[2024-01-24 13:31:57,301] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:57,304] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:57,304] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b77c99c-ec8c-455f-a836-cfb505648d71/dqc_reference
[2024-01-24 13:31:58,671] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:58,672] [INFO] Task started: Prodigal
[2024-01-24 13:31:58,672] [INFO] Running command: gunzip -c /var/lib/cwl/stgfc5fa9df-e936-4d34-842d-28d2299eccf3/GCF_013744875.1_ASM1374487v1_genomic.fna.gz | prodigal -d GCF_013744875.1_ASM1374487v1_genomic.fna/cds.fna -a GCF_013744875.1_ASM1374487v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:38,883] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:38,883] [INFO] Task started: HMMsearch
[2024-01-24 13:32:38,883] [INFO] Running command: hmmsearch --tblout GCF_013744875.1_ASM1374487v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b77c99c-ec8c-455f-a836-cfb505648d71/dqc_reference/reference_markers.hmm GCF_013744875.1_ASM1374487v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:39,310] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:39,311] [INFO] Found 6/6 markers.
[2024-01-24 13:32:39,384] [INFO] Query marker FASTA was written to GCF_013744875.1_ASM1374487v1_genomic.fna/markers.fasta
[2024-01-24 13:32:39,384] [INFO] Task started: Blastn
[2024-01-24 13:32:39,385] [INFO] Running command: blastn -query GCF_013744875.1_ASM1374487v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b77c99c-ec8c-455f-a836-cfb505648d71/dqc_reference/reference_markers.fasta -out GCF_013744875.1_ASM1374487v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:40,778] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:40,782] [INFO] Selected 13 target genomes.
[2024-01-24 13:32:40,782] [INFO] Target genome list was writen to GCF_013744875.1_ASM1374487v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:40,801] [INFO] Task started: fastANI
[2024-01-24 13:32:40,801] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc5fa9df-e936-4d34-842d-28d2299eccf3/GCF_013744875.1_ASM1374487v1_genomic.fna.gz --refList GCF_013744875.1_ASM1374487v1_genomic.fna/target_genomes.txt --output GCF_013744875.1_ASM1374487v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:09,681] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:09,681] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b77c99c-ec8c-455f-a836-cfb505648d71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:09,682] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b77c99c-ec8c-455f-a836-cfb505648d71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:09,694] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:33:09,694] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:09,695] [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 huaxiensis	strain=WCH-YHL-001	GCA_013744875.1	2755382	2755382	type	True	100.0	2779	2779	95	conclusive
Nocardia acididurans	strain=LPG 2	GCA_016741815.1	2802282	2802282	type	True	87.0184	2027	2779	95	below_threshold
Nocardia yamanashiensis	strain=NBRC 100130	GCA_001613325.1	209247	209247	type	True	83.7331	1769	2779	95	below_threshold
Nocardia crassostreae	strain=NBRC 100342	GCA_001613405.1	53428	53428	type	True	83.3315	1647	2779	95	below_threshold
Nocardia seriolae	strain=NBRC 15557	GCA_007990715.1	37332	37332	type	True	83.3141	1549	2779	95	below_threshold
Nocardia concava	strain=NBRC 100430	GCA_000308815.1	257281	257281	type	True	83.2053	1698	2779	95	below_threshold
Nocardia terrae	strain=ET3-3	GCA_009760405.1	2675851	2675851	type	True	83.0583	1679	2779	95	below_threshold
Nocardia niigatensis	strain=NBRC 100131	GCA_000308655.1	209249	209249	type	True	82.9803	1539	2779	95	below_threshold
Nocardia jejuensis	strain=NBRC 103114	GCA_001613145.1	328049	328049	type	True	82.6525	1568	2779	95	below_threshold
Nocardia terpenica	strain=IFM 0706	GCA_013186535.1	455432	455432	type	True	80.9071	1199	2779	95	below_threshold
Nocardia ninae	strain=NBRC 108245	GCA_007990755.1	356145	356145	type	True	79.8626	1128	2779	95	below_threshold
Nocardia colli	strain=CICC 11023	GCA_008704205.1	2545717	2545717	type	True	79.6899	1209	2779	95	below_threshold
Nocardia alba	strain=DSM 44684	GCA_004339125.1	225051	225051	type	True	79.3488	977	2779	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:09,696] [INFO] DFAST Taxonomy check result was written to GCF_013744875.1_ASM1374487v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:09,696] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:09,697] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:09,697] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b77c99c-ec8c-455f-a836-cfb505648d71/dqc_reference/checkm_data
[2024-01-24 13:33:09,698] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:09,782] [INFO] Task started: CheckM
[2024-01-24 13:33:09,782] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013744875.1_ASM1374487v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013744875.1_ASM1374487v1_genomic.fna/checkm_input GCF_013744875.1_ASM1374487v1_genomic.fna/checkm_result
[2024-01-24 13:35:23,056] [INFO] Task succeeded: CheckM
[2024-01-24 13:35:23,058] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:35:23,086] [INFO] ===== Completeness check finished =====
[2024-01-24 13:35:23,087] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:35:23,087] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013744875.1_ASM1374487v1_genomic.fna/markers.fasta)
[2024-01-24 13:35:23,088] [INFO] Task started: Blastn
[2024-01-24 13:35:23,088] [INFO] Running command: blastn -query GCF_013744875.1_ASM1374487v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b77c99c-ec8c-455f-a836-cfb505648d71/dqc_reference/reference_markers_gtdb.fasta -out GCF_013744875.1_ASM1374487v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:35:24,864] [INFO] Task succeeded: Blastn
[2024-01-24 13:35:24,867] [INFO] Selected 13 target genomes.
[2024-01-24 13:35:24,867] [INFO] Target genome list was writen to GCF_013744875.1_ASM1374487v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:35:24,963] [INFO] Task started: fastANI
[2024-01-24 13:35:24,964] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc5fa9df-e936-4d34-842d-28d2299eccf3/GCF_013744875.1_ASM1374487v1_genomic.fna.gz --refList GCF_013744875.1_ASM1374487v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013744875.1_ASM1374487v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:35:51,557] [INFO] Task succeeded: fastANI
[2024-01-24 13:35:51,574] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:35:51,575] [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_013744875.1	s__Nocardia sp013744875	100.0	2778	2779	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_016741815.1	s__Nocardia sp016741815	87.0169	2026	2779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613325.1	s__Nocardia yamanashiensis	83.72	1773	2779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613405.1	s__Nocardia crassostreae	83.3444	1642	2779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007990715.1	s__Nocardia seriolae	83.3032	1552	2779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.94	99.87	0.97	0.93	20	-
GCF_000308815.1	s__Nocardia concava	83.2173	1695	2779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009760405.1	s__Nocardia terrae	83.0677	1679	2779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308655.1	s__Nocardia niigatensis	82.9656	1539	2779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613145.1	s__Nocardia jejuensis	82.6314	1572	2779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007990755.1	s__Nocardia ninae	79.8752	1125	2779	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	79.7072	1206	2779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000710915.1	s__Nocardia brasiliensis_A	79.6666	1183	2779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.2054	98.35	98.32	0.89	0.89	3	-
GCF_001612665.1	s__Nocardia alba	79.3592	982	2779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:35:51,576] [INFO] GTDB search result was written to GCF_013744875.1_ASM1374487v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:35:51,577] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:35:51,580] [INFO] DFAST_QC result json was written to GCF_013744875.1_ASM1374487v1_genomic.fna/dqc_result.json
[2024-01-24 13:35:51,581] [INFO] DFAST_QC completed!
[2024-01-24 13:35:51,581] [INFO] Total running time: 0h3m54s