[2023-06-29 15:04:59,130] [INFO] DFAST_QC pipeline started.
[2023-06-29 15:04:59,133] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 15:04:59,133] [INFO] DQC Reference Directory: /var/lib/cwl/stg15d50eea-0819-4f70-a68f-b67ba2b96a82/dqc_reference
[2023-06-29 15:05:00,376] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 15:05:00,377] [INFO] Task started: Prodigal
[2023-06-29 15:05:00,377] [INFO] Running command: gunzip -c /var/lib/cwl/stg60fdc5d4-4429-4229-a4d8-169010a51c3e/GCA_023417985.1_ASM2341798v1_genomic.fna.gz | prodigal -d GCA_023417985.1_ASM2341798v1_genomic.fna/cds.fna -a GCA_023417985.1_ASM2341798v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 15:05:12,207] [INFO] Task succeeded: Prodigal
[2023-06-29 15:05:12,207] [INFO] Task started: HMMsearch
[2023-06-29 15:05:12,207] [INFO] Running command: hmmsearch --tblout GCA_023417985.1_ASM2341798v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg15d50eea-0819-4f70-a68f-b67ba2b96a82/dqc_reference/reference_markers.hmm GCA_023417985.1_ASM2341798v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 15:05:12,471] [INFO] Task succeeded: HMMsearch
[2023-06-29 15:05:12,472] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg60fdc5d4-4429-4229-a4d8-169010a51c3e/GCA_023417985.1_ASM2341798v1_genomic.fna.gz]
[2023-06-29 15:05:12,516] [INFO] Query marker FASTA was written to GCA_023417985.1_ASM2341798v1_genomic.fna/markers.fasta
[2023-06-29 15:05:12,517] [INFO] Task started: Blastn
[2023-06-29 15:05:12,517] [INFO] Running command: blastn -query GCA_023417985.1_ASM2341798v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15d50eea-0819-4f70-a68f-b67ba2b96a82/dqc_reference/reference_markers.fasta -out GCA_023417985.1_ASM2341798v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:05:13,447] [INFO] Task succeeded: Blastn
[2023-06-29 15:05:13,451] [INFO] Selected 14 target genomes.
[2023-06-29 15:05:13,452] [INFO] Target genome list was writen to GCA_023417985.1_ASM2341798v1_genomic.fna/target_genomes.txt
[2023-06-29 15:05:13,456] [INFO] Task started: fastANI
[2023-06-29 15:05:13,457] [INFO] Running command: fastANI --query /var/lib/cwl/stg60fdc5d4-4429-4229-a4d8-169010a51c3e/GCA_023417985.1_ASM2341798v1_genomic.fna.gz --refList GCA_023417985.1_ASM2341798v1_genomic.fna/target_genomes.txt --output GCA_023417985.1_ASM2341798v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 15:05:25,345] [INFO] Task succeeded: fastANI
[2023-06-29 15:05:25,345] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg15d50eea-0819-4f70-a68f-b67ba2b96a82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 15:05:25,346] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg15d50eea-0819-4f70-a68f-b67ba2b96a82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 15:05:25,359] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 15:05:25,359] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 15:05:25,360] [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 coprophilus	strain=NBRC 100603	GCA_001895045.1	38310	38310	type	True	91.6374	1149	1265	95	below_threshold
Rhodococcus coprophilus	strain=NCTC10994	GCA_900478115.1	38310	38310	type	True	91.622	1157	1265	95	below_threshold
Rhodococcus rhodochrous	strain=DSM 43241	GCA_001646825.1	1829	1829	suspected-type	True	81.2174	802	1265	95	below_threshold
Rhodococcus rhodochrous	strain=NBRC 16069	GCA_001047055.1	1829	1829	suspected-type	True	81.1501	818	1265	95	below_threshold
Rhodococcus rhodochrous	strain=NCTC10210	GCA_900187265.1	1829	1829	suspected-type	True	81.0889	830	1265	95	below_threshold
Rhodococcus phenolicus	strain=DSM 44812	GCA_001646785.1	263849	263849	type	True	80.4582	722	1265	95	below_threshold
Rhodococcus yananensis	strain=FBM22-1	GCA_020515525.1	2879464	2879464	type	True	80.2661	636	1265	95	below_threshold
Prescottella defluvii	strain=Ca11	GCA_000738775.1	1323361	1323361	type	True	79.0692	488	1265	95	below_threshold
Prescottella agglutinans	strain=CCTCC AB2014297	GCA_004011865.1	1644129	1644129	type	True	79.0003	523	1265	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 15:05:25,362] [INFO] DFAST Taxonomy check result was written to GCA_023417985.1_ASM2341798v1_genomic.fna/tc_result.tsv
