.txt
[2023-06-18 10:25:35,892] [INFO] Task started: fastANI
[2023-06-18 10:25:35,893] [INFO] Running command: fastANI --query /var/lib/cwl/stg70e2e8e1-0271-4552-86fd-af355492244f/GCA_018654345.1_ASM1865434v1_genomic.fna.gz --refList GCA_018654345.1_ASM1865434v1_genomic.fna/target_genomes.txt --output GCA_018654345.1_ASM1865434v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 10:25:52,694] [INFO] Task succeeded: fastANI
[2023-06-18 10:25:52,695] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d6d91b4-44af-4c39-b83b-f56b087bc63f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 10:25:52,695] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d6d91b4-44af-4c39-b83b-f56b087bc63f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 10:25:52,697] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 10:25:52,697] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 10:25:52,698] [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
--------------------------------------------------------------------------------
[2023-06-18 10:25:52,704] [INFO] DFAST Taxonomy check result was written to GCA_018654345.1_ASM1865434v1_genomic.fna/tc_result.tsv
[2023-06-18 10:25:52,705] [INFO] ===== Taxonomy check completed =====
[2023-06-18 10:25:52,705] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 10:25:52,705] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d6d91b4-44af-4c39-b83b-f56b087bc63f/dqc_reference/checkm_data
[2023-06-18 10:25:52,709] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 10:25:52,737] [INFO] Task started: CheckM
[2023-06-18 10:25:52,737] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018654345.1_ASM1865434v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018654345.1_ASM1865434v1_genomic.fna/checkm_input GCA_018654345.1_ASM1865434v1_genomic.fna/checkm_result
[2023-06-18 10:26:10,438] [INFO] Task succeeded: CheckM
[2023-06-18 10:26:10,441] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 2.08%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-18 10:26:10,483] [INFO] ===== Completeness check finished =====
[2023-06-18 10:26:10,483] [INFO] ===== Start GTDB Search =====
[2023-06-18 10:26:10,484] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018654345.1_ASM1865434v1_genomic.fna/markers.fasta)
[2023-06-18 10:26:10,484] [INFO] Task started: Blastn
[2023-06-18 10:26:10,485] [INFO] Running command: blastn -query GCA_018654345.1_ASM1865434v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d6d91b4-44af-4c39-b83b-f56b087bc63f/dqc_reference/reference_markers_gtdb.fasta -out GCA_018654345.1_ASM1865434v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 10:26:11,475] [INFO] Task succeeded: Blastn
[2023-06-18 10:26:11,480] [INFO] Selected 9 target genomes.
[2023-06-18 10:26:11,481] [INFO] Target genome list was writen to GCA_018654345.1_ASM1865434v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 10:26:11,487] [INFO] Task started: fastANI
[2023-06-18 10:26:11,487] [INFO] Running command: fastANI --query /var/lib/cwl/stg70e2e8e1-0271-4552-86fd-af355492244f/GCA_018654345.1_ASM1865434v1_genomic.fna.gz --refList GCA_018654345.1_ASM1865434v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018654345.1_ASM1865434v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 10:26:13,646] [INFO] Task succeeded: fastANI
[2023-06-18 10:26:13,658] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 10:26:13,659] [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_018646865.1	s__MED-G11 sp014239615	99.7982	346	377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	99.76	99.49	0.92	0.80	17	conclusive
GCA_902514615.1	s__MED-G11 sp902514615	86.7379	253	377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004214015.1	s__MED-G11 sp004214015	86.4064	216	377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	97.90	97.77	0.83	0.80	4	-
GCA_902509805.1	s__MED-G11 sp902509805	85.5459	168	377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	97.79	97.79	0.58	0.58	2	-
GCA_016777325.1	s__MED-G11 sp016777325	85.3799	217	377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239665.1	s__MED-G11 sp014239665	84.2873	272	377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	96.49	96.27	0.81	0.77	10	-
GCA_002457075.1	s__MED-G11 sp002457075	83.6328	224	377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	98.35	98.35	0.79	0.79	2	-
GCA_004213645.1	s__MED-G11 sp004213645	80.4019	200	377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	97.96	97.96	0.74	0.74	2	-
--------------------------------------------------------------------------------
[2023-06-18 10:26:13,661] [INFO] GTDB search result was written to GCA_018654345.1_ASM1865434v1_genomic.fna/result_gtdb.tsv
[2023-06-18 10:26:13,665] [INFO] ===== GTDB Search completed =====
[2023-06-18 10:26:13,669] [INFO] DFAST_QC result json was written to GCA_018654345.1_ASM1865434v1_genomic.fna/dqc_result.json
[2023-06-18 10:26:13,669] [INFO] DFAST_QC completed!
[2023-06-18 10:26:13,669] [INFO] Total running time: 0h0m43s