[2024-01-24 14:07:30,895] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:07:30,902] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:07:30,902] [INFO] DQC Reference Directory: /var/lib/cwl/stgf7b38957-c34b-48a4-ac32-572dc797c4b1/dqc_reference
[2024-01-24 14:07:32,135] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:07:32,136] [INFO] Task started: Prodigal
[2024-01-24 14:07:32,137] [INFO] Running command: gunzip -c /var/lib/cwl/stgeb223ec3-c453-4ea1-bb7d-487748f0a572/GCF_014648595.1_ASM1464859v1_genomic.fna.gz | prodigal -d GCF_014648595.1_ASM1464859v1_genomic.fna/cds.fna -a GCF_014648595.1_ASM1464859v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:07:45,231] [INFO] Task succeeded: Prodigal
[2024-01-24 14:07:45,232] [INFO] Task started: HMMsearch
[2024-01-24 14:07:45,232] [INFO] Running command: hmmsearch --tblout GCF_014648595.1_ASM1464859v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf7b38957-c34b-48a4-ac32-572dc797c4b1/dqc_reference/reference_markers.hmm GCF_014648595.1_ASM1464859v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:07:45,565] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:07:45,567] [INFO] Found 6/6 markers.
[2024-01-24 14:07:45,623] [INFO] Query marker FASTA was written to GCF_014648595.1_ASM1464859v1_genomic.fna/markers.fasta
[2024-01-24 14:07:45,624] [INFO] Task started: Blastn
[2024-01-24 14:07:45,624] [INFO] Running command: blastn -query GCF_014648595.1_ASM1464859v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7b38957-c34b-48a4-ac32-572dc797c4b1/dqc_reference/reference_markers.fasta -out GCF_014648595.1_ASM1464859v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:46,858] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:46,862] [INFO] Selected 14 target genomes.
[2024-01-24 14:07:46,862] [INFO] Target genome list was writen to GCF_014648595.1_ASM1464859v1_genomic.fna/target_genomes.txt
[2024-01-24 14:07:46,871] [INFO] Task started: fastANI
[2024-01-24 14:07:46,871] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb223ec3-c453-4ea1-bb7d-487748f0a572/GCF_014648595.1_ASM1464859v1_genomic.fna.gz --refList GCF_014648595.1_ASM1464859v1_genomic.fna/target_genomes.txt --output GCF_014648595.1_ASM1464859v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:08:02,770] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:02,771] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf7b38957-c34b-48a4-ac32-572dc797c4b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:08:02,772] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf7b38957-c34b-48a4-ac32-572dc797c4b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:08:02,790] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:08:02,790] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:08:02,790] [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
Nocardioides luteus	strain=JCM 3358	GCA_014648595.1	1844	1844	type	True	100.0	1624	1626	95	conclusive
Nocardioides albus	strain=JCM 3185	GCA_014648255.1	1841	1841	type	True	88.2716	1298	1626	95	below_threshold
Nocardioides panzhihuensis	strain=DSM 26487	GCA_013408335.1	860243	860243	type	True	88.1552	1335	1626	95	below_threshold
Nocardioides albertanoniae	strain=DSM 25218	GCA_006716315.1	1175486	1175486	type	True	87.3028	1279	1626	95	below_threshold
Nocardioides nematodiphilus	strain=R-N-C8	GCA_020216525.1	2849669	2849669	type	True	80.2678	643	1626	95	below_threshold
Nocardioides panaciterrulae	strain=DSM 21350	GCA_013409645.1	661492	661492	type	True	79.6987	597	1626	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	79.5752	606	1626	95	below_threshold
Nocardioides soli	strain=DSM 105498	GCA_014191495.1	1036020	1036020	type	True	79.5035	690	1626	95	below_threshold
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	79.4855	625	1626	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	79.4731	610	1626	95	below_threshold
Nocardioides solisilvae	strain=Ka25	GCA_003194625.1	1542435	1542435	type	True	79.4095	543	1626	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	79.3951	597	1626	95	below_threshold
Nocardioides malaquae	strain=Y6	GCA_015070385.1	2773426	2773426	type	True	79.3738	477	1626	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	79.2087	685	1626	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:08:02,792] [INFO] DFAST Taxonomy check result was written to GCF_014648595.1_ASM1464859v1_genomic.fna/tc_result.tsv
[2024-01-24 14:08:02,793] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:08:02,793] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:08:02,794] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf7b38957-c34b-48a4-ac32-572dc797c4b1/dqc_reference/checkm_data
[2024-01-24 14:08:02,795] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:08:02,847] [INFO] Task started: CheckM
[2024-01-24 14:08:02,848] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014648595.1_ASM1464859v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014648595.1_ASM1464859v1_genomic.fna/checkm_input GCF_014648595.1_ASM1464859v1_genomic.fna/checkm_result
[2024-01-24 14:09:03,331] [INFO] Task succeeded: CheckM
[2024-01-24 14:09:03,332] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:09:03,354] [INFO] ===== Completeness check finished =====
[2024-01-24 14:09:03,354] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:09:03,355] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014648595.1_ASM1464859v1_genomic.fna/markers.fasta)
[2024-01-24 14:09:03,355] [INFO] Task started: Blastn
[2024-01-24 14:09:03,355] [INFO] Running command: blastn -query GCF_014648595.1_ASM1464859v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7b38957-c34b-48a4-ac32-572dc797c4b1/dqc_reference/reference_markers_gtdb.fasta -out GCF_014648595.1_ASM1464859v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:09:05,209] [INFO] Task succeeded: Blastn
[2024-01-24 14:09:05,213] [INFO] Selected 9 target genomes.
[2024-01-24 14:09:05,213] [INFO] Target genome list was writen to GCF_014648595.1_ASM1464859v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:09:05,220] [INFO] Task started: fastANI
[2024-01-24 14:09:05,220] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb223ec3-c453-4ea1-bb7d-487748f0a572/GCF_014648595.1_ASM1464859v1_genomic.fna.gz --refList GCF_014648595.1_ASM1464859v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014648595.1_ASM1464859v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:09:18,790] [INFO] Task succeeded: fastANI
[2024-01-24 14:09:18,801] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:09:18,801] [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_014648595.1	s__Nocardioides luteus	100.0	1624	1626	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000960475.2	s__Nocardioides luteus_A	89.2366	1324	1626	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015752315.1	s__Nocardioides sp000192415	89.2272	1344	1626	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.29	98.29	0.91	0.91	2	-
GCF_011045035.1	s__Nocardioides sp011045035	89.1172	1320	1626	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715835.1	s__Nocardioides sp006715835	89.04	1379	1626	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009858265.1	s__Nocardioides sp009858265	88.989	1380	1626	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715515.1	s__Nocardioides sp006715515	88.9495	1341	1626	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101045.1	s__Nocardioides sp900101045	88.9356	1385	1626	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648255.1	s__Nocardioides albus	88.2787	1297	1626	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:09:18,805] [INFO] GTDB search result was written to GCF_014648595.1_ASM1464859v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:09:18,805] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:09:18,808] [INFO] DFAST_QC result json was written to GCF_014648595.1_ASM1464859v1_genomic.fna/dqc_result.json
[2024-01-24 14:09:18,809] [INFO] DFAST_QC completed!
[2024-01-24 14:09:18,809] [INFO] Total running time: 0h1m48s