[2024-01-24 15:02:24,279] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:24,282] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:24,282] [INFO] DQC Reference Directory: /var/lib/cwl/stg1d5c32c4-f499-4a60-a384-9af156d4dc53/dqc_reference
[2024-01-24 15:02:26,427] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:26,428] [INFO] Task started: Prodigal
[2024-01-24 15:02:26,429] [INFO] Running command: gunzip -c /var/lib/cwl/stgc087f623-b213-4d2c-b23c-ece402a5e676/GCF_005863225.1_ASM586322v1_genomic.fna.gz | prodigal -d GCF_005863225.1_ASM586322v1_genomic.fna/cds.fna -a GCF_005863225.1_ASM586322v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:46,690] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:46,690] [INFO] Task started: HMMsearch
[2024-01-24 15:02:46,690] [INFO] Running command: hmmsearch --tblout GCF_005863225.1_ASM586322v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1d5c32c4-f499-4a60-a384-9af156d4dc53/dqc_reference/reference_markers.hmm GCF_005863225.1_ASM586322v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:47,032] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:47,034] [INFO] Found 6/6 markers.
[2024-01-24 15:02:47,089] [INFO] Query marker FASTA was written to GCF_005863225.1_ASM586322v1_genomic.fna/markers.fasta
[2024-01-24 15:02:47,090] [INFO] Task started: Blastn
[2024-01-24 15:02:47,090] [INFO] Running command: blastn -query GCF_005863225.1_ASM586322v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d5c32c4-f499-4a60-a384-9af156d4dc53/dqc_reference/reference_markers.fasta -out GCF_005863225.1_ASM586322v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:48,380] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:48,384] [INFO] Selected 21 target genomes.
[2024-01-24 15:02:48,384] [INFO] Target genome list was writen to GCF_005863225.1_ASM586322v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:48,400] [INFO] Task started: fastANI
[2024-01-24 15:02:48,400] [INFO] Running command: fastANI --query /var/lib/cwl/stgc087f623-b213-4d2c-b23c-ece402a5e676/GCF_005863225.1_ASM586322v1_genomic.fna.gz --refList GCF_005863225.1_ASM586322v1_genomic.fna/target_genomes.txt --output GCF_005863225.1_ASM586322v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:24,245] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:24,245] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1d5c32c4-f499-4a60-a384-9af156d4dc53/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:24,246] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1d5c32c4-f499-4a60-a384-9af156d4dc53/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:24,262] [INFO] Found 21 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:03:24,262] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:24,262] [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
Nocardia cyriacigeorgica	strain=DSM 44484	GCA_005863225.1	135487	135487	type	True	100.0	2048	2058	95	conclusive
Nocardia cyriacigeorgica	strain=NBRC 100375	GCA_000308555.1	135487	135487	type	True	99.8947	1904	2058	95	conclusive
Nocardia bhagyanarayanae	strain=DSM 103495	GCA_006716565.1	1215925	1215925	type	True	82.1164	1234	2058	95	below_threshold
Nocardia lijiangensis	strain=NBRC 108240	GCA_001613045.1	299618	299618	type	True	82.0672	1156	2058	95	below_threshold
Nocardia amikacinitolerans	strain=NBRC 108937	GCA_001612615.1	756689	756689	type	True	81.899	1205	2058	95	below_threshold
Nocardia amikacinitolerans	strain=DSM 45539	GCA_024172045.1	756689	756689	type	True	81.8983	1212	2058	95	below_threshold
Nocardia xishanensis	strain=NBRC 101358	GCA_001613365.1	238964	238964	type	True	81.8171	1177	2058	95	below_threshold
Nocardia asteroides	strain=DSM 43373	GCA_900114685.1	1824	1824	suspected-type	True	81.7039	1172	2058	95	below_threshold
Nocardia asteroides	strain=NBRC 15531	GCA_000308355.2	1824	1824	suspected-type	True	81.6805	1165	2058	95	below_threshold
Nocardia barduliensis	strain=335427	GCA_013315795.1	2736643	2736643	type	True	81.6726	1181	2058	95	below_threshold
Nocardia asteroides	strain=ATCC 19247	GCA_005863255.1	1824	1824	suspected-type	True	81.6721	1165	2058	95	below_threshold
Nocardia neocaledoniensis	strain=NBRC 108232	GCA_007990735.1	236511	236511	type	True	81.5414	1067	2058	95	below_threshold
Nocardia suismassiliense	strain=S-137	GCA_900269665.1	2077092	2077092	type	True	81.4848	1157	2058	95	below_threshold
Nocardia arthritidis	strain=NBRC 100137	GCA_001612765.1	228602	228602	type	True	81.4723	1135	2058	95	below_threshold
Nocardia colli	strain=CICC 11023	GCA_008704205.1	2545717	2545717	type	True	81.4606	1165	2058	95	below_threshold
