[2024-01-24 11:59:35,621] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:35,623] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:35,623] [INFO] DQC Reference Directory: /var/lib/cwl/stgd75b2799-85e3-44a7-98bc-53d7741b1b7e/dqc_reference
[2024-01-24 11:59:36,843] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:36,843] [INFO] Task started: Prodigal
[2024-01-24 11:59:36,844] [INFO] Running command: gunzip -c /var/lib/cwl/stgcb62a8c0-4c61-45ac-ba0d-0b6bb6897022/GCF_006716565.1_ASM671656v1_genomic.fna.gz | prodigal -d GCF_006716565.1_ASM671656v1_genomic.fna/cds.fna -a GCF_006716565.1_ASM671656v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:00:07,470] [INFO] Task succeeded: Prodigal
[2024-01-24 12:00:07,471] [INFO] Task started: HMMsearch
[2024-01-24 12:00:07,472] [INFO] Running command: hmmsearch --tblout GCF_006716565.1_ASM671656v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd75b2799-85e3-44a7-98bc-53d7741b1b7e/dqc_reference/reference_markers.hmm GCF_006716565.1_ASM671656v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:00:07,880] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:00:07,881] [INFO] Found 6/6 markers.
[2024-01-24 12:00:07,945] [INFO] Query marker FASTA was written to GCF_006716565.1_ASM671656v1_genomic.fna/markers.fasta
[2024-01-24 12:00:07,945] [INFO] Task started: Blastn
[2024-01-24 12:00:07,945] [INFO] Running command: blastn -query GCF_006716565.1_ASM671656v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd75b2799-85e3-44a7-98bc-53d7741b1b7e/dqc_reference/reference_markers.fasta -out GCF_006716565.1_ASM671656v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:09,217] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:09,221] [INFO] Selected 8 target genomes.
[2024-01-24 12:00:09,222] [INFO] Target genome list was writen to GCF_006716565.1_ASM671656v1_genomic.fna/target_genomes.txt
[2024-01-24 12:00:09,224] [INFO] Task started: fastANI
[2024-01-24 12:00:09,224] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb62a8c0-4c61-45ac-ba0d-0b6bb6897022/GCF_006716565.1_ASM671656v1_genomic.fna.gz --refList GCF_006716565.1_ASM671656v1_genomic.fna/target_genomes.txt --output GCF_006716565.1_ASM671656v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:00:25,267] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:25,267] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd75b2799-85e3-44a7-98bc-53d7741b1b7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:00:25,267] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd75b2799-85e3-44a7-98bc-53d7741b1b7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:00:25,275] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:00:25,276] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:00:25,276] [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 bhagyanarayanae	strain=DSM 103495	GCA_006716565.1	1215925	1215925	type	True	100.0	2517	2517	95	conclusive
Nocardia amikacinitolerans	strain=NBRC 108937	GCA_001612615.1	756689	756689	type	True	93.316	2028	2517	95	below_threshold
Nocardia amikacinitolerans	strain=DSM 45539	GCA_024172045.1	756689	756689	type	True	93.2619	2056	2517	95	below_threshold
Nocardia lijiangensis	strain=NBRC 108240	GCA_001613045.1	299618	299618	type	True	89.9191	1924	2517	95	below_threshold
Nocardia xishanensis	strain=NBRC 101358	GCA_001613365.1	238964	238964	type	True	89.2201	1937	2517	95	below_threshold
Nocardia farcinica	strain=NBRC 15532	GCA_001612925.1	37329	37329	type	True	83.528	1274	2517	95	below_threshold
Nocardia farcinica	strain=DSM 43257	GCA_900156775.1	37329	37329	type	True	83.5061	1344	2517	95	below_threshold
Nocardia farcinica	strain=NCTC11134	GCA_001182745.2	37329	37329	type	True	83.4903	1356	2517	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:00:25,278] [INFO] DFAST Taxonomy check result was written to GCF_006716565.1_ASM671656v1_genomic.fna/tc_result.tsv
[2024-01-24 12:00:25,279] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:00:25,279] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:00:25,279] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd75b2799-85e3-44a7-98bc-53d7741b1b7e/dqc_reference/checkm_data
[2024-01-24 12:00:25,281] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:00:25,351] [INFO] Task started: CheckM
[2024-01-24 12:00:25,351] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006716565.1_ASM671656v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006716565.1_ASM671656v1_genomic.fna/checkm_input GCF_006716565.1_ASM671656v1_genomic.fna/checkm_result
[2024-01-24 12:01:56,689] [INFO] Task succeeded: CheckM
[2024-01-24 12:01:56,691] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.31%
Strain heterogeneity: 40.00%
--------------------------------------------------------------------------------
[2024-01-24 12:01:56,718] [INFO] ===== Completeness check finished =====
[2024-01-24 12:01:56,718] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:01:56,719] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006716565.1_ASM671656v1_genomic.fna/markers.fasta)
[2024-01-24 12:01:56,719] [INFO] Task started: Blastn
[2024-01-24 12:01:56,719] [INFO] Running command: blastn -query GCF_006716565.1_ASM671656v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd75b2799-85e3-44a7-98bc-53d7741b1b7e/dqc_reference/reference_markers_gtdb.fasta -out GCF_006716565.1_ASM671656v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:01:58,592] [INFO] Task succeeded: Blastn
[2024-01-24 12:01:58,596] [INFO] Selected 11 target genomes.
[2024-01-24 12:01:58,596] [INFO] Target genome list was writen to GCF_006716565.1_ASM671656v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:01:58,604] [INFO] Task started: fastANI
[2024-01-24 12:01:58,604] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb62a8c0-4c61-45ac-ba0d-0b6bb6897022/GCF_006716565.1_ASM671656v1_genomic.fna.gz --refList GCF_006716565.1_ASM671656v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006716565.1_ASM671656v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:02:21,366] [INFO] Task succeeded: fastANI
[2024-01-24 12:02:21,382] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:02:21,383] [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_006716565.1	s__Nocardia bhagyanarayanae	100.0	2517	2517	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_001612615.1	s__Nocardia amikacinitolerans	93.3068	2029	2517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	97.80	97.80	0.89	0.89	2	-
GCF_001613045.1	s__Nocardia lijiangensis	89.9179	1924	2517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613365.1	s__Nocardia xishanensis	89.2247	1937	2517	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	83.9379	1517	2517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.66	99.46	0.95	0.92	4	-
GCF_001182745.1	s__Nocardia farcinica	83.5133	1348	2517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.16	98.59	0.93	0.88	42	-
GCF_009829325.1	s__Nocardia sp009829325	82.3824	1459	2517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	96.48	96.48	0.88	0.88	2	-
GCF_008704205.1	s__Nocardia colli	82.3612	1447	2517	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	82.2617	1402	2517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.8238	100.00	100.00	0.99	0.99	2	-
GCF_000710915.1	s__Nocardia brasiliensis_A	82.2095	1365	2517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.2054	98.35	98.32	0.89	0.89	3	-
GCF_001612685.1	s__Nocardia altamirensis	82.0433	1406	2517	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 12:02:21,384] [INFO] GTDB search result was written to GCF_006716565.1_ASM671656v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:02:21,386] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:02:21,388] [INFO] DFAST_QC result json was written to GCF_006716565.1_ASM671656v1_genomic.fna/dqc_result.json
[2024-01-24 12:02:21,389] [INFO] DFAST_QC completed!
[2024-01-24 12:02:21,389] [INFO] Total running time: 0h2m46s