[2023-06-28 04:37:17,098] [INFO] DFAST_QC pipeline started.
[2023-06-28 04:37:17,100] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 04:37:17,101] [INFO] DQC Reference Directory: /var/lib/cwl/stgde2681d4-ca92-4c21-a038-fd80a6d3ca93/dqc_reference
[2023-06-28 04:37:18,403] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 04:37:18,404] [INFO] Task started: Prodigal
[2023-06-28 04:37:18,404] [INFO] Running command: gunzip -c /var/lib/cwl/stg71149ca0-66b9-4c87-996f-72cf63776f77/GCA_017397655.1_ASM1739765v1_genomic.fna.gz | prodigal -d GCA_017397655.1_ASM1739765v1_genomic.fna/cds.fna -a GCA_017397655.1_ASM1739765v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 04:37:24,228] [INFO] Task succeeded: Prodigal
[2023-06-28 04:37:24,228] [INFO] Task started: HMMsearch
[2023-06-28 04:37:24,228] [INFO] Running command: hmmsearch --tblout GCA_017397655.1_ASM1739765v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgde2681d4-ca92-4c21-a038-fd80a6d3ca93/dqc_reference/reference_markers.hmm GCA_017397655.1_ASM1739765v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 04:37:24,513] [INFO] Task succeeded: HMMsearch
[2023-06-28 04:37:24,515] [INFO] Found 6/6 markers.
[2023-06-28 04:37:24,548] [INFO] Query marker FASTA was written to GCA_017397655.1_ASM1739765v1_genomic.fna/markers.fasta
[2023-06-28 04:37:24,549] [INFO] Task started: Blastn
[2023-06-28 04:37:24,549] [INFO] Running command: blastn -query GCA_017397655.1_ASM1739765v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde2681d4-ca92-4c21-a038-fd80a6d3ca93/dqc_reference/reference_markers.fasta -out GCA_017397655.1_ASM1739765v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 04:37:25,189] [INFO] Task succeeded: Blastn
[2023-06-28 04:37:25,193] [INFO] Selected 17 target genomes.
[2023-06-28 04:37:25,193] [INFO] Target genome list was writen to GCA_017397655.1_ASM1739765v1_genomic.fna/target_genomes.txt
[2023-06-28 04:37:25,198] [INFO] Task started: fastANI
[2023-06-28 04:37:25,198] [INFO] Running command: fastANI --query /var/lib/cwl/stg71149ca0-66b9-4c87-996f-72cf63776f77/GCA_017397655.1_ASM1739765v1_genomic.fna.gz --refList GCA_017397655.1_ASM1739765v1_genomic.fna/target_genomes.txt --output GCA_017397655.1_ASM1739765v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 04:37:34,407] [INFO] Task succeeded: fastANI
[2023-06-28 04:37:34,408] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgde2681d4-ca92-4c21-a038-fd80a6d3ca93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 04:37:34,409] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgde2681d4-ca92-4c21-a038-fd80a6d3ca93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 04:37:34,411] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 04:37:34,411] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 04:37:34,411] [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 04:37:34,414] [INFO] DFAST Taxonomy check result was written to GCA_017397655.1_ASM1739765v1_genomic.fna/tc_result.tsv
[2023-06-28 04:37:34,414] [INFO] ===== Taxonomy check completed =====
[2023-06-28 04:37:34,415] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 04:37:34,415] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgde2681d4-ca92-4c21-a038-fd80a6d3ca93/dqc_reference/checkm_data
[2023-06-28 04:37:34,420] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 04:37:34,450] [INFO] Task started: CheckM
[2023-06-28 04:37:34,451] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017397655.1_ASM1739765v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017397655.1_ASM1739765v1_genomic.fna/checkm_input GCA_017397655.1_ASM1739765v1_genomic.fna/checkm_result
[2023-06-28 04:37:59,330] [INFO] Task succeeded: CheckM
[2023-06-28 04:37:59,333] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.42%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 04:37:59,360] [INFO] ===== Completeness check finished =====
[2023-06-28 04:37:59,360] [INFO] ===== Start GTDB Search =====
[2023-06-28 04:37:59,361] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017397655.1_ASM1739765v1_genomic.fna/markers.fasta)
[2023-06-28 04:37:59,361] [INFO] Task started: Blastn
[2023-06-28 04:37:59,361] [INFO] Running command: blastn -query GCA_017397655.1_ASM1739765v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde2681d4-ca92-4c21-a038-fd80a6d3ca93/dqc_reference/reference_markers_gtdb.fasta -out GCA_017397655.1_ASM1739765v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 04:38:00,435] [INFO] Task succeeded: Blastn
[2023-06-28 04:38:00,440] [INFO] Selected 26 target genomes.
[2023-06-28 04:38:00,441] [INFO] Target genome list was writen to GCA_017397655.1_ASM1739765v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 04:38:00,457] [INFO] Task started: fastANI
[2023-06-28 04:38:00,457] [INFO] Running command: fastANI --query /var/lib/cwl/stg71149ca0-66b9-4c87-996f-72cf63776f77/GCA_017397655.1_ASM1739765v1_genomic.fna.gz --refList GCA_017397655.1_ASM1739765v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017397655.1_ASM1739765v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 04:38:10,933] [INFO] Task succeeded: fastANI
[2023-06-28 04:38:10,944] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 04:38:10,945] [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_017397655.1	s__UBA1425 sp017397655	100.0	807	811	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1425	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017409845.1	s__CAG-177 sp017409845	77.9473	94	811	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-177	95.0	97.27	97.27	0.85	0.85	2	-
GCA_017403185.1	s__CAG-177 sp017403185	77.5059	84	811	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-177	95.0	98.23	98.23	0.86	0.86	2	-
GCA_017481575.1	s__CAG-488 sp017481575	77.2472	68	811	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-488	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017380575.1	s__CAG-488 sp017380575	77.1068	87	811	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-488	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017935325.1	s__SIG575 sp017935325	77.0064	55	811	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__SIG575	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017548045.1	s__CAG-177 sp017548045	76.8631	91	811	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-177	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017468425.1	s__SIG575 sp017468425	76.8219	54	811	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__SIG575	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017410195.1	s__CAG-177 sp017410195	76.788	76	811	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-177	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017935265.1	s__CAG-488 sp017935265	76.5922	63	811	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-488	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000434915.1	s__CAG-488 sp000434915	76.3484	50	811	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-488	95.0	98.43	98.24	0.92	0.89	3	-
--------------------------------------------------------------------------------
[2023-06-28 04:38:10,946] [INFO] GTDB search result was written to GCA_017397655.1_ASM1739765v1_genomic.fna/result_gtdb.tsv
[2023-06-28 04:38:10,947] [INFO] ===== GTDB Search completed =====
[2023-06-28 04:38:10,950] [INFO] DFAST_QC result json was written to GCA_017397655.1_ASM1739765v1_genomic.fna/dqc_result.json
[2023-06-28 04:38:10,950] [INFO] DFAST_QC completed!
[2023-06-28 04:38:10,950] [INFO] Total running time: 0h0m54s