[2024-01-24 15:27:02,479] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:02,481] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:02,481] [INFO] DQC Reference Directory: /var/lib/cwl/stg153014f1-0ceb-4eee-add8-d9bb1332c4cf/dqc_reference
[2024-01-24 15:27:03,680] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:03,681] [INFO] Task started: Prodigal
[2024-01-24 15:27:03,681] [INFO] Running command: gunzip -c /var/lib/cwl/stg07748340-65cf-49f7-af93-80c4d24cc238/GCF_001612945.1_ASM161294v1_genomic.fna.gz | prodigal -d GCF_001612945.1_ASM161294v1_genomic.fna/cds.fna -a GCF_001612945.1_ASM161294v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:39,908] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:39,909] [INFO] Task started: HMMsearch
[2024-01-24 15:27:39,909] [INFO] Running command: hmmsearch --tblout GCF_001612945.1_ASM161294v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg153014f1-0ceb-4eee-add8-d9bb1332c4cf/dqc_reference/reference_markers.hmm GCF_001612945.1_ASM161294v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:40,326] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:40,328] [INFO] Found 6/6 markers.
[2024-01-24 15:27:40,402] [INFO] Query marker FASTA was written to GCF_001612945.1_ASM161294v1_genomic.fna/markers.fasta
[2024-01-24 15:27:40,403] [INFO] Task started: Blastn
[2024-01-24 15:27:40,403] [INFO] Running command: blastn -query GCF_001612945.1_ASM161294v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg153014f1-0ceb-4eee-add8-d9bb1332c4cf/dqc_reference/reference_markers.fasta -out GCF_001612945.1_ASM161294v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:41,665] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:41,669] [INFO] Selected 13 target genomes.
[2024-01-24 15:27:41,669] [INFO] Target genome list was writen to GCF_001612945.1_ASM161294v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:41,676] [INFO] Task started: fastANI
[2024-01-24 15:27:41,677] [INFO] Running command: fastANI --query /var/lib/cwl/stg07748340-65cf-49f7-af93-80c4d24cc238/GCF_001612945.1_ASM161294v1_genomic.fna.gz --refList GCF_001612945.1_ASM161294v1_genomic.fna/target_genomes.txt --output GCF_001612945.1_ASM161294v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:28:08,797] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:08,798] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg153014f1-0ceb-4eee-add8-d9bb1332c4cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:28:08,798] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg153014f1-0ceb-4eee-add8-d9bb1332c4cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:28:08,813] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:28:08,813] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:28:08,813] [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 inohanensis	strain=NBRC 100128	GCA_001612945.1	209246	209246	type	True	100.0	2693	2694	95	conclusive
Nocardia yamanashiensis	strain=NBRC 100130	GCA_001613325.1	209247	209247	type	True	89.0741	2221	2694	95	below_threshold
Nocardia seriolae	strain=NBRC 15557	GCA_007990715.1	37332	37332	type	True	83.513	1589	2694	95	below_threshold
Nocardia concava	strain=NBRC 100430	GCA_000308815.1	257281	257281	type	True	83.4201	1698	2694	95	below_threshold
Nocardia huaxiensis	strain=WCH-YHL-001	GCA_013744875.1	2755382	2755382	type	True	83.2986	1728	2694	95	below_threshold
Nocardia yunnanensis	strain=CFH S0054	GCA_003626895.1	2382165	2382165	type	True	83.233	1659	2694	95	below_threshold
Nocardia tengchongensis	strain=CFH S0057	GCA_018362975.1	2055889	2055889	type	True	83.2017	1631	2694	95	below_threshold
Nocardia terrae	strain=ET3-3	GCA_009760405.1	2675851	2675851	type	True	83.1926	1750	2694	95	below_threshold
Nocardia niigatensis	strain=NBRC 100131	GCA_000308655.1	209249	209249	type	True	83.104	1591	2694	95	below_threshold
Nocardia crassostreae	strain=NBRC 100342	GCA_001613405.1	53428	53428	type	True	83.0547	1618	2694	95	below_threshold
Nocardia jejuensis	strain=NBRC 103114	GCA_001613145.1	328049	328049	type	True	82.6609	1632	2694	95	below_threshold
Nocardia otitidiscaviarum	strain=NCTC1934	GCA_900454305.1	1823	1823	type	True	82.0904	1487	2694	95	below_threshold
