[2024-01-24 15:27:41,309] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:41,311] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:41,311] [INFO] DQC Reference Directory: /var/lib/cwl/stgab34d765-bdb4-4ce8-80e5-4cfa582dfcac/dqc_reference
[2024-01-24 15:27:43,882] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:43,883] [INFO] Task started: Prodigal
[2024-01-24 15:27:43,883] [INFO] Running command: gunzip -c /var/lib/cwl/stg52bd8e98-1040-44b9-a54d-da88baccc8a9/GCF_013466785.1_ASM1346678v1_genomic.fna.gz | prodigal -d GCF_013466785.1_ASM1346678v1_genomic.fna/cds.fna -a GCF_013466785.1_ASM1346678v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:55,464] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:55,464] [INFO] Task started: HMMsearch
[2024-01-24 15:27:55,464] [INFO] Running command: hmmsearch --tblout GCF_013466785.1_ASM1346678v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgab34d765-bdb4-4ce8-80e5-4cfa582dfcac/dqc_reference/reference_markers.hmm GCF_013466785.1_ASM1346678v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:55,729] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:55,730] [INFO] Found 6/6 markers.
[2024-01-24 15:27:55,772] [INFO] Query marker FASTA was written to GCF_013466785.1_ASM1346678v1_genomic.fna/markers.fasta
[2024-01-24 15:27:55,773] [INFO] Task started: Blastn
[2024-01-24 15:27:55,773] [INFO] Running command: blastn -query GCF_013466785.1_ASM1346678v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab34d765-bdb4-4ce8-80e5-4cfa582dfcac/dqc_reference/reference_markers.fasta -out GCF_013466785.1_ASM1346678v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:56,997] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:57,001] [INFO] Selected 10 target genomes.
[2024-01-24 15:27:57,001] [INFO] Target genome list was writen to GCF_013466785.1_ASM1346678v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:57,007] [INFO] Task started: fastANI
[2024-01-24 15:27:57,007] [INFO] Running command: fastANI --query /var/lib/cwl/stg52bd8e98-1040-44b9-a54d-da88baccc8a9/GCF_013466785.1_ASM1346678v1_genomic.fna.gz --refList GCF_013466785.1_ASM1346678v1_genomic.fna/target_genomes.txt --output GCF_013466785.1_ASM1346678v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:28:09,249] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:09,250] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgab34d765-bdb4-4ce8-80e5-4cfa582dfcac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:28:09,250] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgab34d765-bdb4-4ce8-80e5-4cfa582dfcac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:28:09,268] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:28:09,268] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:28:09,268] [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 marinisabuli	strain=DSM 18965	GCA_013466785.1	419476	419476	type	True	100.0	1390	1390	95	conclusive
Nocardioides marinisabuli	strain=DSM 18965	GCA_013409965.1	419476	419476	type	True	99.9897	1388	1390	95	conclusive
Nocardioides salarius	strain=DSM 18239	GCA_015070765.1	374513	374513	type	True	90.4865	1161	1390	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015339545.1	374513	374513	type	True	90.4752	1161	1390	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_016907435.1	374513	374513	type	True	90.4554	1166	1390	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	81.0375	722	1390	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	80.9489	702	1390	95	below_threshold
Nocardioides coralli	strain=SCSIO 67246	GCA_019880385.1	2872154	2872154	type	True	80.6259	683	1390	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	80.2831	719	1390	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	80.2798	756	1390	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:28:09,270] [INFO] DFAST Taxonomy check result was written to GCF_013466785.1_ASM1346678v1_genomic.fna/tc_result.tsv
[2024-01-24 15:28:09,271] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:28:09,272] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:28:09,272] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgab34d765-bdb4-4ce8-80e5-4cfa582dfcac/dqc_reference/checkm_data
[2024-01-24 15:28:09,274] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:28:09,322] [INFO] Task started: CheckM
[2024-01-24 15:28:09,323] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013466785.1_ASM1346678v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013466785.1_ASM1346678v1_genomic.fna/checkm_input GCF_013466785.1_ASM1346678v1_genomic.fna/checkm_result
[2024-01-24 15:29:12,140] [INFO] Task succeeded: CheckM
[2024-01-24 15:29:12,141] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:29:12,157] [INFO] ===== Completeness check finished =====
[2024-01-24 15:29:12,158] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:29:12,158] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013466785.1_ASM1346678v1_genomic.fna/markers.fasta)
[2024-01-24 15:29:12,159] [INFO] Task started: Blastn
[2024-01-24 15:29:12,159] [INFO] Running command: blastn -query GCF_013466785.1_ASM1346678v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab34d765-bdb4-4ce8-80e5-4cfa582dfcac/dqc_reference/reference_markers_gtdb.fasta -out GCF_013466785.1_ASM1346678v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:29:14,256] [INFO] Task succeeded: Blastn
[2024-01-24 15:29:14,260] [INFO] Selected 19 target genomes.
[2024-01-24 15:29:14,260] [INFO] Target genome list was writen to GCF_013466785.1_ASM1346678v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:29:14,274] [INFO] Task started: fastANI
[2024-01-24 15:29:14,275] [INFO] Running command: fastANI --query /var/lib/cwl/stg52bd8e98-1040-44b9-a54d-da88baccc8a9/GCF_013466785.1_ASM1346678v1_genomic.fna.gz --refList GCF_013466785.1_ASM1346678v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013466785.1_ASM1346678v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:29:37,210] [INFO] Task succeeded: fastANI
[2024-01-24 15:29:37,227] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:29:37,227] [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_013466785.1	s__Nocardioides marinisabuli	100.0	1390	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_016907435.1	s__Nocardioides salarius	90.4495	1167	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	3	-
GCF_001653335.1	s__Nocardioides dokdonensis	87.5042	1093	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015070375.1	s__Nocardioides kribbensis	83.538	854	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.79	97.79	0.94	0.92	3	-
GCF_013408145.1	s__Nocardioides marinus	83.4214	909	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	96.85	95.82	0.82	0.73	3	-
GCF_014127485.1	s__Nocardioides sp014127485	82.7184	828	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.37	99.37	0.97	0.97	2	-
GCF_013177455.1	s__Nocardioides sp013177455	82.5916	856	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.28	98.92	0.97	0.95	4	-
GCF_013155365.1	s__Nocardioides sp013155365	82.4149	790	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011420305.2	s__Nocardioides sp011420305	82.2907	803	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.38	99.38	0.96	0.96	2	-
GCF_003660455.1	s__Nocardioides ferulae	82.1116	855	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409645.1	s__Nocardioides panaciterrulae	82.037	781	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506435.1	s__Nocardioides sp902506435	81.8391	750	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018459925.1	s__Nocardioides aquaticus	81.5835	795	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015319165.1	s__Nocardioides acrostichi	81.5578	778	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001429625.1	s__Nocardioides sp001429625	81.5284	732	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003047295.1	s__Nocardioides sediminis	81.3359	747	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014842875.1	s__Nocardioides sp014842875	80.9853	698	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004785795.1	s__Nocardioides eburneiflavus	80.8527	732	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003076135.1	s__Nocardioides gansuensis	80.7704	680	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:29:37,229] [INFO] GTDB search result was written to GCF_013466785.1_ASM1346678v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:29:37,230] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:29:37,269] [INFO] DFAST_QC result json was written to GCF_013466785.1_ASM1346678v1_genomic.fna/dqc_result.json
[2024-01-24 15:29:37,269] [INFO] DFAST_QC completed!
[2024-01-24 15:29:37,270] [INFO] Total running time: 0h1m56s