[2024-01-25 18:59:50,748] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:59:50,750] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:59:50,750] [INFO] DQC Reference Directory: /var/lib/cwl/stg952823ee-0b87-4107-9974-f99c945bd56a/dqc_reference
[2024-01-25 18:59:51,861] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:59:51,862] [INFO] Task started: Prodigal
[2024-01-25 18:59:51,862] [INFO] Running command: gunzip -c /var/lib/cwl/stg5c0ffd14-e093-4144-8085-567a47ad6042/GCF_014635145.1_ASM1463514v1_genomic.fna.gz | prodigal -d GCF_014635145.1_ASM1463514v1_genomic.fna/cds.fna -a GCF_014635145.1_ASM1463514v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:00:00,967] [INFO] Task succeeded: Prodigal
[2024-01-25 19:00:00,967] [INFO] Task started: HMMsearch
[2024-01-25 19:00:00,967] [INFO] Running command: hmmsearch --tblout GCF_014635145.1_ASM1463514v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg952823ee-0b87-4107-9974-f99c945bd56a/dqc_reference/reference_markers.hmm GCF_014635145.1_ASM1463514v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:00:01,183] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:00:01,184] [INFO] Found 6/6 markers.
[2024-01-25 19:00:01,213] [INFO] Query marker FASTA was written to GCF_014635145.1_ASM1463514v1_genomic.fna/markers.fasta
[2024-01-25 19:00:01,213] [INFO] Task started: Blastn
[2024-01-25 19:00:01,214] [INFO] Running command: blastn -query GCF_014635145.1_ASM1463514v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg952823ee-0b87-4107-9974-f99c945bd56a/dqc_reference/reference_markers.fasta -out GCF_014635145.1_ASM1463514v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:00:02,364] [INFO] Task succeeded: Blastn
[2024-01-25 19:00:02,366] [INFO] Selected 13 target genomes.
[2024-01-25 19:00:02,366] [INFO] Target genome list was writen to GCF_014635145.1_ASM1463514v1_genomic.fna/target_genomes.txt
[2024-01-25 19:00:02,376] [INFO] Task started: fastANI
[2024-01-25 19:00:02,376] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c0ffd14-e093-4144-8085-567a47ad6042/GCF_014635145.1_ASM1463514v1_genomic.fna.gz --refList GCF_014635145.1_ASM1463514v1_genomic.fna/target_genomes.txt --output GCF_014635145.1_ASM1463514v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:00:13,638] [INFO] Task succeeded: fastANI
[2024-01-25 19:00:13,639] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg952823ee-0b87-4107-9974-f99c945bd56a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:00:13,639] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg952823ee-0b87-4107-9974-f99c945bd56a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:00:13,648] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:00:13,648] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:00:13,649] [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 daphniae	strain=CCM 7403	GCA_014635145.1	402297	402297	type	True	100.0	1177	1177	95	conclusive
Nocardioides daphniae	strain=JCM 16608	GCA_004777465.1	402297	402297	type	True	99.9391	1176	1177	95	conclusive
Nocardioides jishulii	strain=dk3136	GCA_006007965.1	2575440	2575440	type	True	87.2981	905	1177	95	below_threshold
Nocardioides malaquae	strain=Y6	GCA_015070385.1	2773426	2773426	type	True	84.4469	782	1177	95	below_threshold
Nocardioides gilvus	strain=XZ17	GCA_003194605.1	1735589	1735589	type	True	82.378	699	1177	95	below_threshold
Nocardioides yefusunii	strain=HY056	GCA_004014875.1	2500546	2500546	type	True	81.733	604	1177	95	below_threshold
Nocardioides solisilvae	strain=Ka25	GCA_003194625.1	1542435	1542435	type	True	81.705	685	1177	95	below_threshold
Nocardioides marinus	strain=DSM 18248	GCA_013408145.1	374514	374514	type	True	80.9144	579	1177	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	80.8549	648	1177	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	80.7993	617	1177	95	below_threshold
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	80.6533	593	1177	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	80.5919	606	1177	95	below_threshold
Nocardioides panaciterrulae	strain=DSM 21350	GCA_013409645.1	661492	661492	type	True	80.321	582	1177	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:00:13,650] [INFO] DFAST Taxonomy check result was written to GCF_014635145.1_ASM1463514v1_genomic.fna/tc_result.tsv
[2024-01-25 19:00:13,650] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:00:13,651] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:00:13,651] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg952823ee-0b87-4107-9974-f99c945bd56a/dqc_reference/checkm_data
