[2024-01-24 13:41:20,406] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:20,409] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:20,409] [INFO] DQC Reference Directory: /var/lib/cwl/stg25dda0cc-df5d-49e9-9828-1c62352166fd/dqc_reference
[2024-01-24 13:41:21,739] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:21,740] [INFO] Task started: Prodigal
[2024-01-24 13:41:21,740] [INFO] Running command: gunzip -c /var/lib/cwl/stg67c95b85-c3e0-45f3-9bb3-c2e5e45d504d/GCF_013408715.1_ASM1340871v1_genomic.fna.gz | prodigal -d GCF_013408715.1_ASM1340871v1_genomic.fna/cds.fna -a GCF_013408715.1_ASM1340871v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:38,969] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:38,969] [INFO] Task started: HMMsearch
[2024-01-24 13:41:38,970] [INFO] Running command: hmmsearch --tblout GCF_013408715.1_ASM1340871v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25dda0cc-df5d-49e9-9828-1c62352166fd/dqc_reference/reference_markers.hmm GCF_013408715.1_ASM1340871v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:39,312] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:39,313] [INFO] Found 6/6 markers.
[2024-01-24 13:41:39,364] [INFO] Query marker FASTA was written to GCF_013408715.1_ASM1340871v1_genomic.fna/markers.fasta
[2024-01-24 13:41:39,364] [INFO] Task started: Blastn
[2024-01-24 13:41:39,364] [INFO] Running command: blastn -query GCF_013408715.1_ASM1340871v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25dda0cc-df5d-49e9-9828-1c62352166fd/dqc_reference/reference_markers.fasta -out GCF_013408715.1_ASM1340871v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:40,773] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:40,776] [INFO] Selected 7 target genomes.
[2024-01-24 13:41:40,776] [INFO] Target genome list was writen to GCF_013408715.1_ASM1340871v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:40,777] [INFO] Task started: fastANI
[2024-01-24 13:41:40,778] [INFO] Running command: fastANI --query /var/lib/cwl/stg67c95b85-c3e0-45f3-9bb3-c2e5e45d504d/GCF_013408715.1_ASM1340871v1_genomic.fna.gz --refList GCF_013408715.1_ASM1340871v1_genomic.fna/target_genomes.txt --output GCF_013408715.1_ASM1340871v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:55,954] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:55,955] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25dda0cc-df5d-49e9-9828-1c62352166fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:55,955] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25dda0cc-df5d-49e9-9828-1c62352166fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:55,966] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:55,966] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:55,966] [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 antarctica	strain=DSM 44749	GCA_013408715.1	237656	237656	type	True	100.0	2080	2080	95	conclusive
Pseudonocardia ammonioxydans	strain=CGMCC 4.1877	GCA_900115005.1	260086	260086	type	True	84.5449	1419	2080	95	below_threshold
Pseudonocardia parietis	strain=DSM 45256	GCA_017876315.1	570936	570936	type	True	84.4784	1418	2080	95	below_threshold
Pseudonocardia autotrophica	strain=DSM 535	GCA_004361965.1	2074	2074	suspected-type	True	84.3333	1439	2080	95	below_threshold
Pseudonocardia autotrophica	strain=DSM 535	GCA_002119215.1	2074	2074	suspected-type	True	84.2717	1416	2080	95	below_threshold
Pseudonocardia autotrophica	strain=NBRC 12743	GCA_003945385.1	2074	2074	suspected-type	True	84.2339	1451	2080	95	below_threshold
Pseudonocardia sediminis	strain=DSM 45779	GCA_004217185.1	1397368	1397368	type	True	82.2586	1302	2080	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:55,970] [INFO] DFAST Taxonomy check result was written to GCF_013408715.1_ASM1340871v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:55,972] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:55,973] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:55,973] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25dda0cc-df5d-49e9-9828-1c62352166fd/dqc_reference/checkm_data
[2024-01-24 13:41:55,976] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:56,034] [INFO] Task started: CheckM
[2024-01-24 13:41:56,034] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013408715.1_ASM1340871v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013408715.1_ASM1340871v1_genomic.fna/checkm_input GCF_013408715.1_ASM1340871v1_genomic.fna/checkm_result
[2024-01-24 13:43:32,907] [INFO] Task succeeded: CheckM
[2024-01-24 13:43:32,909] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:43:32,932] [INFO] ===== Completeness check finished =====
[2024-01-24 13:43:32,933] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:43:32,933] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013408715.1_ASM1340871v1_genomic.fna/markers.fasta)
[2024-01-24 13:43:32,933] [INFO] Task started: Blastn
[2024-01-24 13:43:32,933] [INFO] Running command: blastn -query GCF_013408715.1_ASM1340871v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25dda0cc-df5d-49e9-9828-1c62352166fd/dqc_reference/reference_markers_gtdb.fasta -out GCF_013408715.1_ASM1340871v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:34,930] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:34,933] [INFO] Selected 8 target genomes.
[2024-01-24 13:43:34,934] [INFO] Target genome list was writen to GCF_013408715.1_ASM1340871v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:43:34,946] [INFO] Task started: fastANI
[2024-01-24 13:43:34,946] [INFO] Running command: fastANI --query /var/lib/cwl/stg67c95b85-c3e0-45f3-9bb3-c2e5e45d504d/GCF_013408715.1_ASM1340871v1_genomic.fna.gz --refList GCF_013408715.1_ASM1340871v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013408715.1_ASM1340871v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:52,292] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:52,307] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:52,308] [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
GCA_002813375.1	s__Pseudonocardia alni	98.5446	1860	2080	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	97.52	96.72	0.89	0.85	6	conclusive
GCF_001294645.1	s__Pseudonocardia sp001294645	92.4944	1572	2080	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	85.2998	1528	2080	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	99.03	98.66	0.91	0.86	8	-
GCF_900115005.1	s__Pseudonocardia ammonioxydans	84.5118	1423	2080	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876315.1	s__Pseudonocardia parietis	84.478	1419	2080	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014267175.1	s__Pseudonocardia sp014267175	84.2874	1294	2080	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	84.2775	1447	2080	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	100.00	100.00	1.00	1.00	4	-
GCF_001698125.1	s__Pseudonocardia sp001698125	84.188	1348	2080	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 13:43:52,310] [INFO] GTDB search result was written to GCF_013408715.1_ASM1340871v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:52,310] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:52,313] [INFO] DFAST_QC result json was written to GCF_013408715.1_ASM1340871v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:52,313] [INFO] DFAST_QC completed!
[2024-01-24 13:43:52,313] [INFO] Total running time: 0h2m32s