[2024-01-24 13:36:32,003] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:32,005] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:32,005] [INFO] DQC Reference Directory: /var/lib/cwl/stgcd3bccd0-36fb-4fb4-9388-39c409ec9ac8/dqc_reference
[2024-01-24 13:36:33,413] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:33,414] [INFO] Task started: Prodigal
[2024-01-24 13:36:33,414] [INFO] Running command: gunzip -c /var/lib/cwl/stg62b8a797-5ce7-4de2-bb09-e4e4ce190be9/GCF_009604425.1_ASM960442v1_genomic.fna.gz | prodigal -d GCF_009604425.1_ASM960442v1_genomic.fna/cds.fna -a GCF_009604425.1_ASM960442v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:01,617] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:01,617] [INFO] Task started: HMMsearch
[2024-01-24 13:37:01,617] [INFO] Running command: hmmsearch --tblout GCF_009604425.1_ASM960442v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcd3bccd0-36fb-4fb4-9388-39c409ec9ac8/dqc_reference/reference_markers.hmm GCF_009604425.1_ASM960442v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:02,001] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:02,003] [INFO] Found 6/6 markers.
[2024-01-24 13:37:02,075] [INFO] Query marker FASTA was written to GCF_009604425.1_ASM960442v1_genomic.fna/markers.fasta
[2024-01-24 13:37:02,075] [INFO] Task started: Blastn
[2024-01-24 13:37:02,075] [INFO] Running command: blastn -query GCF_009604425.1_ASM960442v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd3bccd0-36fb-4fb4-9388-39c409ec9ac8/dqc_reference/reference_markers.fasta -out GCF_009604425.1_ASM960442v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:03,395] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:03,399] [INFO] Selected 18 target genomes.
[2024-01-24 13:37:03,400] [INFO] Target genome list was writen to GCF_009604425.1_ASM960442v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:03,411] [INFO] Task started: fastANI
[2024-01-24 13:37:03,411] [INFO] Running command: fastANI --query /var/lib/cwl/stg62b8a797-5ce7-4de2-bb09-e4e4ce190be9/GCF_009604425.1_ASM960442v1_genomic.fna.gz --refList GCF_009604425.1_ASM960442v1_genomic.fna/target_genomes.txt --output GCF_009604425.1_ASM960442v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:35,775] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:35,775] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcd3bccd0-36fb-4fb4-9388-39c409ec9ac8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:35,775] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcd3bccd0-36fb-4fb4-9388-39c409ec9ac8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:35,791] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:35,791] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:35,791] [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 aurantia	strain=RB56	GCA_009604425.1	2585199	2585199	type	True	100.0	2841	2844	95	conclusive
Nocardia terpenica	strain=IFM 0706	GCA_013186535.1	455432	455432	type	True	81.2228	1257	2844	95	below_threshold
Nocardia transvalensis	strain=NBRC 15921	GCA_000308875.1	37333	37333	type	True	81.1069	1319	2844	95	below_threshold
Nocardia transvalensis	strain=DSM 43582	GCA_014203315.1	37333	37333	type	True	81.0929	1347	2844	95	below_threshold
Nocardia mexicana	strain=NBRC 108244	GCA_001613165.1	279262	279262	type	True	80.8894	1243	2844	95	below_threshold
Nocardia mexicana	strain=DSM 44952	GCA_003350525.1	279262	279262	type	True	80.8632	1320	2844	95	below_threshold
Nocardia elegans	strain=NBRC 108235	GCA_001612845.1	300029	300029	type	True	80.5272	1178	2844	95	below_threshold
Nocardia aobensis	strain=NBRC 100429	GCA_000308375.1	257277	257277	type	True	80.5044	1162	2844	95	below_threshold
Nocardia nova	strain=NBRC 15556	GCA_001613005.1	37330	37330	type	True	80.4802	1162	2844	95	below_threshold
Nocardia macrotermitis	strain=RB20	GCA_009604405.1	2585198	2585198	type	True	80.2962	1297	2844	95	below_threshold
Nocardia albiluteola	strain=NEAU-G5	GCA_018860155.1	2842303	2842303	type	True	80.2951	1233	2844	95	below_threshold
Nocardia farcinica	strain=NCTC11134	GCA_001182745.2	37329	37329	type	True	80.1608	1068	2844	95	below_threshold
Nocardia farcinica	strain=DSM 43257	GCA_900156775.1	37329	37329	type	True	80.0969	1052	2844	95	below_threshold
Nocardia stercoris	strain=NEAU-LL90	GCA_003696265.1	2483361	2483361	type	True	79.8975	1147	2844	95	below_threshold
Nocardia puris	strain=DSM 44599	GCA_003315035.1	208602	208602	type	True	79.8686	1064	2844	95	below_threshold
Nocardia pneumoniae	strain=NBRC 100136	GCA_000308755.1	228601	228601	type	True	79.751	1035	2844	95	below_threshold
