[2024-01-24 14:05:34,161] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:34,162] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:34,162] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c4d6018-bcde-4017-bedb-8d2968dcda36/dqc_reference
[2024-01-24 14:05:35,540] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:35,541] [INFO] Task started: Prodigal
[2024-01-24 14:05:35,541] [INFO] Running command: gunzip -c /var/lib/cwl/stgf2ee9126-1694-4346-9147-5f1d6de6f620/GCF_004217185.1_ASM421718v1_genomic.fna.gz | prodigal -d GCF_004217185.1_ASM421718v1_genomic.fna/cds.fna -a GCF_004217185.1_ASM421718v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:54,535] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:54,535] [INFO] Task started: HMMsearch
[2024-01-24 14:05:54,535] [INFO] Running command: hmmsearch --tblout GCF_004217185.1_ASM421718v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c4d6018-bcde-4017-bedb-8d2968dcda36/dqc_reference/reference_markers.hmm GCF_004217185.1_ASM421718v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:54,845] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:54,846] [INFO] Found 6/6 markers.
[2024-01-24 14:05:54,901] [INFO] Query marker FASTA was written to GCF_004217185.1_ASM421718v1_genomic.fna/markers.fasta
[2024-01-24 14:05:54,901] [INFO] Task started: Blastn
[2024-01-24 14:05:54,901] [INFO] Running command: blastn -query GCF_004217185.1_ASM421718v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c4d6018-bcde-4017-bedb-8d2968dcda36/dqc_reference/reference_markers.fasta -out GCF_004217185.1_ASM421718v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:56,199] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:56,203] [INFO] Selected 12 target genomes.
[2024-01-24 14:05:56,203] [INFO] Target genome list was writen to GCF_004217185.1_ASM421718v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:56,212] [INFO] Task started: fastANI
[2024-01-24 14:05:56,213] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2ee9126-1694-4346-9147-5f1d6de6f620/GCF_004217185.1_ASM421718v1_genomic.fna.gz --refList GCF_004217185.1_ASM421718v1_genomic.fna/target_genomes.txt --output GCF_004217185.1_ASM421718v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:17,712] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:17,712] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c4d6018-bcde-4017-bedb-8d2968dcda36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:17,713] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c4d6018-bcde-4017-bedb-8d2968dcda36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:17,725] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:17,725] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:17,725] [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 sediminis	strain=DSM 45779	GCA_004217185.1	1397368	1397368	type	True	100.0	2203	2203	95	conclusive
Pseudonocardia endophytica	strain=DSM 44969	GCA_004339565.1	401976	401976	type	True	82.6452	1395	2203	95	below_threshold
Pseudonocardia antarctica	strain=DSM 44749	GCA_013408715.1	237656	237656	type	True	82.268	1288	2203	95	below_threshold
Pseudonocardia parietis	strain=DSM 45256	GCA_017876315.1	570936	570936	type	True	81.7708	1286	2203	95	below_threshold
Pseudonocardia ammonioxydans	strain=CGMCC 4.1877	GCA_900115005.1	260086	260086	type	True	81.6761	1315	2203	95	below_threshold
Pseudonocardia autotrophica	strain=NBRC 12743	GCA_003945385.1	2074	2074	suspected-type	True	81.5177	1260	2203	95	below_threshold
Pseudonocardia autotrophica	strain=DSM 535	GCA_004361965.1	2074	2074	suspected-type	True	81.5012	1254	2203	95	below_threshold
Pseudonocardia autotrophica	strain=DSM 535	GCA_002119215.1	2074	2074	suspected-type	True	81.4192	1234	2203	95	below_threshold
Pseudonocardia terrae	strain=RS11V-5	GCA_021343995.1	2905831	2905831	type	True	80.1334	1156	2203	95	below_threshold
Pseudonocardia bannensis	strain=DSM 45300	GCA_012911875.1	630973	630973	type	True	80.1189	981	2203	95	below_threshold
Pseudonocardia pini	strain=CAP47R	GCA_013870575.1	2758030	2758030	type	True	80.0943	688	2203	95	below_threshold
Pseudonocardia kujensis	strain=KCTC 29062	GCA_021283305.1	1128675	1128675	type	True	79.979	1177	2203	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:17,727] [INFO] DFAST Taxonomy check result was written to GCF_004217185.1_ASM421718v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:17,728] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:17,728] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:17,728] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c4d6018-bcde-4017-bedb-8d2968dcda36/dqc_reference/checkm_data
[2024-01-24 14:06:17,729] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:17,790] [INFO] Task started: CheckM
[2024-01-24 14:06:17,791] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004217185.1_ASM421718v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004217185.1_ASM421718v1_genomic.fna/checkm_input GCF_004217185.1_ASM421718v1_genomic.fna/checkm_result
[2024-01-24 14:07:59,711] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:59,712] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:59,745] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:59,745] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:59,746] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004217185.1_ASM421718v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:59,746] [INFO] Task started: Blastn
[2024-01-24 14:07:59,746] [INFO] Running command: blastn -query GCF_004217185.1_ASM421718v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c4d6018-bcde-4017-bedb-8d2968dcda36/dqc_reference/reference_markers_gtdb.fasta -out GCF_004217185.1_ASM421718v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:08:01,932] [INFO] Task succeeded: Blastn
[2024-01-24 14:08:01,936] [INFO] Selected 12 target genomes.
[2024-01-24 14:08:01,936] [INFO] Target genome list was writen to GCF_004217185.1_ASM421718v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:08:01,944] [INFO] Task started: fastANI
[2024-01-24 14:08:01,945] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2ee9126-1694-4346-9147-5f1d6de6f620/GCF_004217185.1_ASM421718v1_genomic.fna.gz --refList GCF_004217185.1_ASM421718v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004217185.1_ASM421718v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:25,286] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:25,297] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:08:25,297] [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_004217185.1	s__Pseudonocardia sediminis	100.0	2203	2203	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_019263595.1	s__Pseudonocardia sp019263595	89.0324	1353	2203	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339565.1	s__Pseudonocardia endophytica	82.6074	1403	2203	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002813375.1	s__Pseudonocardia alni	82.3639	1290	2203	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	97.52	96.72	0.89	0.85	6	-
GCF_001294645.1	s__Pseudonocardia sp001294645	81.905	1246	2203	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	96.56	96.19	0.82	0.80	7	-
GCF_001420995.1	s__Pseudonocardia sp001420995	81.8331	1327	2203	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	99.03	98.66	0.91	0.86	8	-
GCF_017876315.1	s__Pseudonocardia parietis	81.7785	1282	2203	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115005.1	s__Pseudonocardia ammonioxydans	81.7594	1300	2203	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003945385.1	s__Pseudonocardia autotrophica	81.5283	1254	2203	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	100.00	100.00	1.00	1.00	4	-
GCF_000717175.1	s__Pseudonocardia autotrophica_A	80.2817	1181	2203	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911875.1	s__Pseudonocardia bannensis	80.1343	982	2203	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	79.7477	996	2203	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:08:25,299] [INFO] GTDB search result was written to GCF_004217185.1_ASM421718v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:25,299] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:25,302] [INFO] DFAST_QC result json was written to GCF_004217185.1_ASM421718v1_genomic.fna/dqc_result.json
[2024-01-24 14:08:25,303] [INFO] DFAST_QC completed!
[2024-01-24 14:08:25,303] [INFO] Total running time: 0h2m51s