[2023-06-29 00:22:52,795] [INFO] DFAST_QC pipeline started.
[2023-06-29 00:22:52,797] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 00:22:52,797] [INFO] DQC Reference Directory: /var/lib/cwl/stg954d47fd-9d4a-4b17-9e02-bdcc2626003e/dqc_reference
[2023-06-29 00:22:54,259] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 00:22:54,260] [INFO] Task started: Prodigal
[2023-06-29 00:22:54,260] [INFO] Running command: gunzip -c /var/lib/cwl/stg4001e091-50f1-4d9a-8626-fbe79e3d742b/GCA_005887735.1_ASM588773v1_genomic.fna.gz | prodigal -d GCA_005887735.1_ASM588773v1_genomic.fna/cds.fna -a GCA_005887735.1_ASM588773v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 00:23:08,959] [INFO] Task succeeded: Prodigal
[2023-06-29 00:23:08,960] [INFO] Task started: HMMsearch
[2023-06-29 00:23:08,960] [INFO] Running command: hmmsearch --tblout GCA_005887735.1_ASM588773v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg954d47fd-9d4a-4b17-9e02-bdcc2626003e/dqc_reference/reference_markers.hmm GCA_005887735.1_ASM588773v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 00:23:09,212] [INFO] Task succeeded: HMMsearch
[2023-06-29 00:23:09,214] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4001e091-50f1-4d9a-8626-fbe79e3d742b/GCA_005887735.1_ASM588773v1_genomic.fna.gz]
[2023-06-29 00:23:09,248] [INFO] Query marker FASTA was written to GCA_005887735.1_ASM588773v1_genomic.fna/markers.fasta
[2023-06-29 00:23:09,248] [INFO] Task started: Blastn
[2023-06-29 00:23:09,248] [INFO] Running command: blastn -query GCA_005887735.1_ASM588773v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg954d47fd-9d4a-4b17-9e02-bdcc2626003e/dqc_reference/reference_markers.fasta -out GCA_005887735.1_ASM588773v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:23:09,874] [INFO] Task succeeded: Blastn
[2023-06-29 00:23:09,882] [INFO] Selected 13 target genomes.
[2023-06-29 00:23:09,883] [INFO] Target genome list was writen to GCA_005887735.1_ASM588773v1_genomic.fna/target_genomes.txt
[2023-06-29 00:23:09,885] [INFO] Task started: fastANI
[2023-06-29 00:23:09,885] [INFO] Running command: fastANI --query /var/lib/cwl/stg4001e091-50f1-4d9a-8626-fbe79e3d742b/GCA_005887735.1_ASM588773v1_genomic.fna.gz --refList GCA_005887735.1_ASM588773v1_genomic.fna/target_genomes.txt --output GCA_005887735.1_ASM588773v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 00:23:20,081] [INFO] Task succeeded: fastANI
[2023-06-29 00:23:20,081] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg954d47fd-9d4a-4b17-9e02-bdcc2626003e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 00:23:20,082] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg954d47fd-9d4a-4b17-9e02-bdcc2626003e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 00:23:20,089] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 00:23:20,089] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 00:23:20,089] [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
Nonomuraea harbinensis	strain=CGMCC 4.7106	GCA_019396385.1	1286938	1286938	type	True	75.0175	62	742	95	below_threshold
Nocardioides humi	strain=DCY24	GCA_006494775.1	449461	449461	type	True	74.9965	63	742	95	below_threshold
Nocardioides nitrophenolicus	strain=DSM 15529	GCA_016907515.1	60489	60489	type	True	74.903	55	742	95	below_threshold
Saccharothrix texasensis	strain=DSM 44231	GCA_003752005.1	103734	103734	type	True	74.8246	70	742	95	below_threshold
Actinomycetospora cinnamomea	strain=DSM 45771	GCA_003096675.1	663609	663609	type	True	74.7976	80	742	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 00:23:20,091] [INFO] DFAST Taxonomy check result was written to GCA_005887735.1_ASM588773v1_genomic.fna/tc_result.tsv
[2023-06-29 00:23:20,092] [INFO] ===== Taxonomy check completed =====
[2023-06-29 00:23:20,092] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 00:23:20,092] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg954d47fd-9d4a-4b17-9e02-bdcc2626003e/dqc_reference/checkm_data
[2023-06-29 00:23:20,093] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 00:23:20,132] [INFO] Task started: CheckM
[2023-06-29 00:23:20,133] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_005887735.1_ASM588773v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_005887735.1_ASM588773v1_genomic.fna/checkm_input GCA_005887735.1_ASM588773v1_genomic.fna/checkm_result
[2023-06-29 00:24:03,081] [INFO] Task succeeded: CheckM
[2023-06-29 00:24:03,115] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.92%
Contamintation: 1.39%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 00:24:03,144] [INFO] ===== Completeness check finished =====
[2023-06-29 00:24:03,144] [INFO] ===== Start GTDB Search =====
[2023-06-29 00:24:03,145] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_005887735.1_ASM588773v1_genomic.fna/markers.fasta)
[2023-06-29 00:24:03,145] [INFO] Task started: Blastn
[2023-06-29 00:24:03,145] [INFO] Running command: blastn -query GCA_005887735.1_ASM588773v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg954d47fd-9d4a-4b17-9e02-bdcc2626003e/dqc_reference/reference_markers_gtdb.fasta -out GCA_005887735.1_ASM588773v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:24:03,955] [INFO] Task succeeded: Blastn
[2023-06-29 00:24:03,961] [INFO] Selected 9 target genomes.
