[2024-01-24 13:31:33,595] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:33,599] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:33,599] [INFO] DQC Reference Directory: /var/lib/cwl/stgd1c871d2-de58-4c63-9f34-5d23a8c93dd7/dqc_reference
[2024-01-24 13:31:34,898] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:34,899] [INFO] Task started: Prodigal
[2024-01-24 13:31:34,899] [INFO] Running command: gunzip -c /var/lib/cwl/stg50b83e3d-7187-4ddf-b2ea-09e741ee3b28/GCF_003350585.1_ASM335058v1_genomic.fna.gz | prodigal -d GCF_003350585.1_ASM335058v1_genomic.fna/cds.fna -a GCF_003350585.1_ASM335058v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:06,148] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:06,149] [INFO] Task started: HMMsearch
[2024-01-24 13:32:06,149] [INFO] Running command: hmmsearch --tblout GCF_003350585.1_ASM335058v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd1c871d2-de58-4c63-9f34-5d23a8c93dd7/dqc_reference/reference_markers.hmm GCF_003350585.1_ASM335058v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:06,542] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:06,544] [INFO] Found 6/6 markers.
[2024-01-24 13:32:06,613] [INFO] Query marker FASTA was written to GCF_003350585.1_ASM335058v1_genomic.fna/markers.fasta
[2024-01-24 13:32:06,614] [INFO] Task started: Blastn
[2024-01-24 13:32:06,614] [INFO] Running command: blastn -query GCF_003350585.1_ASM335058v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1c871d2-de58-4c63-9f34-5d23a8c93dd7/dqc_reference/reference_markers.fasta -out GCF_003350585.1_ASM335058v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:07,827] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:07,832] [INFO] Selected 15 target genomes.
[2024-01-24 13:32:07,832] [INFO] Target genome list was writen to GCF_003350585.1_ASM335058v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:07,843] [INFO] Task started: fastANI
[2024-01-24 13:32:07,843] [INFO] Running command: fastANI --query /var/lib/cwl/stg50b83e3d-7187-4ddf-b2ea-09e741ee3b28/GCF_003350585.1_ASM335058v1_genomic.fna.gz --refList GCF_003350585.1_ASM335058v1_genomic.fna/target_genomes.txt --output GCF_003350585.1_ASM335058v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:37,347] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:37,348] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd1c871d2-de58-4c63-9f34-5d23a8c93dd7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:37,348] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd1c871d2-de58-4c63-9f34-5d23a8c93dd7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:37,361] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:32:37,361] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:37,361] [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 pseudobrasiliensis	strain=DSM 44290	GCA_003350585.1	45979	45979	type	True	100.0	2783	2785	95	conclusive
Nocardia pseudobrasiliensis	strain=NBRC 108224	GCA_001613105.1	45979	45979	type	True	99.9767	2727	2785	95	conclusive
Nocardia terpenica	strain=IFM 0706	GCA_013186535.1	455432	455432	type	True	82.4295	1557	2785	95	below_threshold
Nocardia transvalensis	strain=DSM 43582	GCA_014203315.1	37333	37333	type	True	81.9762	1446	2785	95	below_threshold
Nocardia transvalensis	strain=NBRC 15921	GCA_000308875.1	37333	37333	type	True	81.8911	1439	2785	95	below_threshold
Nocardia aobensis	strain=NBRC 100429	GCA_000308375.1	257277	257277	type	True	81.1364	1204	2785	95	below_threshold
Nocardia mikamii	strain=NBRC 108933	GCA_001613505.1	508464	508464	type	True	81.0962	1198	2785	95	below_threshold
Nocardia jiangxiensis	strain=NBRC 101359	GCA_000308615.1	282685	282685	type	True	81.0458	1284	2785	95	below_threshold
Nocardia miyunensis	strain=NBRC 108239	GCA_001613065.1	282684	282684	type	True	80.9771	1252	2785	95	below_threshold
Nocardia coffeae	strain=CA2R105	GCA_019890715.1	2873381	2873381	type	True	80.9083	1285	2785	95	below_threshold
Nocardia albiluteola	strain=NEAU-G5	GCA_018860155.1	2842303	2842303	type	True	80.9049	1317	2785	95	below_threshold
Nocardia aurantia	strain=RB56	GCA_009604425.1	2585199	2585199	type	True	80.4329	1247	2785	95	below_threshold
Nocardia suismassiliense	strain=S-137	GCA_900269665.1	2077092	2077092	type	True	79.7698	1216	2785	95	below_threshold
Nocardia colli	strain=CICC 11023	GCA_008704205.1	2545717	2545717	type	True	79.7355	1349	2785	95	below_threshold
