[2024-01-25 20:07:35,723] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:07:35,737] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:07:35,737] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f1282b9-72ea-427b-918b-063848c95134/dqc_reference
[2024-01-25 20:07:36,940] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:07:36,941] [INFO] Task started: Prodigal
[2024-01-25 20:07:36,941] [INFO] Running command: gunzip -c /var/lib/cwl/stg5eff5a9a-5809-40a5-a54e-fb875c1a7960/GCF_013624435.2_ASM1362443v2_genomic.fna.gz | prodigal -d GCF_013624435.2_ASM1362443v2_genomic.fna/cds.fna -a GCF_013624435.2_ASM1362443v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:07:47,338] [INFO] Task succeeded: Prodigal
[2024-01-25 20:07:47,338] [INFO] Task started: HMMsearch
[2024-01-25 20:07:47,338] [INFO] Running command: hmmsearch --tblout GCF_013624435.2_ASM1362443v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f1282b9-72ea-427b-918b-063848c95134/dqc_reference/reference_markers.hmm GCF_013624435.2_ASM1362443v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:07:47,561] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:07:47,562] [INFO] Found 6/6 markers.
[2024-01-25 20:07:47,597] [INFO] Query marker FASTA was written to GCF_013624435.2_ASM1362443v2_genomic.fna/markers.fasta
[2024-01-25 20:07:47,597] [INFO] Task started: Blastn
[2024-01-25 20:07:47,598] [INFO] Running command: blastn -query GCF_013624435.2_ASM1362443v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f1282b9-72ea-427b-918b-063848c95134/dqc_reference/reference_markers.fasta -out GCF_013624435.2_ASM1362443v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:07:48,866] [INFO] Task succeeded: Blastn
[2024-01-25 20:07:48,869] [INFO] Selected 22 target genomes.
[2024-01-25 20:07:48,869] [INFO] Target genome list was writen to GCF_013624435.2_ASM1362443v2_genomic.fna/target_genomes.txt
[2024-01-25 20:07:48,900] [INFO] Task started: fastANI
[2024-01-25 20:07:48,900] [INFO] Running command: fastANI --query /var/lib/cwl/stg5eff5a9a-5809-40a5-a54e-fb875c1a7960/GCF_013624435.2_ASM1362443v2_genomic.fna.gz --refList GCF_013624435.2_ASM1362443v2_genomic.fna/target_genomes.txt --output GCF_013624435.2_ASM1362443v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:08:09,168] [INFO] Task succeeded: fastANI
[2024-01-25 20:08:09,168] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f1282b9-72ea-427b-918b-063848c95134/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:08:09,169] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f1282b9-72ea-427b-918b-063848c95134/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:08:09,181] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:08:09,181] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:08:09,181] [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 solisilvae	strain=Ka25	GCA_003194625.1	1542435	1542435	type	True	84.4918	938	1402	95	below_threshold
Nocardioides houyundeii	strain=78	GCA_002865585.1	2045452	2045452	type	True	83.2121	902	1402	95	below_threshold
Nocardioides daphniae	strain=CCM 7403	GCA_014635145.1	402297	402297	type	True	81.305	693	1402	95	below_threshold
Nocardioides malaquae	strain=Y6	GCA_015070385.1	2773426	2773426	type	True	81.2348	630	1402	95	below_threshold
Nocardioides sediminis	strain=KCTC 19271	GCA_003047295.1	433648	433648	type	True	80.9982	683	1402	95	below_threshold
Nocardioides jishulii	strain=dk3136	GCA_006007965.1	2575440	2575440	type	True	80.9832	701	1402	95	below_threshold
Nocardioides terrigena	strain=KCTC 19217	GCA_003047265.1	424797	424797	type	True	80.9513	685	1402	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013466785.1	419476	419476	type	True	80.8672	681	1402	95	below_threshold
Nocardioides gansuensis	strain=WSJ-1	GCA_003076135.1	2138300	2138300	type	True	80.8383	640	1402	95	below_threshold
Nocardioides dokdonensis	strain=FR1436	GCA_001653335.1	450734	450734	type	True	80.8345	658	1402	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	80.828	712	1402	95	below_threshold
Nocardioides ungokensis	strain=LMG 28591	GCA_013466985.1	1643322	1643322	type	True	80.7854	656	1402	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	80.755	595	1402	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	80.6932	673	1402	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	80.6873	663	1402	95	below_threshold
Nocardioides marinus	strain=DSM 18248	GCA_013408145.1	374514	374514	type	True	80.6831	644	1402	95	below_threshold
Nocardioides rotundus	strain=MCCC 1A10561	GCA_019931675.1	1774216	1774216	type	True	80.629	600	1402	95	below_threshold
Nocardioides exalbidus	strain=DSM 22017	GCA_900105585.1	402596	402596	type	True	80.4189	693	1402	95	below_threshold
