[2024-01-24 14:47:08,612] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:08,615] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:08,615] [INFO] DQC Reference Directory: /var/lib/cwl/stg605b065d-c5af-48b3-bcb2-0f627d117dd1/dqc_reference
[2024-01-24 14:47:10,016] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:10,016] [INFO] Task started: Prodigal
[2024-01-24 14:47:10,017] [INFO] Running command: gunzip -c /var/lib/cwl/stgc893f4f0-ee26-4f16-a22a-ac085ee5a98b/GCF_900269665.1_PRJEB24498_genomic.fna.gz | prodigal -d GCF_900269665.1_PRJEB24498_genomic.fna/cds.fna -a GCF_900269665.1_PRJEB24498_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:48:11,158] [INFO] Task succeeded: Prodigal
[2024-01-24 14:48:11,159] [INFO] Task started: HMMsearch
[2024-01-24 14:48:11,159] [INFO] Running command: hmmsearch --tblout GCF_900269665.1_PRJEB24498_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg605b065d-c5af-48b3-bcb2-0f627d117dd1/dqc_reference/reference_markers.hmm GCF_900269665.1_PRJEB24498_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:48:11,566] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:48:11,568] [INFO] Found 6/6 markers.
[2024-01-24 14:48:11,647] [INFO] Query marker FASTA was written to GCF_900269665.1_PRJEB24498_genomic.fna/markers.fasta
[2024-01-24 14:48:11,647] [INFO] Task started: Blastn
[2024-01-24 14:48:11,647] [INFO] Running command: blastn -query GCF_900269665.1_PRJEB24498_genomic.fna/markers.fasta -db /var/lib/cwl/stg605b065d-c5af-48b3-bcb2-0f627d117dd1/dqc_reference/reference_markers.fasta -out GCF_900269665.1_PRJEB24498_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:12,930] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:12,933] [INFO] Selected 15 target genomes.
[2024-01-24 14:48:12,934] [INFO] Target genome list was writen to GCF_900269665.1_PRJEB24498_genomic.fna/target_genomes.txt
[2024-01-24 14:48:12,943] [INFO] Task started: fastANI
[2024-01-24 14:48:12,943] [INFO] Running command: fastANI --query /var/lib/cwl/stgc893f4f0-ee26-4f16-a22a-ac085ee5a98b/GCF_900269665.1_PRJEB24498_genomic.fna.gz --refList GCF_900269665.1_PRJEB24498_genomic.fna/target_genomes.txt --output GCF_900269665.1_PRJEB24498_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:48:41,541] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:41,542] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg605b065d-c5af-48b3-bcb2-0f627d117dd1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:48:41,542] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg605b065d-c5af-48b3-bcb2-0f627d117dd1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:48:41,556] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:48:41,556] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:48:41,556] [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 suismassiliense	strain=S-137	GCA_900269665.1	2077092	2077092	type	True	100.0	3141	3141	95	conclusive
Nocardia ninae	strain=NBRC 108245	GCA_007990755.1	356145	356145	type	True	94.9074	2594	3141	95	below_threshold
Nocardia colli	strain=CICC 11023	GCA_008704205.1	2545717	2545717	type	True	87.4244	2264	3141	95	below_threshold
Nocardia iowensis	strain=NRRL 5646	GCA_019222765.1	204891	204891	type	True	87.1552	2131	3141	95	below_threshold
Nocardia tenerifensis	strain=DSM 44704	GCA_003202065.1	228006	228006	type	True	86.7305	2154	3141	95	below_threshold
Nocardia tenerifensis	strain=NBRC 101015	GCA_000308715.1	228006	228006	type	True	86.6549	1938	3141	95	below_threshold
Nocardia altamirensis	strain=NBRC 108246	GCA_001612685.1	472158	472158	type	True	85.1319	1989	3141	95	below_threshold
Nocardia vulneris	strain=W9851	GCA_000811985.1	1141657	1141657	type	True	85.0001	2030	3141	95	below_threshold
Nocardia vulneris	strain=NBRC 108936	GCA_001613425.1	1141657	1141657	type	True	84.9945	2043	3141	95	below_threshold
Nocardia rhizosphaerihabitans	strain=CGMCC 4.7329	GCA_014646295.1	1691570	1691570	type	True	81.1237	1274	3141	95	below_threshold
Gordonia zhaorongruii	strain=HY186	GCA_007559005.1	2597659	2597659	type	True	77.6172	297	3141	95	below_threshold
Gordonia jinhuaensis	strain=CGMCC 1.12827	GCA_014639795.1	1517702	1517702	type	True	77.5302	386	3141	95	below_threshold
Gordonia spumicola	strain=NBRC 107696	GCA_009932475.1	589161	589161	type	True	77.5177	426	3141	95	below_threshold
Gordonia hydrophobica	strain=NBRC 16057	GCA_001592365.1	40516	40516	type	True	77.2757	399	3141	95	below_threshold
Amycolatopsis albispora	strain=WP1	GCA_003312875.1	1804986	1804986	type	True	76.9111	675	3141	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:48:41,558] [INFO] DFAST Taxonomy check result was written to GCF_900269665.1_PRJEB24498_genomic.fna/tc_result.tsv
