[2023-06-28 00:41:23,984] [INFO] DFAST_QC pipeline started.
[2023-06-28 00:41:23,986] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 00:41:23,986] [INFO] DQC Reference Directory: /var/lib/cwl/stgf97bf161-d737-4901-b692-39d4b95c12b6/dqc_reference
[2023-06-28 00:41:25,341] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 00:41:25,342] [INFO] Task started: Prodigal
[2023-06-28 00:41:25,342] [INFO] Running command: gunzip -c /var/lib/cwl/stgc973de88-af1e-4e5b-8b30-879e00a6dbc7/GCA_017457345.1_ASM1745734v1_genomic.fna.gz | prodigal -d GCA_017457345.1_ASM1745734v1_genomic.fna/cds.fna -a GCA_017457345.1_ASM1745734v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 00:41:28,106] [INFO] Task succeeded: Prodigal
[2023-06-28 00:41:28,107] [INFO] Task started: HMMsearch
[2023-06-28 00:41:28,107] [INFO] Running command: hmmsearch --tblout GCA_017457345.1_ASM1745734v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf97bf161-d737-4901-b692-39d4b95c12b6/dqc_reference/reference_markers.hmm GCA_017457345.1_ASM1745734v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 00:41:28,316] [INFO] Task succeeded: HMMsearch
[2023-06-28 00:41:28,318] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc973de88-af1e-4e5b-8b30-879e00a6dbc7/GCA_017457345.1_ASM1745734v1_genomic.fna.gz]
[2023-06-28 00:41:28,339] [INFO] Query marker FASTA was written to GCA_017457345.1_ASM1745734v1_genomic.fna/markers.fasta
[2023-06-28 00:41:28,339] [INFO] Task started: Blastn
[2023-06-28 00:41:28,339] [INFO] Running command: blastn -query GCA_017457345.1_ASM1745734v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf97bf161-d737-4901-b692-39d4b95c12b6/dqc_reference/reference_markers.fasta -out GCA_017457345.1_ASM1745734v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:41:28,919] [INFO] Task succeeded: Blastn
[2023-06-28 00:41:28,924] [INFO] Selected 19 target genomes.
[2023-06-28 00:41:28,924] [INFO] Target genome list was writen to GCA_017457345.1_ASM1745734v1_genomic.fna/target_genomes.txt
[2023-06-28 00:41:28,931] [INFO] Task started: fastANI
[2023-06-28 00:41:28,932] [INFO] Running command: fastANI --query /var/lib/cwl/stgc973de88-af1e-4e5b-8b30-879e00a6dbc7/GCA_017457345.1_ASM1745734v1_genomic.fna.gz --refList GCA_017457345.1_ASM1745734v1_genomic.fna/target_genomes.txt --output GCA_017457345.1_ASM1745734v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 00:41:41,959] [INFO] Task succeeded: fastANI
[2023-06-28 00:41:41,960] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf97bf161-d737-4901-b692-39d4b95c12b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 00:41:41,960] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf97bf161-d737-4901-b692-39d4b95c12b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 00:41:41,962] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 00:41:41,962] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 00:41:41,963] [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 00:41:41,965] [INFO] DFAST Taxonomy check result was written to GCA_017457345.1_ASM1745734v1_genomic.fna/tc_result.tsv
[2023-06-28 00:41:41,966] [INFO] ===== Taxonomy check completed =====
[2023-06-28 00:41:41,966] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 00:41:41,966] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf97bf161-d737-4901-b692-39d4b95c12b6/dqc_reference/checkm_data
[2023-06-28 00:41:41,969] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 00:41:41,987] [INFO] Task started: CheckM
[2023-06-28 00:41:41,987] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017457345.1_ASM1745734v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017457345.1_ASM1745734v1_genomic.fna/checkm_input GCA_017457345.1_ASM1745734v1_genomic.fna/checkm_result
[2023-06-28 00:41:58,376] [INFO] Task succeeded: CheckM
[2023-06-28 00:41:58,378] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.38%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 00:41:58,401] [INFO] ===== Completeness check finished =====
[2023-06-28 00:41:58,401] [INFO] ===== Start GTDB Search =====
[2023-06-28 00:41:58,402] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017457345.1_ASM1745734v1_genomic.fna/markers.fasta)
[2023-06-28 00:41:58,402] [INFO] Task started: Blastn
[2023-06-28 00:41:58,402] [INFO] Running command: blastn -query GCA_017457345.1_ASM1745734v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf97bf161-d737-4901-b692-39d4b95c12b6/dqc_reference/reference_markers_gtdb.fasta -out GCA_017457345.1_ASM1745734v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:41:59,154] [INFO] Task succeeded: Blastn
[2023-06-28 00:41:59,158] [INFO] Selected 20 target genomes.