Nocardia beijingensis	strain=NBRC 16342	GCA_001612785.1	95162	95162	type	True	79.6252	1067	2785	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:37,363] [INFO] DFAST Taxonomy check result was written to GCF_003350585.1_ASM335058v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:37,363] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:37,364] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:37,364] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd1c871d2-de58-4c63-9f34-5d23a8c93dd7/dqc_reference/checkm_data
[2024-01-24 13:32:37,365] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:37,445] [INFO] Task started: CheckM
[2024-01-24 13:32:37,445] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003350585.1_ASM335058v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003350585.1_ASM335058v1_genomic.fna/checkm_input GCF_003350585.1_ASM335058v1_genomic.fna/checkm_result
[2024-01-24 13:34:08,662] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:08,664] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.31%
Strain heterogeneity: 40.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:08,692] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:08,693] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:08,693] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003350585.1_ASM335058v1_genomic.fna/markers.fasta)
[2024-01-24 13:34:08,694] [INFO] Task started: Blastn
[2024-01-24 13:34:08,694] [INFO] Running command: blastn -query GCF_003350585.1_ASM335058v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1c871d2-de58-4c63-9f34-5d23a8c93dd7/dqc_reference/reference_markers_gtdb.fasta -out GCF_003350585.1_ASM335058v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:10,332] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:10,336] [INFO] Selected 17 target genomes.
[2024-01-24 13:34:10,337] [INFO] Target genome list was writen to GCF_003350585.1_ASM335058v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:10,360] [INFO] Task started: fastANI
[2024-01-24 13:34:10,361] [INFO] Running command: fastANI --query /var/lib/cwl/stg50b83e3d-7187-4ddf-b2ea-09e741ee3b28/GCF_003350585.1_ASM335058v1_genomic.fna.gz --refList GCF_003350585.1_ASM335058v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003350585.1_ASM335058v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:40,582] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:40,599] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:40,599] [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_001613105.1	s__Nocardia pseudobrasiliensis	99.9767	2727	2785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_015477765.1	s__Nocardia transvalensis_A	83.6603	1579	2785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013186535.1	s__Nocardia terpenica	82.4287	1557	2785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	98.12	95.64	0.89	0.79	9	-
GCF_000308875.1	s__Nocardia transvalensis	81.869	1444	2785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015477355.1	s__Nocardia blacklockiae	81.8571	1439	2785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014466955.1	s__Nocardia wallacei	81.8157	1341	2785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308375.1	s__Nocardia aobensis	81.1222	1207	2785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.6988	98.11	97.03	0.89	0.86	3	-
GCF_000308615.1	s__Nocardia jiangxiensis	81.0439	1282	2785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613505.1	s__Nocardia mikamii	81.0376	1208	2785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015354405.1	s__Nocardia sp015354405	81.0132	1186	2785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613065.1	s__Nocardia miyunensis	80.9948	1247	2785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009604425.1	s__Nocardia sp009604425	80.42	1249	2785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000284035.1	s__Nocardia cyriacigeorgica_B	80.3565	1024	2785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	98.41	98.27	0.93	0.91	5	-
GCF_010858045.1	s__Nocardia cyriacigeorgica_E	80.2145	991	2785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	98.94	98.91	0.92	0.91	4	-
GCF_008704205.1	s__Nocardia colli	79.7416	1346	2785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001612785.1	s__Nocardia beijingensis	79.6416	1062	2785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	98.03	98.03	0.92	0.92	2	-
GCF_015477775.1	s__Nocardia abscessus_A	79.5314	1094	2785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:40,601] [INFO] GTDB search result was written to GCF_003350585.1_ASM335058v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:40,601] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:40,605] [INFO] DFAST_QC result json was written to GCF_003350585.1_ASM335058v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:40,605] [INFO] DFAST_QC completed!
[2024-01-24 13:34:40,605] [INFO] Total running time: 0h3m7s