[2024-01-24 10:49:34,342] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:49:34,344] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:49:34,344] [INFO] DQC Reference Directory: /var/lib/cwl/stgc9fae94a-3cdb-48bd-9285-4286085656e0/dqc_reference
[2024-01-24 10:49:35,541] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:49:35,542] [INFO] Task started: Prodigal
[2024-01-24 10:49:35,542] [INFO] Running command: gunzip -c /var/lib/cwl/stg7cd333b1-3f7b-4fe8-a53d-641c8d79a129/GCF_019192965.1_ASM1919296v1_genomic.fna.gz | prodigal -d GCF_019192965.1_ASM1919296v1_genomic.fna/cds.fna -a GCF_019192965.1_ASM1919296v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:49:47,973] [INFO] Task succeeded: Prodigal
[2024-01-24 10:49:47,974] [INFO] Task started: HMMsearch
[2024-01-24 10:49:47,974] [INFO] Running command: hmmsearch --tblout GCF_019192965.1_ASM1919296v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc9fae94a-3cdb-48bd-9285-4286085656e0/dqc_reference/reference_markers.hmm GCF_019192965.1_ASM1919296v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:49:48,310] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:49:48,311] [INFO] Found 6/6 markers.
[2024-01-24 10:49:48,354] [INFO] Query marker FASTA was written to GCF_019192965.1_ASM1919296v1_genomic.fna/markers.fasta
[2024-01-24 10:49:48,355] [INFO] Task started: Blastn
[2024-01-24 10:49:48,355] [INFO] Running command: blastn -query GCF_019192965.1_ASM1919296v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9fae94a-3cdb-48bd-9285-4286085656e0/dqc_reference/reference_markers.fasta -out GCF_019192965.1_ASM1919296v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:49,586] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:49,589] [INFO] Selected 13 target genomes.
[2024-01-24 10:49:49,590] [INFO] Target genome list was writen to GCF_019192965.1_ASM1919296v1_genomic.fna/target_genomes.txt
[2024-01-24 10:49:49,620] [INFO] Task started: fastANI
[2024-01-24 10:49:49,620] [INFO] Running command: fastANI --query /var/lib/cwl/stg7cd333b1-3f7b-4fe8-a53d-641c8d79a129/GCF_019192965.1_ASM1919296v1_genomic.fna.gz --refList GCF_019192965.1_ASM1919296v1_genomic.fna/target_genomes.txt --output GCF_019192965.1_ASM1919296v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:50:07,005] [INFO] Task succeeded: fastANI
[2024-01-24 10:50:07,006] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc9fae94a-3cdb-48bd-9285-4286085656e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:50:07,007] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc9fae94a-3cdb-48bd-9285-4286085656e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:50:07,019] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:50:07,019] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:50:07,019] [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
Nocardioides daeguensis	strain=2C1-5	GCA_019192965.1	908359	908359	type	True	100.0	1534	1534	95	conclusive
Nocardioides kongjuensis	strain=DSM 19082	GCA_013409625.1	349522	349522	type	True	89.4342	1209	1534	95	below_threshold
Nocardioides nitrophenolicus	strain=DSM 15529	GCA_016907515.1	60489	60489	type	True	88.2808	1179	1534	95	below_threshold
Nocardioides humi	strain=DCY24	GCA_006494775.1	449461	449461	type	True	87.2321	1134	1534	95	below_threshold
Nocardioides albidus	strain=CCTCC AB 2015297	GCA_006335005.1	1517589	1517589	type	True	87.086	1042	1534	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	86.8513	1127	1534	95	below_threshold
Pimelobacter simplex	strain=ATCC 6946	GCA_900114845.1	2045	2045	type	True	85.6839	1132	1534	95	below_threshold
Pimelobacter simplex	strain=NBRC 12069	GCA_006538965.1	2045	2045	type	True	85.6251	1132	1534	95	below_threshold
Nocardioides aromaticivorans	strain=DSM 15131	GCA_013408525.1	200618	200618	type	True	85.2896	1086	1534	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	81.5316	818	1534	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	81.517	812	1534	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	79.9985	673	1534	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	79.8542	668	1534	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:50:07,021] [INFO] DFAST Taxonomy check result was written to GCF_019192965.1_ASM1919296v1_genomic.fna/tc_result.tsv
