[2024-01-24 15:26:39,720] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:39,722] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:39,722] [INFO] DQC Reference Directory: /var/lib/cwl/stg8a8c382b-c321-4079-bfbc-769ba17a94c2/dqc_reference
[2024-01-24 15:26:41,039] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:41,040] [INFO] Task started: Prodigal
[2024-01-24 15:26:41,040] [INFO] Running command: gunzip -c /var/lib/cwl/stg382771ac-6792-4126-84e5-379478dff890/GCF_028737265.1_ASM2873726v1_genomic.fna.gz | prodigal -d GCF_028737265.1_ASM2873726v1_genomic.fna/cds.fna -a GCF_028737265.1_ASM2873726v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:57,146] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:57,147] [INFO] Task started: HMMsearch
[2024-01-24 15:26:57,147] [INFO] Running command: hmmsearch --tblout GCF_028737265.1_ASM2873726v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8a8c382b-c321-4079-bfbc-769ba17a94c2/dqc_reference/reference_markers.hmm GCF_028737265.1_ASM2873726v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:26:57,459] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:26:57,460] [INFO] Found 6/6 markers.
[2024-01-24 15:26:57,518] [INFO] Query marker FASTA was written to GCF_028737265.1_ASM2873726v1_genomic.fna/markers.fasta
[2024-01-24 15:26:57,518] [INFO] Task started: Blastn
[2024-01-24 15:26:57,519] [INFO] Running command: blastn -query GCF_028737265.1_ASM2873726v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a8c382b-c321-4079-bfbc-769ba17a94c2/dqc_reference/reference_markers.fasta -out GCF_028737265.1_ASM2873726v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:26:58,856] [INFO] Task succeeded: Blastn
[2024-01-24 15:26:58,860] [INFO] Selected 10 target genomes.
[2024-01-24 15:26:58,860] [INFO] Target genome list was writen to GCF_028737265.1_ASM2873726v1_genomic.fna/target_genomes.txt
[2024-01-24 15:26:58,865] [INFO] Task started: fastANI
[2024-01-24 15:26:58,865] [INFO] Running command: fastANI --query /var/lib/cwl/stg382771ac-6792-4126-84e5-379478dff890/GCF_028737265.1_ASM2873726v1_genomic.fna.gz --refList GCF_028737265.1_ASM2873726v1_genomic.fna/target_genomes.txt --output GCF_028737265.1_ASM2873726v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:17,020] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:17,020] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8a8c382b-c321-4079-bfbc-769ba17a94c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:17,021] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8a8c382b-c321-4079-bfbc-769ba17a94c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:17,035] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:27:17,035] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:27:17,035] [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
Actinomycetospora succinea	strain=DSM 45775	GCA_004363095.1	663603	663603	type	True	86.1463	1589	2014	95	below_threshold
Actinomycetospora cinnamomea	strain=DSM 45771	GCA_003096675.1	663609	663609	type	True	85.378	1444	2014	95	below_threshold
Actinomycetospora soli	strain=SF1	GCA_021026295.1	2893887	2893887	type	True	81.2195	1174	2014	95	below_threshold
Actinomycetospora endophytica	strain=TBRC 5722	GCA_021026375.1	2291215	2291215	type	True	80.9664	1178	2014	95	below_threshold
Actinomycetospora chiangmaiensis	strain=DSM 45062	GCA_000379625.1	402650	402650	type	True	80.9501	1107	2014	95	below_threshold
Actinomycetospora corticicola	strain=DSM 45772	GCA_013409505.1	663602	663602	type	True	80.8919	1153	2014	95	below_threshold
Pseudonocardia oceani	strain=KRD185	GCA_019263585.2	2792013	2792013	type	True	78.0147	938	2014	95	below_threshold
Pseudonocardia hydrocarbonoxydans	strain=NBRC 14498	GCA_006539565.1	76726	76726	type	True	77.9383	826	2014	95	below_threshold
Pseudonocardia cypriaca	strain=DSM 45511	GCA_006717045.1	882449	882449	type	True	77.4123	866	2014	95	below_threshold
Pseudonocardia kunmingensis	strain=DSM 45301	GCA_006716445.1	630975	630975	type	True	77.3371	950	2014	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:17,038] [INFO] DFAST Taxonomy check result was written to GCF_028737265.1_ASM2873726v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:17,039] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:17,039] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:17,039] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8a8c382b-c321-4079-bfbc-769ba17a94c2/dqc_reference/checkm_data
[2024-01-24 15:27:17,041] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:17,098] [INFO] Task started: CheckM
[2024-01-24 15:27:17,099] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028737265.1_ASM2873726v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028737265.1_ASM2873726v1_genomic.fna/checkm_input GCF_028737265.1_ASM2873726v1_genomic.fna/checkm_result
[2024-01-24 15:28:41,005] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:41,006] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:41,029] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:41,029] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:41,030] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028737265.1_ASM2873726v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:41,030] [INFO] Task started: Blastn
[2024-01-24 15:28:41,031] [INFO] Running command: blastn -query GCF_028737265.1_ASM2873726v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a8c382b-c321-4079-bfbc-769ba17a94c2/dqc_reference/reference_markers_gtdb.fasta -out GCF_028737265.1_ASM2873726v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:42,978] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:42,982] [INFO] Selected 10 target genomes.
[2024-01-24 15:28:42,982] [INFO] Target genome list was writen to GCF_028737265.1_ASM2873726v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:42,990] [INFO] Task started: fastANI
[2024-01-24 15:28:42,991] [INFO] Running command: fastANI --query /var/lib/cwl/stg382771ac-6792-4126-84e5-379478dff890/GCF_028737265.1_ASM2873726v1_genomic.fna.gz --refList GCF_028737265.1_ASM2873726v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028737265.1_ASM2873726v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:29:00,680] [INFO] Task succeeded: fastANI
[2024-01-24 15:29:00,693] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 15:29:00,693] [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
GCA_902805495.1	s__Actinomycetospora sp902805495	86.5929	966	2014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinomycetospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363095.1	s__Actinomycetospora succinea	86.1665	1585	2014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinomycetospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003096675.1	s__Actinomycetospora cinnamomea	85.3518	1447	2014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinomycetospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012933465.1	s__Actinomycetospora sp012933465	81.2582	1204	2014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinomycetospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409505.1	s__Actinomycetospora corticicola	80.9192	1146	2014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinomycetospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379625.1	s__Actinomycetospora chiangmaiensis	80.8984	1115	2014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinomycetospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019263585.1	s__Pseudonocardia sp019263585	78.0323	935	2014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	99.90	99.65	0.98	0.94	5	-
GCF_006539565.1	s__Pseudonocardia hydrocarbonoxydans	77.96	820	2014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006717045.1	s__Pseudonocardia cypriaca	77.3896	871	2014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716445.1	s__Pseudonocardia kunmingensis	77.3361	949	2014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:29:00,695] [INFO] GTDB search result was written to GCF_028737265.1_ASM2873726v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:29:00,695] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:29:00,698] [INFO] DFAST_QC result json was written to GCF_028737265.1_ASM2873726v1_genomic.fna/dqc_result.json
[2024-01-24 15:29:00,698] [INFO] DFAST_QC completed!
[2024-01-24 15:29:00,699] [INFO] Total running time: 0h2m21s