[2024-01-24 11:51:49,753] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:49,755] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:49,755] [INFO] DQC Reference Directory: /var/lib/cwl/stg02c24d5b-22c5-492f-8137-40f2853d0651/dqc_reference
[2024-01-24 11:51:51,000] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:51,000] [INFO] Task started: Prodigal
[2024-01-24 11:51:51,001] [INFO] Running command: gunzip -c /var/lib/cwl/stg6d18e78d-f3d0-4fe6-bd07-38238d3dd439/GCF_000802235.1_ASM80223v1_genomic.fna.gz | prodigal -d GCF_000802235.1_ASM80223v1_genomic.fna/cds.fna -a GCF_000802235.1_ASM80223v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:52:03,122] [INFO] Task succeeded: Prodigal
[2024-01-24 11:52:03,123] [INFO] Task started: HMMsearch
[2024-01-24 11:52:03,123] [INFO] Running command: hmmsearch --tblout GCF_000802235.1_ASM80223v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02c24d5b-22c5-492f-8137-40f2853d0651/dqc_reference/reference_markers.hmm GCF_000802235.1_ASM80223v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:52:03,402] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:52:03,405] [INFO] Found 6/6 markers.
[2024-01-24 11:52:03,449] [INFO] Query marker FASTA was written to GCF_000802235.1_ASM80223v1_genomic.fna/markers.fasta
[2024-01-24 11:52:03,450] [INFO] Task started: Blastn
[2024-01-24 11:52:03,450] [INFO] Running command: blastn -query GCF_000802235.1_ASM80223v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02c24d5b-22c5-492f-8137-40f2853d0651/dqc_reference/reference_markers.fasta -out GCF_000802235.1_ASM80223v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:04,526] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:04,530] [INFO] Selected 12 target genomes.
[2024-01-24 11:52:04,530] [INFO] Target genome list was writen to GCF_000802235.1_ASM80223v1_genomic.fna/target_genomes.txt
[2024-01-24 11:52:04,565] [INFO] Task started: fastANI
[2024-01-24 11:52:04,566] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d18e78d-f3d0-4fe6-bd07-38238d3dd439/GCF_000802235.1_ASM80223v1_genomic.fna.gz --refList GCF_000802235.1_ASM80223v1_genomic.fna/target_genomes.txt --output GCF_000802235.1_ASM80223v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:13,833] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:13,834] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02c24d5b-22c5-492f-8137-40f2853d0651/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:13,834] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02c24d5b-22c5-492f-8137-40f2853d0651/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:13,847] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:52:13,847] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:52:13,847] [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
Sinomonas humi	strain=MUSC 117	GCA_000802235.1	1338436	1338436	type	True	100.0	1397	1399	95	conclusive
Sinomonas susongensis	strain=A31	GCA_005877005.1	1324851	1324851	type	True	84.8962	937	1399	95	below_threshold
Sinomonas albida	strain=LC13	GCA_004919045.1	369942	369942	type	True	81.8223	758	1399	95	below_threshold
Sinomonas mesophila	strain=MPKL 26	GCA_001999765.1	1531955	1531955	type	True	80.6498	619	1399	95	below_threshold
Sinomonas atrocyanea	strain=CGMCC 1.1891	GCA_014644475.1	37927	37927	type	True	80.3059	650	1399	95	below_threshold
Sinomonas atrocyanea	strain=NBRC 12956	GCA_006539205.1	37927	37927	type	True	80.2371	662	1399	95	below_threshold
Sinomonas notoginsengisoli	strain=KCTC 29237	GCA_021554725.1	1457311	1457311	type	True	79.4684	520	1399	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	77.8766	288	1399	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	77.7526	273	1399	95	below_threshold
Arthrobacter agilis	strain=DSM 20550	GCA_006494655.1	37921	37921	type	True	77.6472	262	1399	95	below_threshold
Arthrobacter ulcerisalmonis		GCA_900609065.1	2483813	2483813	type	True	77.1304	221	1399	95	below_threshold
Georgenia wutianyii	strain=Z294	GCA_006349365.1	2585135	2585135	type	True	76.7263	196	1399	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:13,849] [INFO] DFAST Taxonomy check result was written to GCF_000802235.1_ASM80223v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:13,849] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:13,850] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:13,850] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02c24d5b-22c5-492f-8137-40f2853d0651/dqc_reference/checkm_data
[2024-01-24 11:52:13,851] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:13,893] [INFO] Task started: CheckM
[2024-01-24 11:52:13,894] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000802235.1_ASM80223v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000802235.1_ASM80223v1_genomic.fna/checkm_input GCF_000802235.1_ASM80223v1_genomic.fna/checkm_result
[2024-01-24 11:52:50,997] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:50,999] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:51,018] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:51,019] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:51,019] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000802235.1_ASM80223v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:51,019] [INFO] Task started: Blastn
[2024-01-24 11:52:51,020] [INFO] Running command: blastn -query GCF_000802235.1_ASM80223v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02c24d5b-22c5-492f-8137-40f2853d0651/dqc_reference/reference_markers_gtdb.fasta -out GCF_000802235.1_ASM80223v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:52,669] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:52,673] [INFO] Selected 9 target genomes.
[2024-01-24 11:52:52,674] [INFO] Target genome list was writen to GCF_000802235.1_ASM80223v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:52,726] [INFO] Task started: fastANI
[2024-01-24 11:52:52,727] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d18e78d-f3d0-4fe6-bd07-38238d3dd439/GCF_000802235.1_ASM80223v1_genomic.fna.gz --refList GCF_000802235.1_ASM80223v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000802235.1_ASM80223v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:01,342] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:01,353] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:53:01,353] [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_000802235.1	s__Sinomonas humi	100.0	1397	1399	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Sinomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005877005.1	s__Sinomonas susongensis	84.9159	935	1399	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Sinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004919045.1	s__Sinomonas albida	81.8446	756	1399	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Sinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005876955.1	s__Sinomonas sp005876955	81.7117	795	1399	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Sinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001999765.1	s__Sinomonas mesophila	80.6421	620	1399	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Sinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001577305.1	s__Sinomonas atrocyanea	80.2287	684	1399	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Sinomonas	95.0	99.98	99.98	1.00	1.00	3	-
GCF_002224485.1	s__Sinomonas sp002224485	80.0373	615	1399	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Sinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656475.1	s__Sinomonas sp014656475	79.8624	591	1399	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Sinomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900016675.1	s__Arthrobacter_B saudimassiliensis	77.6617	258	1399	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:53:01,356] [INFO] GTDB search result was written to GCF_000802235.1_ASM80223v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:01,357] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:01,361] [INFO] DFAST_QC result json was written to GCF_000802235.1_ASM80223v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:01,361] [INFO] DFAST_QC completed!
[2024-01-24 11:53:01,361] [INFO] Total running time: 0h1m12s