Nocardia otitidiscaviarum	strain=NBRC 14405	GCA_000308635.1	1823	1823	type	True	82.0904	1437	2694	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:28:08,815] [INFO] DFAST Taxonomy check result was written to GCF_001612945.1_ASM161294v1_genomic.fna/tc_result.tsv
[2024-01-24 15:28:08,815] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:28:08,815] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:28:08,816] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg153014f1-0ceb-4eee-add8-d9bb1332c4cf/dqc_reference/checkm_data
[2024-01-24 15:28:08,816] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:28:08,888] [INFO] Task started: CheckM
[2024-01-24 15:28:08,888] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001612945.1_ASM161294v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001612945.1_ASM161294v1_genomic.fna/checkm_input GCF_001612945.1_ASM161294v1_genomic.fna/checkm_result
[2024-01-24 15:29:49,674] [INFO] Task succeeded: CheckM
[2024-01-24 15:29:49,676] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:29:49,709] [INFO] ===== Completeness check finished =====
[2024-01-24 15:29:49,709] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:29:49,710] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001612945.1_ASM161294v1_genomic.fna/markers.fasta)
[2024-01-24 15:29:49,711] [INFO] Task started: Blastn
[2024-01-24 15:29:49,711] [INFO] Running command: blastn -query GCF_001612945.1_ASM161294v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg153014f1-0ceb-4eee-add8-d9bb1332c4cf/dqc_reference/reference_markers_gtdb.fasta -out GCF_001612945.1_ASM161294v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:29:51,437] [INFO] Task succeeded: Blastn
[2024-01-24 15:29:51,441] [INFO] Selected 13 target genomes.
[2024-01-24 15:29:51,441] [INFO] Target genome list was writen to GCF_001612945.1_ASM161294v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:29:51,450] [INFO] Task started: fastANI
[2024-01-24 15:29:51,451] [INFO] Running command: fastANI --query /var/lib/cwl/stg07748340-65cf-49f7-af93-80c4d24cc238/GCF_001612945.1_ASM161294v1_genomic.fna.gz --refList GCF_001612945.1_ASM161294v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001612945.1_ASM161294v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:30:18,120] [INFO] Task succeeded: fastANI
[2024-01-24 15:30:18,136] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:30:18,136] [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_001612945.1	s__Nocardia inohanensis	100.0	2693	2694	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_001613325.1	s__Nocardia yamanashiensis	89.0742	2221	2694	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	83.5079	1590	2694	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	83.4203	1699	2694	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013744875.1	s__Nocardia sp013744875	83.3141	1725	2694	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003626895.1	s__Nocardia yunnanensis	83.2265	1661	2694	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	83.2119	1746	2694	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018362975.1	s__Nocardia tengchongensis	83.1935	1632	2694	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	83.0726	1597	2694	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	83.0435	1619	2694	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009708175.1	s__Nocardia sp009708175	82.9866	1495	2694	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	82.6608	1631	2694	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308635.1	s__Nocardia otitidiscaviarum	82.0859	1438	2694	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	97.88	97.41	0.94	0.92	8	-
--------------------------------------------------------------------------------
[2024-01-24 15:30:18,138] [INFO] GTDB search result was written to GCF_001612945.1_ASM161294v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:30:18,138] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:30:18,144] [INFO] DFAST_QC result json was written to GCF_001612945.1_ASM161294v1_genomic.fna/dqc_result.json
[2024-01-24 15:30:18,144] [INFO] DFAST_QC completed!
[2024-01-24 15:30:18,144] [INFO] Total running time: 0h3m16s