[2024-01-24 10:56:34,378] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:56:34,379] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:56:34,380] [INFO] DQC Reference Directory: /var/lib/cwl/stg14d729f0-1380-464f-9763-1081e4693ce3/dqc_reference
[2024-01-24 10:56:36,714] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:56:36,714] [INFO] Task started: Prodigal
[2024-01-24 10:56:36,715] [INFO] Running command: gunzip -c /var/lib/cwl/stg33e44a8f-5ed0-4783-9f4c-8564d9f45930/GCF_017875645.1_ASM1787564v1_genomic.fna.gz | prodigal -d GCF_017875645.1_ASM1787564v1_genomic.fna/cds.fna -a GCF_017875645.1_ASM1787564v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:07,011] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:07,012] [INFO] Task started: HMMsearch
[2024-01-24 10:57:07,012] [INFO] Running command: hmmsearch --tblout GCF_017875645.1_ASM1787564v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg14d729f0-1380-464f-9763-1081e4693ce3/dqc_reference/reference_markers.hmm GCF_017875645.1_ASM1787564v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:07,355] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:07,356] [INFO] Found 6/6 markers.
[2024-01-24 10:57:07,424] [INFO] Query marker FASTA was written to GCF_017875645.1_ASM1787564v1_genomic.fna/markers.fasta
[2024-01-24 10:57:07,425] [INFO] Task started: Blastn
[2024-01-24 10:57:07,425] [INFO] Running command: blastn -query GCF_017875645.1_ASM1787564v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg14d729f0-1380-464f-9763-1081e4693ce3/dqc_reference/reference_markers.fasta -out GCF_017875645.1_ASM1787564v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:08,668] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:08,672] [INFO] Selected 21 target genomes.
[2024-01-24 10:57:08,673] [INFO] Target genome list was writen to GCF_017875645.1_ASM1787564v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:08,708] [INFO] Task started: fastANI
[2024-01-24 10:57:08,708] [INFO] Running command: fastANI --query /var/lib/cwl/stg33e44a8f-5ed0-4783-9f4c-8564d9f45930/GCF_017875645.1_ASM1787564v1_genomic.fna.gz --refList GCF_017875645.1_ASM1787564v1_genomic.fna/target_genomes.txt --output GCF_017875645.1_ASM1787564v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:49,348] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:49,349] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg14d729f0-1380-464f-9763-1081e4693ce3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:49,350] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg14d729f0-1380-464f-9763-1081e4693ce3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:49,367] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:57:49,367] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:49,367] [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 goodfellowii	strain=DSM 45516	GCA_017875645.1	882446	882446	type	True	100.0	2660	2660	95	conclusive
Nocardia bhagyanarayanae	strain=DSM 103495	GCA_006716565.1	1215925	1215925	type	True	81.9484	1362	2660	95	below_threshold
Nocardia lijiangensis	strain=NBRC 108240	GCA_001613045.1	299618	299618	type	True	81.862	1321	2660	95	below_threshold
Nocardia amikacinitolerans	strain=NBRC 108937	GCA_001612615.1	756689	756689	type	True	81.7035	1373	2660	95	below_threshold
Nocardia amikacinitolerans	strain=DSM 45539	GCA_024172045.1	756689	756689	type	True	81.6664	1373	2660	95	below_threshold
Nocardia xishanensis	strain=NBRC 101358	GCA_001613365.1	238964	238964	type	True	81.575	1335	2660	95	below_threshold
Nocardia farcinica	strain=DSM 43257	GCA_900156775.1	37329	37329	type	True	81.3734	1154	2660	95	below_threshold
Nocardia colli	strain=CICC 11023	GCA_008704205.1	2545717	2545717	type	True	81.3625	1429	2660	95	below_threshold
Nocardia tenerifensis	strain=DSM 44704	GCA_003202065.1	228006	228006	type	True	81.3542	1405	2660	95	below_threshold
Nocardia vulneris	strain=NBRC 108936	GCA_001613425.1	1141657	1141657	type	True	81.3039	1341	2660	95	below_threshold
Nocardia tenerifensis	strain=NBRC 101015	GCA_000308715.1	228006	228006	type	True	81.2795	1312	2660	95	below_threshold
Nocardia altamirensis	strain=NBRC 108246	GCA_001612685.1	472158	472158	type	True	81.2781	1307	2660	95	below_threshold
Nocardia vulneris	strain=W9851	GCA_000811985.1	1141657	1141657	type	True	81.2492	1344	2660	95	below_threshold
Nocardia abscessus	strain=FDAARGOS_1596	GCA_020731305.1	120957	120957	suspected-type	True	80.9928	1319	2660	95	below_threshold
Nocardia barduliensis	strain=335427	GCA_013315795.1	2736643	2736643	type	True	80.95	1236	2660	95	below_threshold
Nocardia gamkensis	strain=NBRC 108242	GCA_001612985.1	352869	352869	type	True	80.9372	1250	2660	95	below_threshold
Nocardia arthritidis	strain=NBRC 100137	GCA_001612765.1	228602	228602	type	True	80.9363	1187	2660	95	below_threshold
Nocardia gamkensis	strain=DSM 44956	GCA_012396055.1	352869	352869	type	True	80.8893	1272	2660	95	below_threshold
Nocardia gamkensis	strain=NRRL B-24450	GCA_013181665.1	352869	352869	type	True	80.8703	1268	2660	95	below_threshold
Nocardia anaemiae	strain=NBRC 100462	GCA_001612725.1	263910	263910	type	True	80.846	1255	2660	95	below_threshold
