[2023-06-28 12:34:08,815] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:34:08,821] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:34:08,821] [INFO] DQC Reference Directory: /var/lib/cwl/stg53475d15-a295-4d05-b465-0b8fada1bac7/dqc_reference
[2023-06-28 12:34:10,189] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:34:10,189] [INFO] Task started: Prodigal
[2023-06-28 12:34:10,190] [INFO] Running command: gunzip -c /var/lib/cwl/stg1b71e92b-f242-4001-adea-c9399e7083fe/GCA_017430455.1_ASM1743045v1_genomic.fna.gz | prodigal -d GCA_017430455.1_ASM1743045v1_genomic.fna/cds.fna -a GCA_017430455.1_ASM1743045v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:34:15,193] [INFO] Task succeeded: Prodigal
[2023-06-28 12:34:15,193] [INFO] Task started: HMMsearch
[2023-06-28 12:34:15,193] [INFO] Running command: hmmsearch --tblout GCA_017430455.1_ASM1743045v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg53475d15-a295-4d05-b465-0b8fada1bac7/dqc_reference/reference_markers.hmm GCA_017430455.1_ASM1743045v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:34:15,421] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:34:15,423] [INFO] Found 6/6 markers.
[2023-06-28 12:34:15,457] [INFO] Query marker FASTA was written to GCA_017430455.1_ASM1743045v1_genomic.fna/markers.fasta
[2023-06-28 12:34:15,458] [INFO] Task started: Blastn
[2023-06-28 12:34:15,458] [INFO] Running command: blastn -query GCA_017430455.1_ASM1743045v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg53475d15-a295-4d05-b465-0b8fada1bac7/dqc_reference/reference_markers.fasta -out GCA_017430455.1_ASM1743045v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:34:16,084] [INFO] Task succeeded: Blastn
[2023-06-28 12:34:16,088] [INFO] Selected 5 target genomes.
[2023-06-28 12:34:16,088] [INFO] Target genome list was writen to GCA_017430455.1_ASM1743045v1_genomic.fna/target_genomes.txt
[2023-06-28 12:34:16,089] [INFO] Task started: fastANI
[2023-06-28 12:34:16,089] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b71e92b-f242-4001-adea-c9399e7083fe/GCA_017430455.1_ASM1743045v1_genomic.fna.gz --refList GCA_017430455.1_ASM1743045v1_genomic.fna/target_genomes.txt --output GCA_017430455.1_ASM1743045v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:34:20,592] [INFO] Task succeeded: fastANI
[2023-06-28 12:34:20,592] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg53475d15-a295-4d05-b465-0b8fada1bac7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:34:20,593] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg53475d15-a295-4d05-b465-0b8fada1bac7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:34:20,595] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:34:20,595] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 12:34:20,596] [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 12:34:20,598] [INFO] DFAST Taxonomy check result was written to GCA_017430455.1_ASM1743045v1_genomic.fna/tc_result.tsv
[2023-06-28 12:34:20,599] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:34:20,599] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:34:20,599] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg53475d15-a295-4d05-b465-0b8fada1bac7/dqc_reference/checkm_data
[2023-06-28 12:34:20,604] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:34:20,634] [INFO] Task started: CheckM
[2023-06-28 12:34:20,635] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017430455.1_ASM1743045v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017430455.1_ASM1743045v1_genomic.fna/checkm_input GCA_017430455.1_ASM1743045v1_genomic.fna/checkm_result
[2023-06-28 12:34:42,590] [INFO] Task succeeded: CheckM
[2023-06-28 12:34:42,592] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:34:42,612] [INFO] ===== Completeness check finished =====
[2023-06-28 12:34:42,613] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:34:42,614] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017430455.1_ASM1743045v1_genomic.fna/markers.fasta)
[2023-06-28 12:34:42,614] [INFO] Task started: Blastn
[2023-06-28 12:34:42,614] [INFO] Running command: blastn -query GCA_017430455.1_ASM1743045v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg53475d15-a295-4d05-b465-0b8fada1bac7/dqc_reference/reference_markers_gtdb.fasta -out GCA_017430455.1_ASM1743045v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:34:43,677] [INFO] Task succeeded: Blastn
[2023-06-28 12:34:43,681] [INFO] Selected 18 target genomes.
[2023-06-28 12:34:43,682] [INFO] Target genome list was writen to GCA_017430455.1_ASM1743045v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:34:43,691] [INFO] Task started: fastANI
[2023-06-28 12:34:43,691] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b71e92b-f242-4001-adea-c9399e7083fe/GCA_017430455.1_ASM1743045v1_genomic.fna.gz --refList GCA_017430455.1_ASM1743045v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017430455.1_ASM1743045v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:34:50,509] [INFO] Task succeeded: fastANI
[2023-06-28 12:34:50,521] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 12:34:50,521] [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_017430455.1	s__Limivicinus sp017430455	100.0	683	683	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	98.47	98.47	0.95	0.95	2	conclusive
GCA_902802045.1	s__Limivicinus sp902802045	94.5832	555	683	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	97.63	95.09	0.97	0.95	5	-
GCA_002450075.1	s__Limivicinus sp002450075	77.8747	54	683	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	98.03	97.77	0.79	0.75	6	-
GCA_900320595.1	s__Limivicinus sp900320595	77.7598	60	683	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	99.20	98.25	0.89	0.82	4	-
GCA_902779945.1	s__Limivicinus sp902779945	76.8335	55	683	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_900549545.1	s__Limivicinus sp900549545	76.5986	55	683	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	99.92	99.84	0.93	0.88	3	-
--------------------------------------------------------------------------------
[2023-06-28 12:34:50,523] [INFO] GTDB search result was written to GCA_017430455.1_ASM1743045v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:34:50,523] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:34:50,526] [INFO] DFAST_QC result json was written to GCA_017430455.1_ASM1743045v1_genomic.fna/dqc_result.json
[2023-06-28 12:34:50,527] [INFO] DFAST_QC completed!
[2023-06-28 12:34:50,527] [INFO] Total running time: 0h0m42s