[2024-01-24 14:48:41,559] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:48:41,559] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:48:41,559] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg605b065d-c5af-48b3-bcb2-0f627d117dd1/dqc_reference/checkm_data
[2024-01-24 14:48:41,560] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:48:41,646] [INFO] Task started: CheckM
[2024-01-24 14:48:41,647] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900269665.1_PRJEB24498_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900269665.1_PRJEB24498_genomic.fna/checkm_input GCF_900269665.1_PRJEB24498_genomic.fna/checkm_result
[2024-01-24 14:51:23,550] [INFO] Task succeeded: CheckM
[2024-01-24 14:51:23,551] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 6.48%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2024-01-24 14:51:23,578] [INFO] ===== Completeness check finished =====
[2024-01-24 14:51:23,578] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:51:23,579] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900269665.1_PRJEB24498_genomic.fna/markers.fasta)
[2024-01-24 14:51:23,579] [INFO] Task started: Blastn
[2024-01-24 14:51:23,580] [INFO] Running command: blastn -query GCF_900269665.1_PRJEB24498_genomic.fna/markers.fasta -db /var/lib/cwl/stg605b065d-c5af-48b3-bcb2-0f627d117dd1/dqc_reference/reference_markers_gtdb.fasta -out GCF_900269665.1_PRJEB24498_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:51:25,597] [INFO] Task succeeded: Blastn
[2024-01-24 14:51:25,600] [INFO] Selected 14 target genomes.
[2024-01-24 14:51:25,600] [INFO] Target genome list was writen to GCF_900269665.1_PRJEB24498_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:51:25,610] [INFO] Task started: fastANI
[2024-01-24 14:51:25,610] [INFO] Running command: fastANI --query /var/lib/cwl/stgc893f4f0-ee26-4f16-a22a-ac085ee5a98b/GCF_900269665.1_PRJEB24498_genomic.fna.gz --refList GCF_900269665.1_PRJEB24498_genomic.fna/target_genomes_gtdb.txt --output GCF_900269665.1_PRJEB24498_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:51:56,858] [INFO] Task succeeded: fastANI
[2024-01-24 14:51:56,874] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:51:56,875] [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_900269665.1	s__Nocardia suismassiliense	100.0	3141	3141	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	95.20	95.20	0.87	0.87	2	conclusive
GCF_007990755.1	s__Nocardia ninae	94.9074	2594	3141	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	95.51	95.51	0.86	0.86	2	-
GCF_008704205.1	s__Nocardia colli	87.4325	2262	3141	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019222765.1	s__Nocardia iowensis	87.1484	2130	3141	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308715.1	s__Nocardia tenerifensis	86.6741	1935	3141	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001612685.1	s__Nocardia altamirensis	85.0933	1996	3141	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613425.1	s__Nocardia vulneris	85.0224	2038	3141	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.8238	100.00	100.00	0.99	0.99	2	-
GCF_000284035.1	s__Nocardia cyriacigeorgica_B	81.5192	1196	3141	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	98.41	98.27	0.93	0.91	5	-
GCF_014646295.1	s__Nocardia rhizosphaerihabitans	81.1204	1273	3141	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010868145.1	s__Nocardia cyriacigeorgica_D	80.8913	1107	3141	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.70	99.66	0.98	0.98	4	-
GCF_011290605.1	s__Gordonia sp002009645	77.7531	462	3141	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.70	97.37	0.91	0.88	14	-
GCF_009932475.1	s__Gordonia spumicola	77.4712	426	3141	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001592365.1	s__Gordonia hydrophobica	77.2894	397	3141	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004362825.1	s__Labedaea rhizosphaerae	76.7327	595	3141	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Labedaea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:51:56,881] [INFO] GTDB search result was written to GCF_900269665.1_PRJEB24498_genomic.fna/result_gtdb.tsv
[2024-01-24 14:51:56,882] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:51:56,886] [INFO] DFAST_QC result json was written to GCF_900269665.1_PRJEB24498_genomic.fna/dqc_result.json
[2024-01-24 14:51:56,886] [INFO] DFAST_QC completed!
[2024-01-24 14:51:56,886] [INFO] Total running time: 0h4m48s