[2024-01-25 17:42:20,595] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:42:20,597] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:42:20,597] [INFO] DQC Reference Directory: /var/lib/cwl/stg351de1a8-a06d-4880-8c8f-690ef8715039/dqc_reference
[2024-01-25 17:42:21,724] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:42:21,725] [INFO] Task started: Prodigal
[2024-01-25 17:42:21,725] [INFO] Running command: gunzip -c /var/lib/cwl/stg8deb207b-a2eb-4b19-8544-dbd257d5b6a2/GCF_012911925.1_ASM1291192v1_genomic.fna.gz | prodigal -d GCF_012911925.1_ASM1291192v1_genomic.fna/cds.fna -a GCF_012911925.1_ASM1291192v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:42:40,502] [INFO] Task succeeded: Prodigal
[2024-01-25 17:42:40,502] [INFO] Task started: HMMsearch
[2024-01-25 17:42:40,503] [INFO] Running command: hmmsearch --tblout GCF_012911925.1_ASM1291192v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg351de1a8-a06d-4880-8c8f-690ef8715039/dqc_reference/reference_markers.hmm GCF_012911925.1_ASM1291192v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:42:40,788] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:42:40,789] [INFO] Found 6/6 markers.
[2024-01-25 17:42:40,849] [INFO] Query marker FASTA was written to GCF_012911925.1_ASM1291192v1_genomic.fna/markers.fasta
[2024-01-25 17:42:40,849] [INFO] Task started: Blastn
[2024-01-25 17:42:40,849] [INFO] Running command: blastn -query GCF_012911925.1_ASM1291192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg351de1a8-a06d-4880-8c8f-690ef8715039/dqc_reference/reference_markers.fasta -out GCF_012911925.1_ASM1291192v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:42:42,112] [INFO] Task succeeded: Blastn
[2024-01-25 17:42:42,115] [INFO] Selected 12 target genomes.
[2024-01-25 17:42:42,115] [INFO] Target genome list was writen to GCF_012911925.1_ASM1291192v1_genomic.fna/target_genomes.txt
[2024-01-25 17:42:42,174] [INFO] Task started: fastANI
[2024-01-25 17:42:42,174] [INFO] Running command: fastANI --query /var/lib/cwl/stg8deb207b-a2eb-4b19-8544-dbd257d5b6a2/GCF_012911925.1_ASM1291192v1_genomic.fna.gz --refList GCF_012911925.1_ASM1291192v1_genomic.fna/target_genomes.txt --output GCF_012911925.1_ASM1291192v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:43:04,638] [INFO] Task succeeded: fastANI
[2024-01-25 17:43:04,638] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg351de1a8-a06d-4880-8c8f-690ef8715039/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:43:04,638] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg351de1a8-a06d-4880-8c8f-690ef8715039/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:43:04,647] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:43:04,647] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:43:04,647] [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
Pseudonocardia xinjiangensis	strain=JCM 11839	GCA_012911925.1	75289	75289	type	True	100.0	2417	2431	95	conclusive
Pseudonocardia alaniniphila	strain=Y-16303	GCA_022524485.1	75291	75291	type	True	85.2557	1806	2431	95	below_threshold
Pseudonocardia nigra	strain=DSM 104088	GCA_019396355.1	1921578	1921578	type	True	81.798	1204	2431	95	below_threshold
Pseudonocardia kunmingensis	strain=DSM 45301	GCA_006716445.1	630975	630975	type	True	81.555	1311	2431	95	below_threshold
Pseudonocardia cypriaca	strain=DSM 45511	GCA_006717045.1	882449	882449	type	True	81.3989	1248	2431	95	below_threshold
Pseudonocardia hierapolitana	strain=DSM 45671	GCA_007994075.1	1128676	1128676	type	True	81.2696	1325	2431	95	below_threshold
Pseudonocardia petroleophila	strain=CGMCC 4.1532	GCA_014235185.1	37331	37331	type	True	81.0865	1071	2431	95	below_threshold
Pseudonocardia hydrocarbonoxydans	strain=NBRC 14498	GCA_006539565.1	76726	76726	type	True	81.0008	1007	2431	95	below_threshold
Pseudonocardia oceani	strain=KRD185	GCA_019263585.2	2792013	2792013	type	True	80.9933	1098	2431	95	below_threshold
Pseudonocardia broussonetiae	strain=Gen 01	GCA_013155125.1	2736640	2736640	type	True	80.8077	1143	2431	95	below_threshold
Pseudonocardia sulfidoxydans	strain=NBRC 16205	GCA_007989085.1	54011	54011	type	True	79.7	889	2431	95	below_threshold
Pseudonocardia dioxanivorans	strain=CB1190	GCA_000196675.2	240495	240495	type	True	79.5466	1007	2431	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:43:04,648] [INFO] DFAST Taxonomy check result was written to GCF_012911925.1_ASM1291192v1_genomic.fna/tc_result.tsv
[2024-01-25 17:43:04,649] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:43:04,649] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:43:04,649] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg351de1a8-a06d-4880-8c8f-690ef8715039/dqc_reference/checkm_data
