[2024-01-24 14:46:55,043] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:55,046] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:55,046] [INFO] DQC Reference Directory: /var/lib/cwl/stg719e78b5-c274-4aa9-ba03-6f9f87ea8187/dqc_reference
[2024-01-24 14:46:58,016] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:58,017] [INFO] Task started: Prodigal
[2024-01-24 14:46:58,017] [INFO] Running command: gunzip -c /var/lib/cwl/stgdca08536-17ab-48a5-a070-191bf80978ca/GCF_004519545.1_ASM451954v1_genomic.fna.gz | prodigal -d GCF_004519545.1_ASM451954v1_genomic.fna/cds.fna -a GCF_004519545.1_ASM451954v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:13,234] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:13,235] [INFO] Task started: HMMsearch
[2024-01-24 14:47:13,235] [INFO] Running command: hmmsearch --tblout GCF_004519545.1_ASM451954v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg719e78b5-c274-4aa9-ba03-6f9f87ea8187/dqc_reference/reference_markers.hmm GCF_004519545.1_ASM451954v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:13,581] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:13,583] [INFO] Found 6/6 markers.
[2024-01-24 14:47:13,637] [INFO] Query marker FASTA was written to GCF_004519545.1_ASM451954v1_genomic.fna/markers.fasta
[2024-01-24 14:47:13,637] [INFO] Task started: Blastn
[2024-01-24 14:47:13,637] [INFO] Running command: blastn -query GCF_004519545.1_ASM451954v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg719e78b5-c274-4aa9-ba03-6f9f87ea8187/dqc_reference/reference_markers.fasta -out GCF_004519545.1_ASM451954v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:14,948] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:14,953] [INFO] Selected 23 target genomes.
[2024-01-24 14:47:14,954] [INFO] Target genome list was writen to GCF_004519545.1_ASM451954v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:14,963] [INFO] Task started: fastANI
[2024-01-24 14:47:14,964] [INFO] Running command: fastANI --query /var/lib/cwl/stgdca08536-17ab-48a5-a070-191bf80978ca/GCF_004519545.1_ASM451954v1_genomic.fna.gz --refList GCF_004519545.1_ASM451954v1_genomic.fna/target_genomes.txt --output GCF_004519545.1_ASM451954v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:38,848] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:38,849] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg719e78b5-c274-4aa9-ba03-6f9f87ea8187/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:38,849] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg719e78b5-c274-4aa9-ba03-6f9f87ea8187/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:38,866] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:47:38,867] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:38,867] [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 guangzhouensis	strain=130	GCA_004519545.1	2497878	2497878	type	True	100.0	1686	1692	95	conclusive
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	82.0516	769	1692	95	below_threshold
Nocardioides ginsengisegetis	strain=DSM 21349	GCA_014138045.1	661491	661491	type	True	81.7124	784	1692	95	below_threshold
Nocardioides ungokensis	strain=LMG 28591	GCA_013466985.1	1643322	1643322	type	True	81.6829	854	1692	95	below_threshold
Nocardioides luti	strain=KIGAM211	GCA_014212315.1	2761101	2761101	type	True	81.4991	792	1692	95	below_threshold
Nocardioides panaciterrulae	strain=DSM 21350	GCA_013409645.1	661492	661492	type	True	81.46	791	1692	95	below_threshold
Nocardioides ferulae	strain=SZ4R5S7	GCA_003660455.1	2340821	2340821	type	True	80.9788	732	1692	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	80.8256	769	1692	95	below_threshold
Nocardioides soli	strain=DSM 105498	GCA_014191495.1	1036020	1036020	type	True	80.8219	828	1692	95	below_threshold
Nocardioides currus	strain=IB-3	GCA_003057875.1	2133958	2133958	type	True	80.7989	765	1692	95	below_threshold
Nocardioides deserti	strain=SC8A-24	GCA_014266025.1	1588644	1588644	type	True	80.7902	746	1692	95	below_threshold
Nocardioides sediminis	strain=KCTC 19271	GCA_003047295.1	433648	433648	type	True	80.7854	782	1692	95	below_threshold
Nocardioides deserti	strain=CGMCC 4.7183	GCA_014646035.1	1588644	1588644	type	True	80.7392	752	1692	95	below_threshold
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	80.725	734	1692	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015339545.1	374513	374513	type	True	80.648	731	1692	95	below_threshold
Nocardioides anomalus	strain=HKS04	GCA_011046535.1	2712223	2712223	type	True	80.6183	811	1692	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	80.5421	706	1692	95	below_threshold
Nocardioides halotolerans	strain=DSM 19273	GCA_000422805.1	433660	433660	type	True	80.5238	803	1692	95	below_threshold
Nocardioides marinus	strain=DSM 18248	GCA_013408145.1	374514	374514	type	True	80.4486	704	1692	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	80.3765	677	1692	95	below_threshold
Marmoricola scoriae	strain=DSM 22127	GCA_900104965.1	642780	642780	type	True	80.2867	695	1692	95	below_threshold
Nocardioides solisilvae	strain=Ka25	GCA_003194625.1	1542435	1542435	type	True	80.1821	656	1692	95	below_threshold
