[2024-01-24 14:55:23,377] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:23,380] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:23,380] [INFO] DQC Reference Directory: /var/lib/cwl/stg0aad7602-93ba-4c26-9f47-c2911462cfed/dqc_reference
[2024-01-24 14:55:24,614] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:24,615] [INFO] Task started: Prodigal
[2024-01-24 14:55:24,615] [INFO] Running command: gunzip -c /var/lib/cwl/stgec3aedb9-a9ca-4ab8-951a-6fe7d99dfae4/GCF_001895005.1_ASM189500v1_genomic.fna.gz | prodigal -d GCF_001895005.1_ASM189500v1_genomic.fna/cds.fna -a GCF_001895005.1_ASM189500v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:45,574] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:45,574] [INFO] Task started: HMMsearch
[2024-01-24 14:55:45,575] [INFO] Running command: hmmsearch --tblout GCF_001895005.1_ASM189500v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0aad7602-93ba-4c26-9f47-c2911462cfed/dqc_reference/reference_markers.hmm GCF_001895005.1_ASM189500v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:45,921] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:45,923] [INFO] Found 6/6 markers.
[2024-01-24 14:55:45,986] [INFO] Query marker FASTA was written to GCF_001895005.1_ASM189500v1_genomic.fna/markers.fasta
[2024-01-24 14:55:45,986] [INFO] Task started: Blastn
[2024-01-24 14:55:45,986] [INFO] Running command: blastn -query GCF_001895005.1_ASM189500v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0aad7602-93ba-4c26-9f47-c2911462cfed/dqc_reference/reference_markers.fasta -out GCF_001895005.1_ASM189500v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:47,261] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:47,264] [INFO] Selected 11 target genomes.
[2024-01-24 14:55:47,264] [INFO] Target genome list was writen to GCF_001895005.1_ASM189500v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:47,273] [INFO] Task started: fastANI
[2024-01-24 14:55:47,273] [INFO] Running command: fastANI --query /var/lib/cwl/stgec3aedb9-a9ca-4ab8-951a-6fe7d99dfae4/GCF_001895005.1_ASM189500v1_genomic.fna.gz --refList GCF_001895005.1_ASM189500v1_genomic.fna/target_genomes.txt --output GCF_001895005.1_ASM189500v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:59,991] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:59,992] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0aad7602-93ba-4c26-9f47-c2911462cfed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:59,992] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0aad7602-93ba-4c26-9f47-c2911462cfed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:56:00,002] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:56:00,002] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:56:00,002] [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
Rhodococcus yunnanensis	strain=NBRC 103083	GCA_001895005.1	278209	278209	type	True	100.0	2090	2094	95	conclusive
Rhodococcus kyotonensis	strain=JCM 23211	GCA_900188125.1	398843	398843	type	True	81.9924	1236	2094	95	below_threshold
Rhodococcus fascians	strain=LMG 3623	GCA_000761055.1	1828	1828	type	True	79.9211	741	2094	95	below_threshold
Rhodococcus fascians	strain=NBRC 12155	GCA_001894785.1	1828	1828	type	True	79.873	771	2094	95	below_threshold
Rhodococcus spelaei	strain=C9-5	GCA_006704125.1	2546320	2546320	type	True	78.426	481	2094	95	below_threshold
Rhodococcus oryzae	strain=NEAU-CX67	GCA_005049235.1	2571143	2571143	type	True	78.2885	485	2094	95	below_threshold
Rhodococcus maanshanensis	strain=DSM 44675	GCA_900109405.1	183556	183556	type	True	78.2868	483	2094	95	below_threshold
Prescottella defluvii	strain=Ca11	GCA_000738775.1	1323361	1323361	type	True	78.2523	491	2094	95	below_threshold
Rhodococcus maanshanensis	strain=NBRC 100610	GCA_001894865.1	183556	183556	type	True	78.2502	494	2094	95	below_threshold
Rhodococcus wratislaviensis	strain=NBRC 100605	GCA_000583735.1	44752	44752	suspected-type	True	78.1827	620	2094	95	below_threshold
Nocardia thailandica	strain=NBRC 100428	GCA_000308795.1	257275	257275	type	True	77.5225	405	2094	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:56:00,004] [INFO] DFAST Taxonomy check result was written to GCF_001895005.1_ASM189500v1_genomic.fna/tc_result.tsv