[2024-01-25 17:43:04,650] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:43:04,720] [INFO] Task started: CheckM
[2024-01-25 17:43:04,720] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012911925.1_ASM1291192v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012911925.1_ASM1291192v1_genomic.fna/checkm_input GCF_012911925.1_ASM1291192v1_genomic.fna/checkm_result
[2024-01-25 17:44:39,589] [INFO] Task succeeded: CheckM
[2024-01-25 17:44:39,590] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2024-01-25 17:44:39,616] [INFO] ===== Completeness check finished =====
[2024-01-25 17:44:39,616] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:44:39,617] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012911925.1_ASM1291192v1_genomic.fna/markers.fasta)
[2024-01-25 17:44:39,617] [INFO] Task started: Blastn
[2024-01-25 17:44:39,617] [INFO] Running command: blastn -query GCF_012911925.1_ASM1291192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg351de1a8-a06d-4880-8c8f-690ef8715039/dqc_reference/reference_markers_gtdb.fasta -out GCF_012911925.1_ASM1291192v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:44:41,635] [INFO] Task succeeded: Blastn
[2024-01-25 17:44:41,639] [INFO] Selected 18 target genomes.
[2024-01-25 17:44:41,639] [INFO] Target genome list was writen to GCF_012911925.1_ASM1291192v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:44:41,656] [INFO] Task started: fastANI
[2024-01-25 17:44:41,657] [INFO] Running command: fastANI --query /var/lib/cwl/stg8deb207b-a2eb-4b19-8544-dbd257d5b6a2/GCF_012911925.1_ASM1291192v1_genomic.fna.gz --refList GCF_012911925.1_ASM1291192v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012911925.1_ASM1291192v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:45:12,313] [INFO] Task succeeded: fastANI
[2024-01-25 17:45:12,324] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:45:12,325] [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_012911925.1	s__Pseudonocardia xinjiangensis	100.0	2417	2431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002262885.1	s__Pseudonocardia sp002262885	81.5996	1302	2431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001942415.1	s__Pseudonocardia sp001942415	81.5587	1196	2431	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	81.5582	1309	2431	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	81.3855	1253	2431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899645.1	s__Pseudonocardia sp001899645	81.2686	1089	2431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	99.47	99.47	0.91	0.91	2	-
GCF_007994075.1	s__Pseudonocardia hierapolitana	81.2384	1330	2431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001942185.1	s__Pseudonocardia sp001942185	81.2209	1299	2431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014235185.1	s__Pseudonocardia sp014235185	81.1148	1066	2431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539565.1	s__Pseudonocardia hydrocarbonoxydans	81.0602	999	2431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019263585.1	s__Pseudonocardia sp019263585	80.9725	1102	2431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	99.90	99.65	0.98	0.94	5	-
GCA_019263705.1	s__Pseudonocardia sp019263705	80.86	1049	2431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_013155125.1	s__Pseudonocardia broussonetiae	80.7928	1145	2431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018531445.1	s__Pseudonocardia sp018531445	80.555	1140	2431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007989085.1	s__Pseudonocardia sulfidoxydans	79.7307	883	2431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002583555.1	s__Pseudonocardia sp002583555	79.6346	920	2431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000196675.1	s__Pseudonocardia dioxanivorans	79.5539	1003	2431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	98.76	98.74	0.91	0.91	3	-
GCA_001725415.1	s__Pseudonocardia sp001725415	79.4101	974	2431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	97.90	95.81	0.91	0.83	3	-
--------------------------------------------------------------------------------
[2024-01-25 17:45:12,326] [INFO] GTDB search result was written to GCF_012911925.1_ASM1291192v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:45:12,326] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:45:12,329] [INFO] DFAST_QC result json was written to GCF_012911925.1_ASM1291192v1_genomic.fna/dqc_result.json
[2024-01-25 17:45:12,329] [INFO] DFAST_QC completed!
[2024-01-25 17:45:12,329] [INFO] Total running time: 0h2m52s