[2023-06-29 15:05:25,362] [INFO] ===== Taxonomy check completed =====
[2023-06-29 15:05:25,362] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 15:05:25,363] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg15d50eea-0819-4f70-a68f-b67ba2b96a82/dqc_reference/checkm_data
[2023-06-29 15:05:25,364] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 15:05:25,411] [INFO] Task started: CheckM
[2023-06-29 15:05:25,412] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023417985.1_ASM2341798v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023417985.1_ASM2341798v1_genomic.fna/checkm_input GCA_023417985.1_ASM2341798v1_genomic.fna/checkm_result
[2023-06-29 15:06:05,718] [INFO] Task succeeded: CheckM
[2023-06-29 15:06:05,720] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.56%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 15:06:05,744] [INFO] ===== Completeness check finished =====
[2023-06-29 15:06:05,745] [INFO] ===== Start GTDB Search =====
[2023-06-29 15:06:05,745] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023417985.1_ASM2341798v1_genomic.fna/markers.fasta)
[2023-06-29 15:06:05,746] [INFO] Task started: Blastn
[2023-06-29 15:06:05,746] [INFO] Running command: blastn -query GCA_023417985.1_ASM2341798v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15d50eea-0819-4f70-a68f-b67ba2b96a82/dqc_reference/reference_markers_gtdb.fasta -out GCA_023417985.1_ASM2341798v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:06:07,096] [INFO] Task succeeded: Blastn
[2023-06-29 15:06:07,100] [INFO] Selected 15 target genomes.
[2023-06-29 15:06:07,100] [INFO] Target genome list was writen to GCA_023417985.1_ASM2341798v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 15:06:07,136] [INFO] Task started: fastANI
[2023-06-29 15:06:07,137] [INFO] Running command: fastANI --query /var/lib/cwl/stg60fdc5d4-4429-4229-a4d8-169010a51c3e/GCA_023417985.1_ASM2341798v1_genomic.fna.gz --refList GCA_023417985.1_ASM2341798v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023417985.1_ASM2341798v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 15:06:20,147] [INFO] Task succeeded: fastANI
[2023-06-29 15:06:20,161] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 15:06:20,161] [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_001895045.1	s__Rhodococcus coprophilus	91.6374	1149	1265	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	100.00	100.00	1.00	1.00	3	-
GCF_012844225.1	s__Rhodococcus sp012844225	86.4801	1076	1265	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	99.09	99.02	0.95	0.95	3	-
GCF_001646655.1	s__Rhodococcus gordoniae	81.2892	724	1265	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.98	98.16	0.95	0.93	4	-
GCF_900105195.1	s__Rhodococcus pyridinivorans	81.198	765	1265	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.16	95.17	0.90	0.84	21	-
GCF_013602415.1	s__Rhodococcus sp013602415	81.1262	812	1265	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187265.1	s__Rhodococcus rhodochrous	81.0991	828	1265	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	97.52	95.51	0.91	0.84	11	-
GCF_001646785.1	s__Rhodococcus phenolicus	80.461	721	1265	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012729135.1	s__Rhodococcus sp012729135	80.3727	580	1265	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000738775.1	s__Rhodococcus defluvii	79.0581	488	1265	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004011865.1	s__Rhodococcus agglutinans	78.9721	526	1265	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 15:06:20,163] [INFO] GTDB search result was written to GCA_023417985.1_ASM2341798v1_genomic.fna/result_gtdb.tsv
[2023-06-29 15:06:20,164] [INFO] ===== GTDB Search completed =====
[2023-06-29 15:06:20,167] [INFO] DFAST_QC result json was written to GCA_023417985.1_ASM2341798v1_genomic.fna/dqc_result.json
[2023-06-29 15:06:20,167] [INFO] DFAST_QC completed!
[2023-06-29 15:06:20,167] [INFO] Total running time: 0h1m21s