[2024-01-24 14:05:59,969] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:59,971] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:59,971] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a8ec82c-efc2-4621-83d4-324b449bdc2d/dqc_reference
[2024-01-24 14:06:01,171] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:01,172] [INFO] Task started: Prodigal
[2024-01-24 14:06:01,172] [INFO] Running command: gunzip -c /var/lib/cwl/stg768910a6-c74c-4201-9128-e200e2af7ac6/GCF_000308515.1_ASM30851v1_genomic.fna.gz | prodigal -d GCF_000308515.1_ASM30851v1_genomic.fna/cds.fna -a GCF_000308515.1_ASM30851v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:26,315] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:26,315] [INFO] Task started: HMMsearch
[2024-01-24 14:06:26,315] [INFO] Running command: hmmsearch --tblout GCF_000308515.1_ASM30851v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a8ec82c-efc2-4621-83d4-324b449bdc2d/dqc_reference/reference_markers.hmm GCF_000308515.1_ASM30851v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:26,688] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:26,690] [INFO] Found 6/6 markers.
[2024-01-24 14:06:26,756] [INFO] Query marker FASTA was written to GCF_000308515.1_ASM30851v1_genomic.fna/markers.fasta
[2024-01-24 14:06:26,757] [INFO] Task started: Blastn
[2024-01-24 14:06:26,757] [INFO] Running command: blastn -query GCF_000308515.1_ASM30851v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a8ec82c-efc2-4621-83d4-324b449bdc2d/dqc_reference/reference_markers.fasta -out GCF_000308515.1_ASM30851v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:27,727] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:27,731] [INFO] Selected 9 target genomes.
[2024-01-24 14:06:27,732] [INFO] Target genome list was writen to GCF_000308515.1_ASM30851v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:27,738] [INFO] Task started: fastANI
[2024-01-24 14:06:27,738] [INFO] Running command: fastANI --query /var/lib/cwl/stg768910a6-c74c-4201-9128-e200e2af7ac6/GCF_000308515.1_ASM30851v1_genomic.fna.gz --refList GCF_000308515.1_ASM30851v1_genomic.fna/target_genomes.txt --output GCF_000308515.1_ASM30851v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:42,401] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:42,402] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a8ec82c-efc2-4621-83d4-324b449bdc2d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:42,403] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a8ec82c-efc2-4621-83d4-324b449bdc2d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:42,418] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:42,418] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:42,418] [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 carnea	strain=NBRC 14403	GCA_000308515.1	37328	37328	type	True	100.0	2439	2442	95	conclusive
Nocardia flavorosea	strain=NBRC 108225	GCA_001613385.1	53429	53429	type	True	92.7409	1882	2442	95	below_threshold
Nocardia flavorosea	strain=JCM 3332	GCA_012396035.1	53429	53429	type	True	92.6908	1912	2442	95	below_threshold
Nocardia speluncae	strain=NBRC 108251	GCA_001613245.1	419477	419477	type	True	90.4571	1828	2442	95	below_threshold
Nocardia speluncae	strain=DSM 45078	GCA_012395985.1	419477	419477	type	True	90.4206	1853	2442	95	below_threshold
Nocardia asteroides	strain=DSM 43373	GCA_900114685.1	1824	1824	suspected-type	True	79.1041	856	2442	95	below_threshold
Nocardia asteroides	strain=NBRC 15531	GCA_000308355.2	1824	1824	suspected-type	True	79.0817	863	2442	95	below_threshold
Nocardia asteroides	strain=ATCC 19247	GCA_005863255.1	1824	1824	suspected-type	True	79.0702	854	2442	95	below_threshold
Nocardia asteroides	strain=NCTC11293	GCA_900637185.1	1824	1824	suspected-type	True	79.0296	865	2442	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:42,420] [INFO] DFAST Taxonomy check result was written to GCF_000308515.1_ASM30851v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:42,420] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:42,420] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:42,421] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a8ec82c-efc2-4621-83d4-324b449bdc2d/dqc_reference/checkm_data
[2024-01-24 14:06:42,422] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:42,496] [INFO] Task started: CheckM
[2024-01-24 14:06:42,497] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000308515.1_ASM30851v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000308515.1_ASM30851v1_genomic.fna/checkm_input GCF_000308515.1_ASM30851v1_genomic.fna/checkm_result
[2024-01-24 14:07:51,545] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:51,547] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:51,568] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:51,569] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:51,569] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000308515.1_ASM30851v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:51,570] [INFO] Task started: Blastn
[2024-01-24 14:07:51,570] [INFO] Running command: blastn -query GCF_000308515.1_ASM30851v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a8ec82c-efc2-4621-83d4-324b449bdc2d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000308515.1_ASM30851v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:53,000] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:53,003] [INFO] Selected 10 target genomes.
[2024-01-24 14:07:53,003] [INFO] Target genome list was writen to GCF_000308515.1_ASM30851v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:53,011] [INFO] Task started: fastANI
[2024-01-24 14:07:53,012] [INFO] Running command: fastANI --query /var/lib/cwl/stg768910a6-c74c-4201-9128-e200e2af7ac6/GCF_000308515.1_ASM30851v1_genomic.fna.gz --refList GCF_000308515.1_ASM30851v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000308515.1_ASM30851v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:10,455] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:10,472] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:08:10,472] [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_000308515.1	s__Nocardia carnea	100.0	2439	2442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_001613385.1	s__Nocardia flavorosea	92.7445	1882	2442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001613245.1	s__Nocardia speluncae	90.458	1829	2442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015477805.1	s__Nocardia flavorosea_A	89.2296	1742	2442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001618425.1	s__Nocardia fusca	83.3629	1531	2442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308775.1	s__Nocardia testacea	83.2795	1404	2442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613445.1	s__Nocardia grenadensis	83.0881	1359	2442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645735.1	s__Nocardia jinanensis	83.0067	1440	2442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.99	99.97	1.00	1.00	3	-
GCF_002081715.1	s__Nocardia donostiensis	80.2418	895	2442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.79	99.59	0.98	0.98	3	-
GCF_900637185.1	s__Nocardia asteroides	79.0402	863	2442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	5	-
--------------------------------------------------------------------------------
[2024-01-24 14:08:10,474] [INFO] GTDB search result was written to GCF_000308515.1_ASM30851v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:10,475] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:10,478] [INFO] DFAST_QC result json was written to GCF_000308515.1_ASM30851v1_genomic.fna/dqc_result.json
[2024-01-24 14:08:10,478] [INFO] DFAST_QC completed!
[2024-01-24 14:08:10,478] [INFO] Total running time: 0h2m11s