[2024-01-24 10:50:07,022] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:50:07,022] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:50:07,022] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc9fae94a-3cdb-48bd-9285-4286085656e0/dqc_reference/checkm_data
[2024-01-24 10:50:07,023] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:50:07,070] [INFO] Task started: CheckM
[2024-01-24 10:50:07,070] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019192965.1_ASM1919296v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019192965.1_ASM1919296v1_genomic.fna/checkm_input GCF_019192965.1_ASM1919296v1_genomic.fna/checkm_result
[2024-01-24 10:51:08,629] [INFO] Task succeeded: CheckM
[2024-01-24 10:51:08,630] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:51:08,653] [INFO] ===== Completeness check finished =====
[2024-01-24 10:51:08,654] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:51:08,654] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019192965.1_ASM1919296v1_genomic.fna/markers.fasta)
[2024-01-24 10:51:08,654] [INFO] Task started: Blastn
[2024-01-24 10:51:08,654] [INFO] Running command: blastn -query GCF_019192965.1_ASM1919296v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9fae94a-3cdb-48bd-9285-4286085656e0/dqc_reference/reference_markers_gtdb.fasta -out GCF_019192965.1_ASM1919296v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:51:10,713] [INFO] Task succeeded: Blastn
[2024-01-24 10:51:10,717] [INFO] Selected 11 target genomes.
[2024-01-24 10:51:10,717] [INFO] Target genome list was writen to GCF_019192965.1_ASM1919296v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:51:10,725] [INFO] Task started: fastANI
[2024-01-24 10:51:10,726] [INFO] Running command: fastANI --query /var/lib/cwl/stg7cd333b1-3f7b-4fe8-a53d-641c8d79a129/GCF_019192965.1_ASM1919296v1_genomic.fna.gz --refList GCF_019192965.1_ASM1919296v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019192965.1_ASM1919296v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:51:26,797] [INFO] Task succeeded: fastANI
[2024-01-24 10:51:26,815] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:51:26,816] [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_019192965.1	s__Nocardioides daeguensis	100.0	1534	1534	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013409625.1	s__Nocardioides kongjuensis	89.4779	1206	1534	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016803235.1	s__Nocardioides simplex_A	89.4016	1183	1534	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715725.1	s__Nocardioides sp006715725	89.1833	1221	1534	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907515.1	s__Nocardioides nitrophenolicus	88.2824	1178	1534	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006494775.1	s__Nocardioides humi	87.2388	1133	1534	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006335005.1	s__Nocardioides albidus	87.1138	1040	1534	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114845.1	s__Nocardioides simplex	85.7055	1130	1534	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.16	97.49	0.97	0.92	4	-
GCF_013408525.1	s__Nocardioides aromaticivorans	85.2878	1086	1534	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.43	98.36	0.91	0.91	3	-
GCF_001428825.1	s__Nocardioides sp001428825	85.145	1075	1534	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_018388425.1	s__Nocardioides sp018388425	83.3092	839	1534	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.59	99.18	0.98	0.96	3	-
--------------------------------------------------------------------------------
[2024-01-24 10:51:26,818] [INFO] GTDB search result was written to GCF_019192965.1_ASM1919296v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:51:26,820] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:51:26,825] [INFO] DFAST_QC result json was written to GCF_019192965.1_ASM1919296v1_genomic.fna/dqc_result.json
[2024-01-24 10:51:26,825] [INFO] DFAST_QC completed!
[2024-01-24 10:51:26,825] [INFO] Total running time: 0h1m52s