[2023-06-05 13:47:48,405] [INFO] DFAST_QC pipeline started.
[2023-06-05 13:47:48,408] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 13:47:48,408] [INFO] DQC Reference Directory: /var/lib/cwl/stgcd3fa5b6-e26a-4a22-a4c4-970bd145ef01/dqc_reference
[2023-06-05 13:47:50,100] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 13:47:50,101] [INFO] Task started: Prodigal
[2023-06-05 13:47:50,101] [INFO] Running command: gunzip -c /var/lib/cwl/stg9a23289e-56c1-4eef-b1ca-ce36cb20d8b1/GCA_902770045.1_Rumen_uncultured_genome_RUG11534_genomic.fna.gz | prodigal -d GCA_902770045.1_Rumen_uncultured_genome_RUG11534_genomic.fna/cds.fna -a GCA_902770045.1_Rumen_uncultured_genome_RUG11534_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 13:47:55,923] [INFO] Task succeeded: Prodigal
[2023-06-05 13:47:55,923] [INFO] Task started: HMMsearch
[2023-06-05 13:47:55,923] [INFO] Running command: hmmsearch --tblout GCA_902770045.1_Rumen_uncultured_genome_RUG11534_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcd3fa5b6-e26a-4a22-a4c4-970bd145ef01/dqc_reference/reference_markers.hmm GCA_902770045.1_Rumen_uncultured_genome_RUG11534_genomic.fna/protein.faa > /dev/null
[2023-06-05 13:47:56,108] [INFO] Task succeeded: HMMsearch
[2023-06-05 13:47:56,109] [INFO] Found 6/6 markers.
[2023-06-05 13:47:56,132] [INFO] Query marker FASTA was written to GCA_902770045.1_Rumen_uncultured_genome_RUG11534_genomic.fna/markers.fasta
[2023-06-05 13:47:56,132] [INFO] Task started: Blastn
[2023-06-05 13:47:56,132] [INFO] Running command: blastn -query GCA_902770045.1_Rumen_uncultured_genome_RUG11534_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd3fa5b6-e26a-4a22-a4c4-970bd145ef01/dqc_reference/reference_markers.fasta -out GCA_902770045.1_Rumen_uncultured_genome_RUG11534_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 13:47:56,756] [INFO] Task succeeded: Blastn
[2023-06-05 13:47:56,759] [INFO] Selected 35 target genomes.
[2023-06-05 13:47:56,760] [INFO] Target genome list was writen to GCA_902770045.1_Rumen_uncultured_genome_RUG11534_genomic.fna/target_genomes.txt
[2023-06-05 13:47:56,767] [INFO] Task started: fastANI
[2023-06-05 13:47:56,768] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a23289e-56c1-4eef-b1ca-ce36cb20d8b1/GCA_902770045.1_Rumen_uncultured_genome_RUG11534_genomic.fna.gz --refList GCA_902770045.1_Rumen_uncultured_genome_RUG11534_genomic.fna/target_genomes.txt --output GCA_902770045.1_Rumen_uncultured_genome_RUG11534_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 13:48:18,592] [INFO] Task succeeded: fastANI
[2023-06-05 13:48:18,593] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcd3fa5b6-e26a-4a22-a4c4-970bd145ef01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 13:48:18,593] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcd3fa5b6-e26a-4a22-a4c4-970bd145ef01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 13:48:18,601] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 13:48:18,601] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 13:48:18,601] [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
Agrococcus carbonis	strain=DSM 22965	GCA_900104705.1	684552	684552	type	True	75.4426	63	715	95	below_threshold
Thermomonospora umbrina	strain=DSM 43927	GCA_003386555.1	111806	111806	type	True	75.2215	56	715	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	75.0875	70	715	95	below_threshold
Motilibacter deserti	strain=E257	GCA_011250635.1	2714956	2714956	type	True	75.0076	56	715	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	75.0016	68	715	95	below_threshold
Nonomuraea cavernae	strain=CGMCC 4.7368	GCA_014646355.1	2045107	2045107	type	True	74.887	55	715	95	below_threshold
Nonomuraea cavernae	strain=SYSU K10005	GCA_020215905.1	2045107	2045107	type	True	74.887	55	715	95	below_threshold
Nonomuraea indica	strain=DRQ-2	GCA_002850745.1	1581193	1581193	type	True	74.8321	79	715	95	below_threshold
Planotetraspora mira	strain=NBRC 15435	GCA_016863275.1	58121	58121	type	True	74.7413	56	715	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	74.6422	79	715	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 13:48:18,603] [INFO] DFAST Taxonomy check result was written to GCA_902770045.1_Rumen_uncultured_genome_RUG11534_genomic.fna/tc_result.tsv
[2023-06-05 13:48:18,604] [INFO] ===== Taxonomy check completed =====
