[2023-06-28 12:59:25,216] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:59:25,220] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:59:25,220] [INFO] DQC Reference Directory: /var/lib/cwl/stg3314a59b-897a-4e40-b6b2-c7463b00c0b6/dqc_reference
[2023-06-28 12:59:26,622] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:59:26,623] [INFO] Task started: Prodigal
[2023-06-28 12:59:26,623] [INFO] Running command: gunzip -c /var/lib/cwl/stg59d38488-8a15-444d-a289-6801ddd774f9/GCA_017632815.1_ASM1763281v1_genomic.fna.gz | prodigal -d GCA_017632815.1_ASM1763281v1_genomic.fna/cds.fna -a GCA_017632815.1_ASM1763281v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:59:29,687] [INFO] Task succeeded: Prodigal
[2023-06-28 12:59:29,687] [INFO] Task started: HMMsearch
[2023-06-28 12:59:29,687] [INFO] Running command: hmmsearch --tblout GCA_017632815.1_ASM1763281v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3314a59b-897a-4e40-b6b2-c7463b00c0b6/dqc_reference/reference_markers.hmm GCA_017632815.1_ASM1763281v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:59:29,876] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:59:29,878] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg59d38488-8a15-444d-a289-6801ddd774f9/GCA_017632815.1_ASM1763281v1_genomic.fna.gz]
[2023-06-28 12:59:29,901] [INFO] Query marker FASTA was written to GCA_017632815.1_ASM1763281v1_genomic.fna/markers.fasta
[2023-06-28 12:59:29,902] [INFO] Task started: Blastn
[2023-06-28 12:59:29,902] [INFO] Running command: blastn -query GCA_017632815.1_ASM1763281v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3314a59b-897a-4e40-b6b2-c7463b00c0b6/dqc_reference/reference_markers.fasta -out GCA_017632815.1_ASM1763281v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:59:30,465] [INFO] Task succeeded: Blastn
[2023-06-28 12:59:30,469] [INFO] Selected 18 target genomes.
[2023-06-28 12:59:30,469] [INFO] Target genome list was writen to GCA_017632815.1_ASM1763281v1_genomic.fna/target_genomes.txt
[2023-06-28 12:59:30,470] [INFO] Task started: fastANI
[2023-06-28 12:59:30,470] [INFO] Running command: fastANI --query /var/lib/cwl/stg59d38488-8a15-444d-a289-6801ddd774f9/GCA_017632815.1_ASM1763281v1_genomic.fna.gz --refList GCA_017632815.1_ASM1763281v1_genomic.fna/target_genomes.txt --output GCA_017632815.1_ASM1763281v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:59:44,208] [INFO] Task succeeded: fastANI
[2023-06-28 12:59:44,209] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3314a59b-897a-4e40-b6b2-c7463b00c0b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:59:44,210] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3314a59b-897a-4e40-b6b2-c7463b00c0b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:59:44,212] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:59:44,212] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 12:59:44,212] [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
--------------------------------------------------------------------------------
[2023-06-28 12:59:44,216] [INFO] DFAST Taxonomy check result was written to GCA_017632815.1_ASM1763281v1_genomic.fna/tc_result.tsv
[2023-06-28 12:59:44,217] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:59:44,217] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:59:44,218] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3314a59b-897a-4e40-b6b2-c7463b00c0b6/dqc_reference/checkm_data
[2023-06-28 12:59:44,221] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:59:44,240] [INFO] Task started: CheckM
[2023-06-28 12:59:44,240] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017632815.1_ASM1763281v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017632815.1_ASM1763281v1_genomic.fna/checkm_input GCA_017632815.1_ASM1763281v1_genomic.fna/checkm_result
[2023-06-28 13:00:02,007] [INFO] Task succeeded: CheckM
[2023-06-28 13:00:02,008] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.01%
Contamintation: 11.98%
Strain heterogeneity: 57.14%
--------------------------------------------------------------------------------
[2023-06-28 13:00:02,035] [INFO] ===== Completeness check finished =====
[2023-06-28 13:00:02,036] [INFO] ===== Start GTDB Search =====
[2023-06-28 13:00:02,036] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017632815.1_ASM1763281v1_genomic.fna/markers.fasta)
[2023-06-28 13:00:02,036] [INFO] Task started: Blastn
[2023-06-28 13:00:02,036] [INFO] Running command: blastn -query GCA_017632815.1_ASM1763281v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3314a59b-897a-4e40-b6b2-c7463b00c0b6/dqc_reference/reference_markers_gtdb.fasta -out GCA_017632815.1_ASM1763281v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:00:02,552] [INFO] Task succeeded: Blastn
[2023-06-28 13:00:02,556] [INFO] Selected 11 target genomes.
[2023-06-28 13:00:02,556] [INFO] Target genome list was writen to GCA_017632815.1_ASM1763281v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 13:00:02,557] [INFO] Task started: fastANI
[2023-06-28 13:00:02,557] [INFO] Running command: fastANI --query /var/lib/cwl/stg59d38488-8a15-444d-a289-6801ddd774f9/GCA_017632815.1_ASM1763281v1_genomic.fna.gz --refList GCA_017632815.1_ASM1763281v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017632815.1_ASM1763281v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 13:00:07,706] [INFO] Task succeeded: fastANI
[2023-06-28 13:00:07,721] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 13:00:07,722] [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_017395085.1	s__Limivicinus sp017395085	87.8926	162	248	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	97.30	96.83	0.71	0.71	3	-
GCA_017458335.1	s__Limivicinus sp017458335	79.717	84	248	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017458065.1	s__Limivicinus sp017458065	79.5608	105	248	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017538965.1	s__Limivicinus sp017538965	79.3572	101	248	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017448455.1	s__Limivicinus sp017448455	79.2414	71	248	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900317375.1	s__Limivicinus sp900317375	79.1199	94	248	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	98.11	95.61	0.84	0.72	56	-
GCA_902778275.1	s__Limivicinus sp902778275	79.0096	67	248	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017470325.1	s__Limivicinus sp017470325	78.8314	53	248	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902789835.1	s__Limivicinus sp902789835	78.8199	84	248	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902798545.1	s__Limivicinus sp902798545	78.7968	84	248	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 13:00:07,724] [INFO] GTDB search result was written to GCA_017632815.1_ASM1763281v1_genomic.fna/result_gtdb.tsv
[2023-06-28 13:00:07,724] [INFO] ===== GTDB Search completed =====
[2023-06-28 13:00:07,730] [INFO] DFAST_QC result json was written to GCA_017632815.1_ASM1763281v1_genomic.fna/dqc_result.json
[2023-06-28 13:00:07,730] [INFO] DFAST_QC completed!
[2023-06-28 13:00:07,730] [INFO] Total running time: 0h0m43s