[2023-06-28 00:41:59,159] [INFO] Target genome list was writen to GCA_017457345.1_ASM1745734v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 00:41:59,173] [INFO] Task started: fastANI
[2023-06-28 00:41:59,173] [INFO] Running command: fastANI --query /var/lib/cwl/stgc973de88-af1e-4e5b-8b30-879e00a6dbc7/GCA_017457345.1_ASM1745734v1_genomic.fna.gz --refList GCA_017457345.1_ASM1745734v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017457345.1_ASM1745734v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 00:42:03,916] [INFO] Task succeeded: fastANI
[2023-06-28 00:42:03,934] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 00:42:03,934] [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_017457345.1	s__Scatosoma sp017457345	100.0	284	286	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Scatosoma	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_015055655.1	s__Scatosoma sp015055655	77.9308	70	286	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Scatosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017505465.1	s__Scatosoma sp017505465	77.8294	65	286	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Scatosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015055865.1	s__Scatosoma sp015055865	77.6908	56	286	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Scatosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017473605.1	s__Scatosoma sp017473605	77.5213	58	286	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Scatosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017625565.1	s__Scatosoma sp017625565	77.4964	67	286	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Scatosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015071005.1	s__Scatosoma sp015071005	77.3765	68	286	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Scatosoma	95.0	97.47	97.47	0.85	0.85	2	-
GCA_015055545.1	s__Scatosoma sp015055545	77.3584	70	286	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Scatosoma	95.0	97.18	97.18	0.77	0.77	2	-
GCA_017536305.1	s__Scatosoma sp017536305	77.3391	52	286	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Scatosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017504065.1	s__Scatosoma sp017504065	77.2023	60	286	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Scatosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017482415.1	s__Scatosoma sp017482415	77.1751	54	286	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Scatosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904501815.1	s__Scatosoma sp904501815	77.0952	62	286	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Scatosoma	95.0	100.00	100.00	0.97	0.97	2	-
GCA_017468085.1	s__Scatosoma sp017468085	77.0767	53	286	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Scatosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017462985.1	s__Scatosoma sp017462985	76.7351	58	286	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Scatosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017623605.1	s__Scatosoma sp017623605	76.7141	54	286	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Scatosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017503525.1	s__Scatosoma sp017503525	76.6597	51	286	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Scatosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017463425.1	s__Scatosoma sp017463425	76.6523	54	286	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Scatosoma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 00:42:03,936] [INFO] GTDB search result was written to GCA_017457345.1_ASM1745734v1_genomic.fna/result_gtdb.tsv
[2023-06-28 00:42:03,937] [INFO] ===== GTDB Search completed =====
[2023-06-28 00:42:03,942] [INFO] DFAST_QC result json was written to GCA_017457345.1_ASM1745734v1_genomic.fna/dqc_result.json
[2023-06-28 00:42:03,943] [INFO] DFAST_QC completed!
[2023-06-28 00:42:03,943] [INFO] Total running time: 0h0m40s