[2023-06-05 13:48:18,604] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 13:48:18,604] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcd3fa5b6-e26a-4a22-a4c4-970bd145ef01/dqc_reference/checkm_data
[2023-06-05 13:48:18,605] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 13:48:18,631] [INFO] Task started: CheckM
[2023-06-05 13:48:18,631] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902770045.1_Rumen_uncultured_genome_RUG11534_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902770045.1_Rumen_uncultured_genome_RUG11534_genomic.fna/checkm_input GCA_902770045.1_Rumen_uncultured_genome_RUG11534_genomic.fna/checkm_result
[2023-06-05 13:48:38,121] [INFO] Task succeeded: CheckM
[2023-06-05 13:48:38,123] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.29%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 13:48:38,137] [INFO] ===== Completeness check finished =====
[2023-06-05 13:48:38,137] [INFO] ===== Start GTDB Search =====
[2023-06-05 13:48:38,137] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902770045.1_Rumen_uncultured_genome_RUG11534_genomic.fna/markers.fasta)
[2023-06-05 13:48:38,137] [INFO] Task started: Blastn
[2023-06-05 13:48:38,137] [INFO] Running command: blastn -query GCA_902770045.1_Rumen_uncultured_genome_RUG11534_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd3fa5b6-e26a-4a22-a4c4-970bd145ef01/dqc_reference/reference_markers_gtdb.fasta -out GCA_902770045.1_Rumen_uncultured_genome_RUG11534_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 13:48:39,141] [INFO] Task succeeded: Blastn
[2023-06-05 13:48:39,144] [INFO] Selected 12 target genomes.
[2023-06-05 13:48:39,144] [INFO] Target genome list was writen to GCA_902770045.1_Rumen_uncultured_genome_RUG11534_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 13:48:39,150] [INFO] Task started: fastANI
[2023-06-05 13:48:39,150] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a23289e-56c1-4eef-b1ca-ce36cb20d8b1/GCA_902770045.1_Rumen_uncultured_genome_RUG11534_genomic.fna.gz --refList GCA_902770045.1_Rumen_uncultured_genome_RUG11534_genomic.fna/target_genomes_gtdb.txt --output GCA_902770045.1_Rumen_uncultured_genome_RUG11534_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 13:48:46,688] [INFO] Task succeeded: fastANI
[2023-06-05 13:48:46,697] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 13:48:46,697] [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_902770045.1	s__UBA1067 sp902770045	100.0	712	715	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	95.51	95.51	0.70	0.70	2	conclusive
GCA_902764415.1	s__UBA1067 sp002351765	94.8636	533	715	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	97.23	96.23	0.86	0.81	5	-
GCA_004551905.1	s__UBA1067 sp004551905	94.1529	424	715	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902800055.1	s__UBA1067 sp902800055	92.3217	489	715	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	96.21	96.21	0.84	0.84	3	-
GCA_017432385.1	s__UBA1067 sp017432385	80.9521	231	715	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900321255.1	s__UBA1067 sp900321255	80.9493	276	715	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.6109	100.00	100.00	1.00	1.00	2	-
GCA_900320855.1	s__UBA1067 sp900320855	80.5241	253	715	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	100.00	100.00	0.99	0.99	2	-
GCA_002321305.1	s__UBA1067 sp002321305	80.4989	272	715	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902799955.1	s__UBA1067 sp902799955	80.2044	255	715	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	95.66	95.66	0.72	0.72	2	-
GCA_017405115.1	s__UBA1067 sp017405115	79.8679	316	715	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902773015.1	s__UBA1067 sp902773015	79.426	219	715	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017514235.1	s__UBA1067 sp017514235	79.2606	250	715	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 13:48:46,698] [INFO] GTDB search result was written to GCA_902770045.1_Rumen_uncultured_genome_RUG11534_genomic.fna/result_gtdb.tsv
[2023-06-05 13:48:46,699] [INFO] ===== GTDB Search completed =====
[2023-06-05 13:48:46,702] [INFO] DFAST_QC result json was written to GCA_902770045.1_Rumen_uncultured_genome_RUG11534_genomic.fna/dqc_result.json
[2023-06-05 13:48:46,702] [INFO] DFAST_QC completed!
[2023-06-05 13:48:46,702] [INFO] Total running time: 0h0m58s