[2023-06-29 00:24:03,961] [INFO] Target genome list was writen to GCA_005887735.1_ASM588773v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 00:24:03,968] [INFO] Task started: fastANI
[2023-06-29 00:24:03,968] [INFO] Running command: fastANI --query /var/lib/cwl/stg4001e091-50f1-4d9a-8626-fbe79e3d742b/GCA_005887735.1_ASM588773v1_genomic.fna.gz --refList GCA_005887735.1_ASM588773v1_genomic.fna/target_genomes_gtdb.txt --output GCA_005887735.1_ASM588773v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 00:24:09,261] [INFO] Task succeeded: fastANI
[2023-06-29 00:24:09,278] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 00:24:09,278] [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_005887735.1	s__40CM-4-65-16 sp005887735	100.0	728	742	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__Dormibacterales;f__Dormibacteraceae;g__40CM-4-65-16	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_005880795.1	s__40CM-4-65-16 sp005880795	88.3343	622	742	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__Dormibacterales;f__Dormibacteraceae;g__40CM-4-65-16	95.0	99.34	99.06	0.87	0.86	4	-
GCA_005887685.1	s__40CM-4-65-16 sp005887685	85.8744	583	742	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__Dormibacterales;f__Dormibacteraceae;g__40CM-4-65-16	95.0	99.31	99.31	0.86	0.86	2	-
GCA_005889085.1	s__40CM-4-65-16 sp005889085	81.0206	433	742	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__Dormibacterales;f__Dormibacteraceae;g__40CM-4-65-16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005880915.1	s__40CM-4-65-16 sp005880915	80.5882	506	742	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__Dormibacterales;f__Dormibacteraceae;g__40CM-4-65-16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005880755.1	s__40CM-4-65-16 sp005880755	80.5662	322	742	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__Dormibacterales;f__Dormibacteraceae;g__40CM-4-65-16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005882135.1	s__40CM-4-65-16 sp005882135	80.4713	413	742	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__Dormibacterales;f__Dormibacteraceae;g__40CM-4-65-16	95.0	99.34	99.09	0.85	0.80	5	-
GCA_005889135.1	s__40CM-4-65-16 sp005889135	80.0925	439	742	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__Dormibacterales;f__Dormibacteraceae;g__40CM-4-65-16	95.0	99.06	98.96	0.92	0.90	3	-
GCA_005880345.1	s__40CM-4-65-16 sp005880345	79.8706	276	742	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__Dormibacterales;f__Dormibacteraceae;g__40CM-4-65-16	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 00:24:09,302] [INFO] GTDB search result was written to GCA_005887735.1_ASM588773v1_genomic.fna/result_gtdb.tsv
[2023-06-29 00:24:09,304] [INFO] ===== GTDB Search completed =====
[2023-06-29 00:24:09,308] [INFO] DFAST_QC result json was written to GCA_005887735.1_ASM588773v1_genomic.fna/dqc_result.json
[2023-06-29 00:24:09,308] [INFO] DFAST_QC completed!
[2023-06-29 00:24:09,308] [INFO] Total running time: 0h1m17s