Nocardia beijingensis	strain=NBRC 16342	GCA_001612785.1	95162	95162	type	True	79.7022	1097	2844	95	below_threshold
Nocardia thailandica	strain=NBRC 100428	GCA_000308795.1	257275	257275	type	True	79.6849	1010	2844	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:35,793] [INFO] DFAST Taxonomy check result was written to GCF_009604425.1_ASM960442v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:35,793] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:35,793] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:35,794] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcd3bccd0-36fb-4fb4-9388-39c409ec9ac8/dqc_reference/checkm_data
[2024-01-24 13:37:35,795] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:35,877] [INFO] Task started: CheckM
[2024-01-24 13:37:35,878] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009604425.1_ASM960442v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009604425.1_ASM960442v1_genomic.fna/checkm_input GCF_009604425.1_ASM960442v1_genomic.fna/checkm_result
[2024-01-24 13:39:10,691] [INFO] Task succeeded: CheckM
[2024-01-24 13:39:10,692] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:39:10,718] [INFO] ===== Completeness check finished =====
[2024-01-24 13:39:10,718] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:39:10,719] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009604425.1_ASM960442v1_genomic.fna/markers.fasta)
[2024-01-24 13:39:10,719] [INFO] Task started: Blastn
[2024-01-24 13:39:10,720] [INFO] Running command: blastn -query GCF_009604425.1_ASM960442v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd3bccd0-36fb-4fb4-9388-39c409ec9ac8/dqc_reference/reference_markers_gtdb.fasta -out GCF_009604425.1_ASM960442v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:39:12,601] [INFO] Task succeeded: Blastn
[2024-01-24 13:39:12,605] [INFO] Selected 14 target genomes.
[2024-01-24 13:39:12,605] [INFO] Target genome list was writen to GCF_009604425.1_ASM960442v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:39:12,622] [INFO] Task started: fastANI
[2024-01-24 13:39:12,622] [INFO] Running command: fastANI --query /var/lib/cwl/stg62b8a797-5ce7-4de2-bb09-e4e4ce190be9/GCF_009604425.1_ASM960442v1_genomic.fna.gz --refList GCF_009604425.1_ASM960442v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009604425.1_ASM960442v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:39:41,398] [INFO] Task succeeded: fastANI
[2024-01-24 13:39:41,414] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:39:41,414] [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_009604425.1	s__Nocardia sp009604425	100.0	2841	2844	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_000381925.1	s__Nocardia sp000381925	90.219	2351	2844	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015477355.1	s__Nocardia blacklockiae	81.2519	1371	2844	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	81.1952	1263	2844	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	81.1327	1314	2844	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014466955.1	s__Nocardia wallacei	80.9614	1290	2844	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613165.1	s__Nocardia mexicana	80.8491	1254	2844	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000308375.1	s__Nocardia aobensis	80.558	1150	2844	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.6988	98.11	97.03	0.89	0.86	3	-
GCF_001612845.1	s__Nocardia elegans	80.5146	1181	2844	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.9334	99.79	99.59	0.97	0.94	3	-
GCF_001613005.1	s__Nocardia nova	80.4817	1159	2844	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.9334	98.75	97.55	0.88	0.84	13	-
GCF_018860155.1	s__Nocardia sp018860155	80.3175	1232	2844	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019038435.1	s__Nocardia sp019038435	79.9566	1280	2844	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315035.1	s__Nocardia puris	79.8466	1069	2844	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.66	99.46	0.95	0.92	4	-
GCF_000308795.1	s__Nocardia thailandica	79.6724	1010	2844	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 13:39:41,418] [INFO] GTDB search result was written to GCF_009604425.1_ASM960442v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:39:41,419] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:39:41,428] [INFO] DFAST_QC result json was written to GCF_009604425.1_ASM960442v1_genomic.fna/dqc_result.json
[2024-01-24 13:39:41,429] [INFO] DFAST_QC completed!
[2024-01-24 13:39:41,429] [INFO] Total running time: 0h3m9s