[2023-06-28 17:15:18,575] [INFO] DFAST_QC pipeline started.
[2023-06-28 17:15:18,578] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 17:15:18,578] [INFO] DQC Reference Directory: /var/lib/cwl/stgedfcb875-a050-4ba3-ac66-fc9e3ccaeab1/dqc_reference
[2023-06-28 17:15:21,084] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 17:15:21,086] [INFO] Task started: Prodigal
[2023-06-28 17:15:21,086] [INFO] Running command: gunzip -c /var/lib/cwl/stg6f18504f-edba-48eb-8010-800d431148ad/GCA_944337025.1_BRZ_MS_bin33_genomic.fna.gz | prodigal -d GCA_944337025.1_BRZ_MS_bin33_genomic.fna/cds.fna -a GCA_944337025.1_BRZ_MS_bin33_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 17:15:26,648] [INFO] Task succeeded: Prodigal
[2023-06-28 17:15:26,649] [INFO] Task started: HMMsearch
[2023-06-28 17:15:26,649] [INFO] Running command: hmmsearch --tblout GCA_944337025.1_BRZ_MS_bin33_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgedfcb875-a050-4ba3-ac66-fc9e3ccaeab1/dqc_reference/reference_markers.hmm GCA_944337025.1_BRZ_MS_bin33_genomic.fna/protein.faa > /dev/null
[2023-06-28 17:15:26,909] [INFO] Task succeeded: HMMsearch
[2023-06-28 17:15:26,911] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6f18504f-edba-48eb-8010-800d431148ad/GCA_944337025.1_BRZ_MS_bin33_genomic.fna.gz]
[2023-06-28 17:15:26,943] [INFO] Query marker FASTA was written to GCA_944337025.1_BRZ_MS_bin33_genomic.fna/markers.fasta
[2023-06-28 17:15:26,944] [INFO] Task started: Blastn
[2023-06-28 17:15:26,944] [INFO] Running command: blastn -query GCA_944337025.1_BRZ_MS_bin33_genomic.fna/markers.fasta -db /var/lib/cwl/stgedfcb875-a050-4ba3-ac66-fc9e3ccaeab1/dqc_reference/reference_markers.fasta -out GCA_944337025.1_BRZ_MS_bin33_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:15:27,618] [INFO] Task succeeded: Blastn
[2023-06-28 17:15:27,622] [INFO] Selected 24 target genomes.
[2023-06-28 17:15:27,623] [INFO] Target genome list was writen to GCA_944337025.1_BRZ_MS_bin33_genomic.fna/target_genomes.txt
[2023-06-28 17:15:27,627] [INFO] Task started: fastANI
[2023-06-28 17:15:27,627] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f18504f-edba-48eb-8010-800d431148ad/GCA_944337025.1_BRZ_MS_bin33_genomic.fna.gz --refList GCA_944337025.1_BRZ_MS_bin33_genomic.fna/target_genomes.txt --output GCA_944337025.1_BRZ_MS_bin33_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 17:15:41,154] [INFO] Task succeeded: fastANI
[2023-06-28 17:15:41,155] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgedfcb875-a050-4ba3-ac66-fc9e3ccaeab1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 17:15:41,155] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgedfcb875-a050-4ba3-ac66-fc9e3ccaeab1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 17:15:41,162] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 17:15:41,162] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 17:15:41,162] [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
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	76.6673	56	581	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 17:15:41,165] [INFO] DFAST Taxonomy check result was written to GCA_944337025.1_BRZ_MS_bin33_genomic.fna/tc_result.tsv
[2023-06-28 17:15:41,165] [INFO] ===== Taxonomy check completed =====
[2023-06-28 17:15:41,166] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 17:15:41,166] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgedfcb875-a050-4ba3-ac66-fc9e3ccaeab1/dqc_reference/checkm_data
[2023-06-28 17:15:41,168] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 17:15:41,191] [INFO] Task started: CheckM
[2023-06-28 17:15:41,191] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944337025.1_BRZ_MS_bin33_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944337025.1_BRZ_MS_bin33_genomic.fna/checkm_input GCA_944337025.1_BRZ_MS_bin33_genomic.fna/checkm_result
[2023-06-28 17:16:03,720] [INFO] Task succeeded: CheckM
[2023-06-28 17:16:03,722] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.07%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 17:16:03,742] [INFO] ===== Completeness check finished =====
[2023-06-28 17:16:03,743] [INFO] ===== Start GTDB Search =====
[2023-06-28 17:16:03,743] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944337025.1_BRZ_MS_bin33_genomic.fna/markers.fasta)
[2023-06-28 17:16:03,744] [INFO] Task started: Blastn
[2023-06-28 17:16:03,744] [INFO] Running command: blastn -query GCA_944337025.1_BRZ_MS_bin33_genomic.fna/markers.fasta -db /var/lib/cwl/stgedfcb875-a050-4ba3-ac66-fc9e3ccaeab1/dqc_reference/reference_markers_gtdb.fasta -out GCA_944337025.1_BRZ_MS_bin33_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:16:04,891] [INFO] Task succeeded: Blastn
[2023-06-28 17:16:04,897] [INFO] Selected 16 target genomes.
