[2024-01-24 10:57:26,694] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:26,696] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:26,696] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c7fe86d-6e36-4f20-b95d-a3d5c9ea0508/dqc_reference
[2024-01-24 10:57:28,095] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:28,096] [INFO] Task started: Prodigal
[2024-01-24 10:57:28,096] [INFO] Running command: gunzip -c /var/lib/cwl/stgc0018dc2-86bc-4c36-933c-2310244462fd/GCF_018860155.1_ASM1886015v1_genomic.fna.gz | prodigal -d GCF_018860155.1_ASM1886015v1_genomic.fna/cds.fna -a GCF_018860155.1_ASM1886015v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:07,267] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:07,268] [INFO] Task started: HMMsearch
[2024-01-24 10:58:07,268] [INFO] Running command: hmmsearch --tblout GCF_018860155.1_ASM1886015v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c7fe86d-6e36-4f20-b95d-a3d5c9ea0508/dqc_reference/reference_markers.hmm GCF_018860155.1_ASM1886015v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:07,639] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:07,641] [INFO] Found 6/6 markers.
[2024-01-24 10:58:07,712] [INFO] Query marker FASTA was written to GCF_018860155.1_ASM1886015v1_genomic.fna/markers.fasta
[2024-01-24 10:58:07,713] [INFO] Task started: Blastn
[2024-01-24 10:58:07,713] [INFO] Running command: blastn -query GCF_018860155.1_ASM1886015v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c7fe86d-6e36-4f20-b95d-a3d5c9ea0508/dqc_reference/reference_markers.fasta -out GCF_018860155.1_ASM1886015v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:09,027] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:09,031] [INFO] Selected 16 target genomes.
[2024-01-24 10:58:09,031] [INFO] Target genome list was writen to GCF_018860155.1_ASM1886015v1_genomic.fna/target_genomes.txt
[2024-01-24 10:58:09,042] [INFO] Task started: fastANI
[2024-01-24 10:58:09,043] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0018dc2-86bc-4c36-933c-2310244462fd/GCF_018860155.1_ASM1886015v1_genomic.fna.gz --refList GCF_018860155.1_ASM1886015v1_genomic.fna/target_genomes.txt --output GCF_018860155.1_ASM1886015v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:39,001] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:39,002] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c7fe86d-6e36-4f20-b95d-a3d5c9ea0508/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:39,002] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c7fe86d-6e36-4f20-b95d-a3d5c9ea0508/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:39,015] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:39,015] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:39,015] [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 albiluteola	strain=NEAU-G5	GCA_018860155.1	2842303	2842303	type	True	100.0	3123	3169	95	conclusive
Nocardia jiangxiensis	strain=NBRC 101359	GCA_000308615.1	282685	282685	type	True	82.9823	1660	3169	95	below_threshold
Nocardia miyunensis	strain=NBRC 108239	GCA_001613065.1	282684	282684	type	True	82.823	1631	3169	95	below_threshold
Nocardia coffeae	strain=CA2R105	GCA_019890715.1	2873381	2873381	type	True	82.7704	1686	3169	95	below_threshold
Nocardia macrotermitis	strain=RB20	GCA_009604405.1	2585198	2585198	type	True	82.6909	1520	3169	95	below_threshold
Nocardia vaccinii	strain=NBRC 15922	GCA_001613305.1	1822	1822	type	True	82.4008	1515	3169	95	below_threshold
Nocardia terpenica	strain=IFM 0706	GCA_013186535.1	455432	455432	type	True	81.9086	1345	3169	95	below_threshold
Nocardia mexicana	strain=DSM 44952	GCA_003350525.1	279262	279262	type	True	81.7381	1399	3169	95	below_threshold
Nocardia mexicana	strain=NBRC 108244	GCA_001613165.1	279262	279262	type	True	81.62	1362	3169	95	below_threshold
Nocardia transvalensis	strain=NBRC 15921	GCA_000308875.1	37333	37333	type	True	81.4868	1359	3169	95	below_threshold
Nocardia nova	strain=NBRC 15556	GCA_001613005.1	37330	37330	type	True	80.6811	1195	3169	95	below_threshold
Nocardia aobensis	strain=NBRC 100429	GCA_000308375.1	257277	257277	type	True	80.675	1175	3169	95	below_threshold
Nocardia mikamii	strain=NBRC 108933	GCA_001613505.1	508464	508464	type	True	80.64	1230	3169	95	below_threshold
Nocardia farcinica	strain=NBRC 15532	GCA_001612925.1	37329	37329	type	True	80.1055	1009	3169	95	below_threshold