Nocardia aurantia	strain=RB56	GCA_009604425.1	2585199	2585199	type	True	79.2789	1039	2660	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:49,369] [INFO] DFAST Taxonomy check result was written to GCF_017875645.1_ASM1787564v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:49,369] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:49,370] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:49,370] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg14d729f0-1380-464f-9763-1081e4693ce3/dqc_reference/checkm_data
[2024-01-24 10:57:49,371] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:49,444] [INFO] Task started: CheckM
[2024-01-24 10:57:49,445] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017875645.1_ASM1787564v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017875645.1_ASM1787564v1_genomic.fna/checkm_input GCF_017875645.1_ASM1787564v1_genomic.fna/checkm_result
[2024-01-24 10:59:15,967] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:15,968] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:15,991] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:15,991] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:15,992] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017875645.1_ASM1787564v1_genomic.fna/markers.fasta)
[2024-01-24 10:59:15,992] [INFO] Task started: Blastn
[2024-01-24 10:59:15,992] [INFO] Running command: blastn -query GCF_017875645.1_ASM1787564v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg14d729f0-1380-464f-9763-1081e4693ce3/dqc_reference/reference_markers_gtdb.fasta -out GCF_017875645.1_ASM1787564v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:17,752] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:17,757] [INFO] Selected 19 target genomes.
[2024-01-24 10:59:17,757] [INFO] Target genome list was writen to GCF_017875645.1_ASM1787564v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:17,814] [INFO] Task started: fastANI
[2024-01-24 10:59:17,814] [INFO] Running command: fastANI --query /var/lib/cwl/stg33e44a8f-5ed0-4783-9f4c-8564d9f45930/GCF_017875645.1_ASM1787564v1_genomic.fna.gz --refList GCF_017875645.1_ASM1787564v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017875645.1_ASM1787564v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:50,912] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:50,932] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:50,932] [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_017875645.1	s__Nocardia goodfellowii	100.0	2659	2660	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_015355755.1	s__Nocardia sp015355755	88.079	1921	2660	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716565.1	s__Nocardia bhagyanarayanae	81.9283	1365	2660	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613045.1	s__Nocardia lijiangensis	81.8524	1320	2660	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001612615.1	s__Nocardia amikacinitolerans	81.7094	1372	2660	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	97.80	97.80	0.89	0.89	2	-
GCF_001613365.1	s__Nocardia xishanensis	81.5984	1331	2660	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011801125.1	s__Nocardia brasiliensis_C	81.4129	1308	2660	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001182745.1	s__Nocardia farcinica	81.3985	1177	2660	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.16	98.59	0.93	0.88	42	-
GCF_008704205.1	s__Nocardia colli	81.3777	1426	2660	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000250675.2	s__Nocardia brasiliensis_B	81.3375	1337	2660	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.2192	100.00	100.00	1.00	1.00	2	-
GCF_000308715.1	s__Nocardia tenerifensis	81.3148	1304	2660	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001613425.1	s__Nocardia vulneris	81.3001	1343	2660	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.8238	100.00	100.00	0.99	0.99	2	-
GCF_001612685.1	s__Nocardia altamirensis	81.2697	1309	2660	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001612765.1	s__Nocardia arthritidis	80.952	1182	2660	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.103	N/A	N/A	N/A	N/A	1	-
GCF_001612985.1	s__Nocardia gamkensis	80.9352	1252	2660	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.7192	100.00	100.00	1.00	0.99	3	-
GCF_015477835.1	s__Nocardia higoensis_A	80.8498	1010	2660	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001612725.1	s__Nocardia anaemiae	80.8381	1259	2660	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000381925.1	s__Nocardia sp000381925	79.3738	1060	2660	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	79.2732	1039	2660	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 10:59:50,934] [INFO] GTDB search result was written to GCF_017875645.1_ASM1787564v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:50,934] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:50,938] [INFO] DFAST_QC result json was written to GCF_017875645.1_ASM1787564v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:50,939] [INFO] DFAST_QC completed!
[2024-01-24 10:59:50,939] [INFO] Total running time: 0h3m17s