[2023-06-28 12:59:19,856] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:59:19,858] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:59:19,858] [INFO] DQC Reference Directory: /var/lib/cwl/stgfb747934-b22f-4c0b-8537-7666169c018b/dqc_reference
[2023-06-28 12:59:21,052] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:59:21,053] [INFO] Task started: Prodigal
[2023-06-28 12:59:21,053] [INFO] Running command: gunzip -c /var/lib/cwl/stgf720c511-a66e-466a-817b-051ba4fcae93/GCA_017512335.1_ASM1751233v1_genomic.fna.gz | prodigal -d GCA_017512335.1_ASM1751233v1_genomic.fna/cds.fna -a GCA_017512335.1_ASM1751233v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:59:29,741] [INFO] Task succeeded: Prodigal
[2023-06-28 12:59:29,742] [INFO] Task started: HMMsearch
[2023-06-28 12:59:29,742] [INFO] Running command: hmmsearch --tblout GCA_017512335.1_ASM1751233v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfb747934-b22f-4c0b-8537-7666169c018b/dqc_reference/reference_markers.hmm GCA_017512335.1_ASM1751233v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:59:30,039] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:59:30,041] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf720c511-a66e-466a-817b-051ba4fcae93/GCA_017512335.1_ASM1751233v1_genomic.fna.gz]
[2023-06-28 12:59:30,083] [INFO] Query marker FASTA was written to GCA_017512335.1_ASM1751233v1_genomic.fna/markers.fasta
[2023-06-28 12:59:30,083] [INFO] Task started: Blastn
[2023-06-28 12:59:30,083] [INFO] Running command: blastn -query GCA_017512335.1_ASM1751233v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb747934-b22f-4c0b-8537-7666169c018b/dqc_reference/reference_markers.fasta -out GCA_017512335.1_ASM1751233v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:59:30,762] [INFO] Task succeeded: Blastn
[2023-06-28 12:59:30,766] [INFO] Selected 30 target genomes.
[2023-06-28 12:59:30,767] [INFO] Target genome list was writen to GCA_017512335.1_ASM1751233v1_genomic.fna/target_genomes.txt
[2023-06-28 12:59:30,770] [INFO] Task started: fastANI
[2023-06-28 12:59:30,770] [INFO] Running command: fastANI --query /var/lib/cwl/stgf720c511-a66e-466a-817b-051ba4fcae93/GCA_017512335.1_ASM1751233v1_genomic.fna.gz --refList GCA_017512335.1_ASM1751233v1_genomic.fna/target_genomes.txt --output GCA_017512335.1_ASM1751233v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:59:48,429] [INFO] Task succeeded: fastANI
[2023-06-28 12:59:48,430] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfb747934-b22f-4c0b-8537-7666169c018b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:59:48,430] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfb747934-b22f-4c0b-8537-7666169c018b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:59:48,442] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:59:48,443] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 12:59:48,443] [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
Geodermatophilus telluris	strain=DSM 45421	GCA_900102745.1	1190417	1190417	type	True	74.9532	50	854	95	below_threshold
Thermomonospora echinospora	strain=DSM 43163	GCA_900108175.1	1992	1992	type	True	74.9214	77	854	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	74.8088	81	854	95	below_threshold
Micromonospora yangpuensis	strain=DSM 45577	GCA_900091615.1	683228	683228	type	True	74.6507	50	854	95	below_threshold
Micromonospora rhizosphaerae	strain=DSM 45431	GCA_900091465.1	568872	568872	type	True	74.6457	64	854	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 12:59:48,445] [INFO] DFAST Taxonomy check result was written to GCA_017512335.1_ASM1751233v1_genomic.fna/tc_result.tsv
[2023-06-28 12:59:48,446] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:59:48,446] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:59:48,447] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfb747934-b22f-4c0b-8537-7666169c018b/dqc_reference/checkm_data
[2023-06-28 12:59:48,448] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:59:48,493] [INFO] Task started: CheckM
[2023-06-28 12:59:48,493] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017512335.1_ASM1751233v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017512335.1_ASM1751233v1_genomic.fna/checkm_input GCA_017512335.1_ASM1751233v1_genomic.fna/checkm_result
[2023-06-28 13:00:19,844] [INFO] Task succeeded: CheckM
[2023-06-28 13:00:19,846] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.41%
Contamintation: 19.44%
Strain heterogeneity: 63.16%
--------------------------------------------------------------------------------
[2023-06-28 13:00:19,875] [INFO] ===== Completeness check finished =====
[2023-06-28 13:00:19,876] [INFO] ===== Start GTDB Search =====
[2023-06-28 13:00:19,876] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017512335.1_ASM1751233v1_genomic.fna/markers.fasta)
[2023-06-28 13:00:19,877] [INFO] Task started: Blastn
[2023-06-28 13:00:19,877] [INFO] Running command: blastn -query GCA_017512335.1_ASM1751233v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb747934-b22f-4c0b-8537-7666169c018b/dqc_reference/reference_markers_gtdb.fasta -out GCA_017512335.1_ASM1751233v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:00:20,979] [INFO] Task succeeded: Blastn
[2023-06-28 13:00:20,983] [INFO] Selected 11 target genomes.
[2023-06-28 13:00:20,984] [INFO] Target genome list was writen to GCA_017512335.1_ASM1751233v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 13:00:20,987] [INFO] Task started: fastANI
[2023-06-28 13:00:20,988] [INFO] Running command: fastANI --query /var/lib/cwl/stgf720c511-a66e-466a-817b-051ba4fcae93/GCA_017512335.1_ASM1751233v1_genomic.fna.gz --refList GCA_017512335.1_ASM1751233v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017512335.1_ASM1751233v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 13:00:29,786] [INFO] Task succeeded: fastANI
[2023-06-28 13:00:29,801] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 13:00:29,801] [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_902765735.1	s__UBA2862 sp002350605	95.1862	616	854	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	99.72	99.72	0.89	0.89	2	conclusive
GCA_017434085.1	s__UBA2862 sp017434085	92.3926	542	854	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902790525.1	s__UBA2862 sp902790525	92.1524	627	854	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017471125.1	s__UBA2862 sp017471125	83.9803	423	854	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902799465.1	s__UBA2862 sp902799465	83.5598	442	854	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	97.80	97.80	0.88	0.88	2	-
GCA_900317565.1	s__UBA2862 sp900317565	82.2986	410	854	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	99.55	99.55	0.85	0.85	2	-
GCA_902777335.1	s__UBA2862 sp902777335	82.198	429	854	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017537105.1	s__UBA2862 sp017537105	82.1173	296	854	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315585.1	s__UBA2862 sp900315585	82.0304	373	854	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	98.00	97.28	0.87	0.83	5	-
GCA_902778995.1	s__UBA2862 sp902778995	81.9238	390	854	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017535865.1	s__Limivicinus sp017535865	77.8572	50	854	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 13:00:29,803] [INFO] GTDB search result was written to GCA_017512335.1_ASM1751233v1_genomic.fna/result_gtdb.tsv
[2023-06-28 13:00:29,803] [INFO] ===== GTDB Search completed =====
[2023-06-28 13:00:29,806] [INFO] DFAST_QC result json was written to GCA_017512335.1_ASM1751233v1_genomic.fna/dqc_result.json
[2023-06-28 13:00:29,806] [INFO] DFAST_QC completed!
[2023-06-28 13:00:29,807] [INFO] Total running time: 0h1m10s