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	80.3019	667	1402	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_900101465.1	1045774	1045774	type	True	80.2901	741	1402	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_013409225.1	1045774	1045774	type	True	80.2626	745	1402	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	79.5181	613	1402	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:08:09,183] [INFO] DFAST Taxonomy check result was written to GCF_013624435.2_ASM1362443v2_genomic.fna/tc_result.tsv
[2024-01-25 20:08:09,183] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:08:09,183] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:08:09,184] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f1282b9-72ea-427b-918b-063848c95134/dqc_reference/checkm_data
[2024-01-25 20:08:09,184] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:08:09,224] [INFO] Task started: CheckM
[2024-01-25 20:08:09,224] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013624435.2_ASM1362443v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013624435.2_ASM1362443v2_genomic.fna/checkm_input GCF_013624435.2_ASM1362443v2_genomic.fna/checkm_result
[2024-01-25 20:09:23,448] [INFO] Task succeeded: CheckM
[2024-01-25 20:09:23,449] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:09:23,465] [INFO] ===== Completeness check finished =====
[2024-01-25 20:09:23,465] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:09:23,466] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013624435.2_ASM1362443v2_genomic.fna/markers.fasta)
[2024-01-25 20:09:23,466] [INFO] Task started: Blastn
[2024-01-25 20:09:23,466] [INFO] Running command: blastn -query GCF_013624435.2_ASM1362443v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f1282b9-72ea-427b-918b-063848c95134/dqc_reference/reference_markers_gtdb.fasta -out GCF_013624435.2_ASM1362443v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:09:25,471] [INFO] Task succeeded: Blastn
[2024-01-25 20:09:25,474] [INFO] Selected 17 target genomes.
[2024-01-25 20:09:25,474] [INFO] Target genome list was writen to GCF_013624435.2_ASM1362443v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:09:25,504] [INFO] Task started: fastANI
[2024-01-25 20:09:25,504] [INFO] Running command: fastANI --query /var/lib/cwl/stg5eff5a9a-5809-40a5-a54e-fb875c1a7960/GCF_013624435.2_ASM1362443v2_genomic.fna.gz --refList GCF_013624435.2_ASM1362443v2_genomic.fna/target_genomes_gtdb.txt --output GCF_013624435.2_ASM1362443v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:09:40,331] [INFO] Task succeeded: fastANI
[2024-01-25 20:09:40,341] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:09:40,342] [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_013624435.2	s__Nocardioides sp013624415	100.0	1402	1402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.04	99.04	0.95	0.95	2	conclusive
GCF_003194625.1	s__Nocardioides solisilvae	84.4958	938	1402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002865585.1	s__Nocardioides houyundeii	83.241	898	1402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.48	96.00	0.92	0.88	3	-
GCA_902805925.1	s__Nocardioides sp902805925	81.2259	577	1402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003710085.1	s__Nocardioides sp003710085	81.0421	721	1402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.05	99.05	0.97	0.97	2	-
GCF_013155365.1	s__Nocardioides sp013155365	81.0263	756	1402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001429625.1	s__Nocardioides sp001429625	81.0179	717	1402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006007965.1	s__Nocardioides sp006007965	81.0023	699	1402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003047265.1	s__Nocardioides terrigena	80.9744	681	1402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	95.44	95.44	0.86	0.86	2	-
GCF_011420305.2	s__Nocardioides sp011420305	80.9637	747	1402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.38	99.38	0.96	0.96	2	-
GCF_003047295.1	s__Nocardioides sediminis	80.9564	688	1402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001653335.1	s__Nocardioides dokdonensis	80.8521	660	1402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408145.1	s__Nocardioides marinus	80.7494	638	1402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	96.85	95.82	0.82	0.73	3	-
GCF_017310035.1	s__Nocardioides sp017310035	80.6946	660	1402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015070375.1	s__Nocardioides kribbensis	80.6369	672	1402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.79	97.79	0.94	0.92	3	-
GCF_017916455.1	s__Nocardioides sp017916455	80.5836	649	1402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.92	98.92	0.96	0.96	2	-
GCF_900105585.1	s__Nocardioides exalbidus	80.4335	695	1402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:09:40,346] [INFO] GTDB search result was written to GCF_013624435.2_ASM1362443v2_genomic.fna/result_gtdb.tsv
[2024-01-25 20:09:40,346] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:09:40,350] [INFO] DFAST_QC result json was written to GCF_013624435.2_ASM1362443v2_genomic.fna/dqc_result.json
[2024-01-25 20:09:40,350] [INFO] DFAST_QC completed!
[2024-01-25 20:09:40,350] [INFO] Total running time: 0h2m5s