Nocardia farcinica	strain=NCTC11134	GCA_001182745.2	37329	37329	type	True	80.0819	1050	3169	95	below_threshold
Nocardia farcinica	strain=DSM 43257	GCA_900156775.1	37329	37329	type	True	80.023	1040	3169	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:39,017] [INFO] DFAST Taxonomy check result was written to GCF_018860155.1_ASM1886015v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:39,018] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:39,018] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:39,018] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c7fe86d-6e36-4f20-b95d-a3d5c9ea0508/dqc_reference/checkm_data
[2024-01-24 10:58:39,019] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:39,103] [INFO] Task started: CheckM
[2024-01-24 10:58:39,104] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018860155.1_ASM1886015v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018860155.1_ASM1886015v1_genomic.fna/checkm_input GCF_018860155.1_ASM1886015v1_genomic.fna/checkm_result
[2024-01-24 11:00:17,989] [INFO] Task succeeded: CheckM
[2024-01-24 11:00:17,990] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:00:18,008] [INFO] ===== Completeness check finished =====
[2024-01-24 11:00:18,009] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:00:18,009] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018860155.1_ASM1886015v1_genomic.fna/markers.fasta)
[2024-01-24 11:00:18,009] [INFO] Task started: Blastn
[2024-01-24 11:00:18,009] [INFO] Running command: blastn -query GCF_018860155.1_ASM1886015v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c7fe86d-6e36-4f20-b95d-a3d5c9ea0508/dqc_reference/reference_markers_gtdb.fasta -out GCF_018860155.1_ASM1886015v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:00:19,833] [INFO] Task succeeded: Blastn
[2024-01-24 11:00:19,836] [INFO] Selected 13 target genomes.
[2024-01-24 11:00:19,836] [INFO] Target genome list was writen to GCF_018860155.1_ASM1886015v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:00:19,844] [INFO] Task started: fastANI
[2024-01-24 11:00:19,844] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0018dc2-86bc-4c36-933c-2310244462fd/GCF_018860155.1_ASM1886015v1_genomic.fna.gz --refList GCF_018860155.1_ASM1886015v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018860155.1_ASM1886015v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:00:45,047] [INFO] Task succeeded: fastANI
[2024-01-24 11:00:45,058] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:00:45,058] [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_018860155.1	s__Nocardia sp018860155	100.0	3133	3169	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_019038435.1	s__Nocardia sp019038435	83.0951	1603	3169	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308615.1	s__Nocardia jiangxiensis	82.9607	1665	3169	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	82.838	1630	3169	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009604405.1	s__Nocardia sp009604405	82.6829	1521	3169	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613305.1	s__Nocardia vaccinii	82.3827	1518	3169	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	81.8492	1355	3169	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	98.12	95.64	0.89	0.79	9	-
GCF_015477765.1	s__Nocardia transvalensis_A	81.3436	1280	3169	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000526215.1	s__Nocardia sp000526215	81.2949	1320	3169	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613005.1	s__Nocardia nova	80.6626	1199	3169	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.9334	98.75	97.55	0.88	0.84	13	-
GCF_001613505.1	s__Nocardia mikamii	80.6498	1228	3169	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	80.0662	1056	3169	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.16	98.59	0.93	0.88	42	-
GCF_003315035.1	s__Nocardia puris	80.0117	1081	3169	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.66	99.46	0.95	0.92	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:00:45,060] [INFO] GTDB search result was written to GCF_018860155.1_ASM1886015v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:00:45,060] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:00:45,063] [INFO] DFAST_QC result json was written to GCF_018860155.1_ASM1886015v1_genomic.fna/dqc_result.json
[2024-01-24 11:00:45,063] [INFO] DFAST_QC completed!
[2024-01-24 11:00:45,064] [INFO] Total running time: 0h3m18s