[2024-01-25 19:24:50,753] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:24:50,755] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:24:50,755] [INFO] DQC Reference Directory: /var/lib/cwl/stge2bd8dda-ec9e-4da6-af1c-141bc6e22828/dqc_reference
[2024-01-25 19:24:51,883] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:24:51,884] [INFO] Task started: Prodigal
[2024-01-25 19:24:51,884] [INFO] Running command: gunzip -c /var/lib/cwl/stg7e50cd1c-484a-4d4b-ae99-60ac36968a25/GCF_009858255.1_ASM985825v1_genomic.fna.gz | prodigal -d GCF_009858255.1_ASM985825v1_genomic.fna/cds.fna -a GCF_009858255.1_ASM985825v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:25:16,278] [INFO] Task succeeded: Prodigal
[2024-01-25 19:25:16,278] [INFO] Task started: HMMsearch
[2024-01-25 19:25:16,278] [INFO] Running command: hmmsearch --tblout GCF_009858255.1_ASM985825v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge2bd8dda-ec9e-4da6-af1c-141bc6e22828/dqc_reference/reference_markers.hmm GCF_009858255.1_ASM985825v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:25:16,530] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:25:16,531] [INFO] Found 6/6 markers.
[2024-01-25 19:25:16,582] [INFO] Query marker FASTA was written to GCF_009858255.1_ASM985825v1_genomic.fna/markers.fasta
[2024-01-25 19:25:16,582] [INFO] Task started: Blastn
[2024-01-25 19:25:16,583] [INFO] Running command: blastn -query GCF_009858255.1_ASM985825v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2bd8dda-ec9e-4da6-af1c-141bc6e22828/dqc_reference/reference_markers.fasta -out GCF_009858255.1_ASM985825v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:25:17,800] [INFO] Task succeeded: Blastn
[2024-01-25 19:25:17,803] [INFO] Selected 8 target genomes.
[2024-01-25 19:25:17,803] [INFO] Target genome list was writen to GCF_009858255.1_ASM985825v1_genomic.fna/target_genomes.txt
[2024-01-25 19:25:17,824] [INFO] Task started: fastANI
[2024-01-25 19:25:17,824] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e50cd1c-484a-4d4b-ae99-60ac36968a25/GCF_009858255.1_ASM985825v1_genomic.fna.gz --refList GCF_009858255.1_ASM985825v1_genomic.fna/target_genomes.txt --output GCF_009858255.1_ASM985825v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:25:32,830] [INFO] Task succeeded: fastANI
[2024-01-25 19:25:32,831] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge2bd8dda-ec9e-4da6-af1c-141bc6e22828/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:25:32,831] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge2bd8dda-ec9e-4da6-af1c-141bc6e22828/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:25:32,837] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:25:32,838] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:25:32,838] [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
Nocardia caishijiensis	strain=DSM 44831	GCA_009858255.1	184756	184756	type	True	100.0	2086	2090	95	conclusive
Nocardia caishijiensis	strain=NBRC 108228	GCA_001612825.1	184756	184756	type	True	99.9854	2054	2090	95	conclusive
Nocardia coubleae	strain=DSM 44960	GCA_012395945.1	356147	356147	type	True	91.7936	1756	2090	95	below_threshold
Nocardia coubleae	strain=NBRC 108252	GCA_001612805.1	356147	356147	type	True	91.7642	1729	2090	95	below_threshold
Nocardia ignorata	strain=NBRC 108230	GCA_001612905.1	145285	145285	type	True	91.6261	1752	2090	95	below_threshold
Nocardia rosealba	strain=NEAU-G4	GCA_020216065.1	2878563	2878563	type	True	91.6055	1770	2090	95	below_threshold
Nocardia ignorata	strain=DSM 44496	GCA_004362495.1	145285	145285	type	True	91.6005	1767	2090	95	below_threshold
Nocardia colli	strain=CICC 11023	GCA_008704205.1	2545717	2545717	type	True	80.8227	1101	2090	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:25:32,839] [INFO] DFAST Taxonomy check result was written to GCF_009858255.1_ASM985825v1_genomic.fna/tc_result.tsv
[2024-01-25 19:25:32,840] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:25:32,840] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:25:32,840] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge2bd8dda-ec9e-4da6-af1c-141bc6e22828/dqc_reference/checkm_data
[2024-01-25 19:25:32,841] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:25:32,898] [INFO] Task started: CheckM
[2024-01-25 19:25:32,898] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009858255.1_ASM985825v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009858255.1_ASM985825v1_genomic.fna/checkm_input GCF_009858255.1_ASM985825v1_genomic.fna/checkm_result
[2024-01-25 19:27:02,068] [INFO] Task succeeded: CheckM
[2024-01-25 19:27:02,069] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:27:02,088] [INFO] ===== Completeness check finished =====
[2024-01-25 19:27:02,088] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:27:02,089] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009858255.1_ASM985825v1_genomic.fna/markers.fasta)
[2024-01-25 19:27:02,089] [INFO] Task started: Blastn
[2024-01-25 19:27:02,089] [INFO] Running command: blastn -query GCF_009858255.1_ASM985825v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2bd8dda-ec9e-4da6-af1c-141bc6e22828/dqc_reference/reference_markers_gtdb.fasta -out GCF_009858255.1_ASM985825v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:27:03,971] [INFO] Task succeeded: Blastn
[2024-01-25 19:27:03,974] [INFO] Selected 10 target genomes.
[2024-01-25 19:27:03,974] [INFO] Target genome list was writen to GCF_009858255.1_ASM985825v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:27:03,980] [INFO] Task started: fastANI
[2024-01-25 19:27:03,980] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e50cd1c-484a-4d4b-ae99-60ac36968a25/GCF_009858255.1_ASM985825v1_genomic.fna.gz --refList GCF_009858255.1_ASM985825v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009858255.1_ASM985825v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:27:21,848] [INFO] Task succeeded: fastANI
[2024-01-25 19:27:21,856] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:27:21,856] [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
GCF_001612825.1	s__Nocardia caishijiensis	99.9854	2054	2090	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001612805.1	s__Nocardia coubleae	91.7623	1730	2090	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.9719	100.00	100.00	1.00	1.00	2	-
GCF_001612905.1	s__Nocardia ignorata	91.6176	1753	2090	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.9719	100.00	100.00	1.00	1.00	2	-
GCF_013839555.1	s__Nocardia sp013839555	91.2933	1390	2090	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.2705	N/A	N/A	N/A	N/A	1	-
GCF_014646295.1	s__Nocardia rhizosphaerihabitans	85.3755	1534	2090	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886715.1	s__Nocardia mangyaensis	84.835	1411	2090	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613085.1	s__Nocardia salmonicida	84.5332	1465	2090	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	97.01	95.63	0.88	0.85	5	-
GCF_000308795.1	s__Nocardia thailandica	82.8321	1241	2090	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008704205.1	s__Nocardia colli	80.8062	1103	2090	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308475.2	s__Nocardia brasiliensis	80.6955	1083	2090	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.8238	100.00	99.99	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-25 19:27:21,859] [INFO] GTDB search result was written to GCF_009858255.1_ASM985825v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:27:21,859] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:27:21,862] [INFO] DFAST_QC result json was written to GCF_009858255.1_ASM985825v1_genomic.fna/dqc_result.json
[2024-01-25 19:27:21,862] [INFO] DFAST_QC completed!
[2024-01-25 19:27:21,862] [INFO] Total running time: 0h2m31s