Nocardia neocaledoniensis	strain=DSM 44717	GCA_003182135.1	236511	236511	type	True	81.4269	1154	2058	95	below_threshold
Nocardia thailandica	strain=NBRC 100428	GCA_000308795.1	257275	257275	type	True	81.2319	1054	2058	95	below_threshold
Nocardia caishijiensis	strain=NBRC 108228	GCA_001612825.1	184756	184756	type	True	81.0717	1027	2058	95	below_threshold
Nocardia caishijiensis	strain=DSM 44831	GCA_009858255.1	184756	184756	type	True	81.0654	1031	2058	95	below_threshold
Nocardia ignorata	strain=NBRC 108230	GCA_001612905.1	145285	145285	type	True	80.9947	1069	2058	95	below_threshold
Nocardia ignorata	strain=DSM 44496	GCA_004362495.1	145285	145285	type	True	80.9911	1095	2058	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:24,264] [INFO] DFAST Taxonomy check result was written to GCF_005863225.1_ASM586322v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:24,265] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:24,265] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:24,265] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1d5c32c4-f499-4a60-a384-9af156d4dc53/dqc_reference/checkm_data
[2024-01-24 15:03:24,266] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:24,325] [INFO] Task started: CheckM
[2024-01-24 15:03:24,325] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005863225.1_ASM586322v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005863225.1_ASM586322v1_genomic.fna/checkm_input GCF_005863225.1_ASM586322v1_genomic.fna/checkm_result
[2024-01-24 15:04:29,578] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:29,579] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:29,600] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:29,600] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:29,601] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005863225.1_ASM586322v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:29,601] [INFO] Task started: Blastn
[2024-01-24 15:04:29,602] [INFO] Running command: blastn -query GCF_005863225.1_ASM586322v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d5c32c4-f499-4a60-a384-9af156d4dc53/dqc_reference/reference_markers_gtdb.fasta -out GCF_005863225.1_ASM586322v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:31,528] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:31,536] [INFO] Selected 9 target genomes.
[2024-01-24 15:04:31,536] [INFO] Target genome list was writen to GCF_005863225.1_ASM586322v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:31,544] [INFO] Task started: fastANI
[2024-01-24 15:04:31,545] [INFO] Running command: fastANI --query /var/lib/cwl/stgc087f623-b213-4d2c-b23c-ece402a5e676/GCF_005863225.1_ASM586322v1_genomic.fna.gz --refList GCF_005863225.1_ASM586322v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005863225.1_ASM586322v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:47,303] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:47,315] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:47,315] [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_000308555.1	s__Nocardia cyriacigeorgica	99.8947	1904	2058	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	96.94	96.19	0.91	0.88	19	conclusive
GCF_005863245.1	s__Nocardia cyriacigeorgica_C	92.525	1757	2058	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	96.66	96.66	0.89	0.89	2	-
GCF_010858045.1	s__Nocardia cyriacigeorgica_E	91.7027	1738	2058	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	98.94	98.91	0.92	0.91	4	-
GCF_000284035.1	s__Nocardia cyriacigeorgica_B	91.0328	1737	2058	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	98.41	98.27	0.93	0.91	5	-
GCF_010868145.1	s__Nocardia cyriacigeorgica_D	86.9618	1545	2058	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.70	99.66	0.98	0.98	4	-
GCF_003315035.1	s__Nocardia puris	81.9569	1212	2058	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.66	99.46	0.95	0.92	4	-
GCF_900637185.1	s__Nocardia asteroides	81.6343	1174	2058	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	5	-
GCF_001886715.1	s__Nocardia mangyaensis	81.2152	1067	2058	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001612825.1	s__Nocardia caishijiensis	81.0557	1030	2058	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:04:47,317] [INFO] GTDB search result was written to GCF_005863225.1_ASM586322v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:47,317] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:47,321] [INFO] DFAST_QC result json was written to GCF_005863225.1_ASM586322v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:47,322] [INFO] DFAST_QC completed!
[2024-01-24 15:04:47,322] [INFO] Total running time: 0h2m23s