[2024-01-24 14:56:00,004] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:56:00,005] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:56:00,005] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0aad7602-93ba-4c26-9f47-c2911462cfed/dqc_reference/checkm_data
[2024-01-24 14:56:00,006] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:56:00,064] [INFO] Task started: CheckM
[2024-01-24 14:56:00,064] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001895005.1_ASM189500v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001895005.1_ASM189500v1_genomic.fna/checkm_input GCF_001895005.1_ASM189500v1_genomic.fna/checkm_result
[2024-01-24 14:57:00,945] [INFO] Task succeeded: CheckM
[2024-01-24 14:57:00,946] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:57:00,967] [INFO] ===== Completeness check finished =====
[2024-01-24 14:57:00,967] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:57:00,968] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001895005.1_ASM189500v1_genomic.fna/markers.fasta)
[2024-01-24 14:57:00,968] [INFO] Task started: Blastn
[2024-01-24 14:57:00,968] [INFO] Running command: blastn -query GCF_001895005.1_ASM189500v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0aad7602-93ba-4c26-9f47-c2911462cfed/dqc_reference/reference_markers_gtdb.fasta -out GCF_001895005.1_ASM189500v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:57:02,803] [INFO] Task succeeded: Blastn
[2024-01-24 14:57:02,806] [INFO] Selected 12 target genomes.
[2024-01-24 14:57:02,806] [INFO] Target genome list was writen to GCF_001895005.1_ASM189500v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:57:02,818] [INFO] Task started: fastANI
[2024-01-24 14:57:02,818] [INFO] Running command: fastANI --query /var/lib/cwl/stgec3aedb9-a9ca-4ab8-951a-6fe7d99dfae4/GCF_001895005.1_ASM189500v1_genomic.fna.gz --refList GCF_001895005.1_ASM189500v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001895005.1_ASM189500v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:57:20,517] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:20,529] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:57:20,529] [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_001895005.1	s__Rhodococcus_B yunnanensis	100.0	2090	2094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900188125.1	s__Rhodococcus_B kyotonensis	81.984	1238	2094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001645385.1	s__Rhodococcus_B kyotonensis_B	81.7836	1101	2094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	98.37	97.70	0.89	0.87	3	-
GCF_000760735.1	s__Rhodococcus_B fascians_E	80.9996	998	2094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	98.84	98.47	0.88	0.82	19	-
GCF_003386655.1	s__Rhodococcus_B sp003386655	80.8279	1041	2094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003641205.1	s__Rhodococcus_B sp003641205	80.8247	961	2094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002259415.1	s__Rhodococcus_B sp002259415	80.7442	1014	2094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	98.80	98.78	0.88	0.88	4	-
GCF_001647195.1	s__Rhodococcus_B sp001647195	80.5964	811	2094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017168235.1	s__Rhodococcus_B sp001942265	80.2423	842	2094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	98.66	98.66	0.86	0.86	2	-
GCF_002258315.1	s__Rhodococcus_B sp002258315	79.9705	790	2094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002258785.1	s__Rhodococcus_B sp002258785	79.937	754	2094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017168335.1	s__Rhodococcus_B sp017168335	79.6808	705	2094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:57:20,531] [INFO] GTDB search result was written to GCF_001895005.1_ASM189500v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:57:20,531] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:57:20,535] [INFO] DFAST_QC result json was written to GCF_001895005.1_ASM189500v1_genomic.fna/dqc_result.json
[2024-01-24 14:57:20,535] [INFO] DFAST_QC completed!
[2024-01-24 14:57:20,535] [INFO] Total running time: 0h1m57s