[2023-06-28 17:16:04,897] [INFO] Target genome list was writen to GCA_944337025.1_BRZ_MS_bin33_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 17:16:04,907] [INFO] Task started: fastANI
[2023-06-28 17:16:04,908] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f18504f-edba-48eb-8010-800d431148ad/GCA_944337025.1_BRZ_MS_bin33_genomic.fna.gz --refList GCA_944337025.1_BRZ_MS_bin33_genomic.fna/target_genomes_gtdb.txt --output GCA_944337025.1_BRZ_MS_bin33_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 17:16:11,641] [INFO] Task succeeded: fastANI
[2023-06-28 17:16:11,661] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 17:16:11,662] [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_900542615.1	s__Pelethousia sp900542615	98.1532	480	581	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__Pelethousia	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCA_900543475.1	s__Pelethousia gallinarum	93.262	500	581	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__Pelethousia	95.0	98.78	98.45	0.84	0.76	5	-
GCA_002409725.1	s__Pelethousia sp002409725	79.3659	198	581	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__Pelethousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902798825.1	s__RUG472 sp902798825	77.696	78	581	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__RUG472	95.0	97.85	97.83	0.89	0.89	3	-
GCA_902786465.1	s__RUG472 sp902786465	77.6795	59	581	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__RUG472	95.0	96.79	96.79	0.84	0.84	2	-
GCA_902801845.1	s__RUG472 sp902801845	77.653	74	581	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__RUG472	95.0	96.79	96.35	0.92	0.91	4	-
GCA_017545535.1	s__RUG472 sp017545535	77.5551	78	581	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__RUG472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017547885.1	s__SFEL01 sp017547885	77.4892	53	581	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__SFEL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015056105.1	s__UBA1685 sp015056105	77.3426	65	581	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__UBA1685	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900546845.1	s__UBA1685 sp900546845	77.2963	76	581	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__UBA1685	95.0	97.42	97.42	0.86	0.86	2	-
GCA_004560435.1	s__UBA1685 sp004560435	77.1358	70	581	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__UBA1685	95.0	97.01	95.84	0.87	0.85	3	-
GCA_016292635.1	s__SFEL01 sp016292635	77.0521	59	581	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__SFEL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018711685.1	s__Excrementavichristensenella intestinipullorum	76.8169	82	581	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Excrementavichristensenella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 17:16:11,663] [INFO] GTDB search result was written to GCA_944337025.1_BRZ_MS_bin33_genomic.fna/result_gtdb.tsv
[2023-06-28 17:16:11,664] [INFO] ===== GTDB Search completed =====
[2023-06-28 17:16:11,667] [INFO] DFAST_QC result json was written to GCA_944337025.1_BRZ_MS_bin33_genomic.fna/dqc_result.json
[2023-06-28 17:16:11,668] [INFO] DFAST_QC completed!
[2023-06-28 17:16:11,668] [INFO] Total running time: 0h0m53s