Nocardioides houyundeii	strain=78	GCA_002865585.1	2045452	2045452	type	True	80.1756	611	1692	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:38,869] [INFO] DFAST Taxonomy check result was written to GCF_004519545.1_ASM451954v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:38,869] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:38,869] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:38,870] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg719e78b5-c274-4aa9-ba03-6f9f87ea8187/dqc_reference/checkm_data
[2024-01-24 14:47:38,871] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:38,921] [INFO] Task started: CheckM
[2024-01-24 14:47:38,921] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004519545.1_ASM451954v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004519545.1_ASM451954v1_genomic.fna/checkm_input GCF_004519545.1_ASM451954v1_genomic.fna/checkm_result
[2024-01-24 14:48:54,778] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:54,779] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:54,804] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:54,804] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:54,805] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004519545.1_ASM451954v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:54,805] [INFO] Task started: Blastn
[2024-01-24 14:48:54,805] [INFO] Running command: blastn -query GCF_004519545.1_ASM451954v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg719e78b5-c274-4aa9-ba03-6f9f87ea8187/dqc_reference/reference_markers_gtdb.fasta -out GCF_004519545.1_ASM451954v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:56,927] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:56,931] [INFO] Selected 22 target genomes.
[2024-01-24 14:48:56,931] [INFO] Target genome list was writen to GCF_004519545.1_ASM451954v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:56,953] [INFO] Task started: fastANI
[2024-01-24 14:48:56,953] [INFO] Running command: fastANI --query /var/lib/cwl/stgdca08536-17ab-48a5-a070-191bf80978ca/GCF_004519545.1_ASM451954v1_genomic.fna.gz --refList GCF_004519545.1_ASM451954v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004519545.1_ASM451954v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:49:21,314] [INFO] Task succeeded: fastANI
[2024-01-24 14:49:21,334] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:49:21,334] [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_004519545.1	s__Nocardioides guangzhouensis	100.0	1686	1692	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_014842875.1	s__Nocardioides sp014842875	82.0309	771	1692	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013466985.1	s__Nocardioides ungokensis	81.6657	856	1692	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014212315.1	s__Nocardioides luti	81.5497	787	1692	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426745.1	s__Nocardioides sp001426745	81.2926	788	1692	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.99	98.75	0.96	0.95	3	-
GCF_016924665.1	s__Nocardioides sp016924665	81.2556	747	1692	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013778305.1	s__Nocardioides sp013778305	81.1427	817	1692	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003660455.1	s__Nocardioides ferulae	80.9935	730	1692	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000015265.1	s__Nocardioides sp000015265	80.9839	804	1692	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902805925.1	s__Nocardioides sp902805925	80.9229	590	1692	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018275325.1	s__Nocardioides sp018275325	80.8973	775	1692	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425175.1	s__Nocardioides sp001425175	80.8515	839	1692	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014191495.1	s__Nocardioides soli	80.8212	827	1692	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.71	98.71	0.90	0.90	2	-
GCF_003047295.1	s__Nocardioides sediminis	80.819	777	1692	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014266025.1	s__Nocardioides deserti	80.8107	744	1692	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	0.99	0.99	2	-
GCF_011046535.1	s__Nocardioides anomalus	80.6283	809	1692	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907435.1	s__Nocardioides salarius	80.5276	754	1692	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	3	-
GCF_017916425.1	s__Nocardioides sp017916425	80.4887	661	1692	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	80.474	702	1692	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	96.85	95.82	0.82	0.73	3	-
GCF_002865585.1	s__Nocardioides houyundeii	80.1656	612	1692	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.48	96.00	0.92	0.88	3	-
GCF_003725535.1	s__Marmoricola pocheonensis	80.1577	676	1692	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003674065.1	s__Marmoricola mangrovicus	79.8987	638	1692	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:49:21,336] [INFO] GTDB search result was written to GCF_004519545.1_ASM451954v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:49:21,337] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:49:21,342] [INFO] DFAST_QC result json was written to GCF_004519545.1_ASM451954v1_genomic.fna/dqc_result.json
[2024-01-24 14:49:21,342] [INFO] DFAST_QC completed!
[2024-01-24 14:49:21,342] [INFO] Total running time: 0h2m26s