[2024-01-25 19:00:13,652] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:00:13,688] [INFO] Task started: CheckM
[2024-01-25 19:00:13,688] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014635145.1_ASM1463514v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014635145.1_ASM1463514v1_genomic.fna/checkm_input GCF_014635145.1_ASM1463514v1_genomic.fna/checkm_result
[2024-01-25 19:01:07,898] [INFO] Task succeeded: CheckM
[2024-01-25 19:01:07,899] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:01:07,914] [INFO] ===== Completeness check finished =====
[2024-01-25 19:01:07,915] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:01:07,915] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014635145.1_ASM1463514v1_genomic.fna/markers.fasta)
[2024-01-25 19:01:07,916] [INFO] Task started: Blastn
[2024-01-25 19:01:07,916] [INFO] Running command: blastn -query GCF_014635145.1_ASM1463514v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg952823ee-0b87-4107-9974-f99c945bd56a/dqc_reference/reference_markers_gtdb.fasta -out GCF_014635145.1_ASM1463514v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:01:09,876] [INFO] Task succeeded: Blastn
[2024-01-25 19:01:09,878] [INFO] Selected 17 target genomes.
[2024-01-25 19:01:09,879] [INFO] Target genome list was writen to GCF_014635145.1_ASM1463514v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:01:09,892] [INFO] Task started: fastANI
[2024-01-25 19:01:09,892] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c0ffd14-e093-4144-8085-567a47ad6042/GCF_014635145.1_ASM1463514v1_genomic.fna.gz --refList GCF_014635145.1_ASM1463514v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014635145.1_ASM1463514v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:01:24,902] [INFO] Task succeeded: fastANI
[2024-01-25 19:01:24,914] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:01:24,914] [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_004777465.1	s__Nocardioides daphniae	99.9391	1176	1177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.94	99.94	1.00	1.00	2	conclusive
GCF_006007965.1	s__Nocardioides sp006007965	87.2866	907	1177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003194605.1	s__Nocardioides gilvus	82.3552	701	1177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004014875.1	s__Nocardioides sp004014875	81.6996	606	1177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003194625.1	s__Nocardioides solisilvae	81.6869	687	1177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013624435.2	s__Nocardioides sp013624415	81.4649	671	1177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.04	99.04	0.95	0.95	2	-
GCF_002865585.1	s__Nocardioides houyundeii	81.2488	651	1177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.48	96.00	0.92	0.88	3	-
GCF_003047295.1	s__Nocardioides sediminis	80.8786	627	1177	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	80.7992	630	1177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	3	-
GCF_900105585.1	s__Nocardioides exalbidus	80.7334	637	1177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001627335.1	s__Nocardioides sp001627335	80.5265	519	1177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.38	96.50	0.91	0.88	12	-
GCF_015024225.1	s__Nocardioides sp015024225	80.3812	602	1177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.48	97.48	0.91	0.91	2	-
GCF_001425175.1	s__Nocardioides sp001425175	80.3727	613	1177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013177455.1	s__Nocardioides sp013177455	80.3643	609	1177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.28	98.92	0.97	0.95	4	-
GCF_013409645.1	s__Nocardioides panaciterrulae	80.3388	581	1177	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	80.2516	611	1177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004919105.1	s__Nocardioides sp004919105	79.9715	563	1177	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 19:01:24,916] [INFO] GTDB search result was written to GCF_014635145.1_ASM1463514v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:01:24,916] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:01:24,919] [INFO] DFAST_QC result json was written to GCF_014635145.1_ASM1463514v1_genomic.fna/dqc_result.json
[2024-01-25 19:01:24,919] [INFO] DFAST_QC completed!
[2024-01-25 19:01:24,920] [INFO] Total running time: 0h1m34s