[2024-01-24 13:32:34,814] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:34,816] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:34,816] [INFO] DQC Reference Directory: /var/lib/cwl/stg574ff35b-6bd2-43e9-8101-5ffe5536746e/dqc_reference
[2024-01-24 13:32:36,221] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:36,222] [INFO] Task started: Prodigal
[2024-01-24 13:32:36,223] [INFO] Running command: gunzip -c /var/lib/cwl/stgec8f04d8-312a-47b6-9adb-cce9a8f968dd/GCF_004361965.1_ASM436196v1_genomic.fna.gz | prodigal -d GCF_004361965.1_ASM436196v1_genomic.fna/cds.fna -a GCF_004361965.1_ASM436196v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:33:01,360] [INFO] Task succeeded: Prodigal
[2024-01-24 13:33:01,361] [INFO] Task started: HMMsearch
[2024-01-24 13:33:01,361] [INFO] Running command: hmmsearch --tblout GCF_004361965.1_ASM436196v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg574ff35b-6bd2-43e9-8101-5ffe5536746e/dqc_reference/reference_markers.hmm GCF_004361965.1_ASM436196v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:33:01,813] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:33:01,815] [INFO] Found 6/6 markers.
[2024-01-24 13:33:01,883] [INFO] Query marker FASTA was written to GCF_004361965.1_ASM436196v1_genomic.fna/markers.fasta
[2024-01-24 13:33:01,883] [INFO] Task started: Blastn
[2024-01-24 13:33:01,883] [INFO] Running command: blastn -query GCF_004361965.1_ASM436196v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg574ff35b-6bd2-43e9-8101-5ffe5536746e/dqc_reference/reference_markers.fasta -out GCF_004361965.1_ASM436196v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:03,277] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:03,280] [INFO] Selected 6 target genomes.
[2024-01-24 13:33:03,280] [INFO] Target genome list was writen to GCF_004361965.1_ASM436196v1_genomic.fna/target_genomes.txt
[2024-01-24 13:33:03,294] [INFO] Task started: fastANI
[2024-01-24 13:33:03,295] [INFO] Running command: fastANI --query /var/lib/cwl/stgec8f04d8-312a-47b6-9adb-cce9a8f968dd/GCF_004361965.1_ASM436196v1_genomic.fna.gz --refList GCF_004361965.1_ASM436196v1_genomic.fna/target_genomes.txt --output GCF_004361965.1_ASM436196v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:17,889] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:17,890] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg574ff35b-6bd2-43e9-8101-5ffe5536746e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:17,890] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg574ff35b-6bd2-43e9-8101-5ffe5536746e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:17,898] [INFO] Found 6 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:33:17,898] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:17,898] [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 autotrophica	strain=DSM 535	GCA_004361965.1	2074	2074	suspected-type	True	100.0	2522	2522	95	conclusive
Pseudonocardia autotrophica	strain=NBRC 12743	GCA_003945385.1	2074	2074	suspected-type	True	99.9917	2508	2522	95	conclusive
Pseudonocardia autotrophica	strain=DSM 535	GCA_002119215.1	2074	2074	suspected-type	True	99.9453	2388	2522	95	conclusive
Pseudonocardia parietis	strain=DSM 45256	GCA_017876315.1	570936	570936	type	True	84.8215	1560	2522	95	below_threshold
Pseudonocardia ammonioxydans	strain=CGMCC 4.1877	GCA_900115005.1	260086	260086	type	True	84.7619	1518	2522	95	below_threshold
Pseudonocardia antarctica	strain=DSM 44749	GCA_013408715.1	237656	237656	type	True	84.1306	1471	2522	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:17,900] [INFO] DFAST Taxonomy check result was written to GCF_004361965.1_ASM436196v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:17,900] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:17,900] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:17,901] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg574ff35b-6bd2-43e9-8101-5ffe5536746e/dqc_reference/checkm_data
[2024-01-24 13:33:17,902] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:17,971] [INFO] Task started: CheckM
[2024-01-24 13:33:17,972] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004361965.1_ASM436196v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004361965.1_ASM436196v1_genomic.fna/checkm_input GCF_004361965.1_ASM436196v1_genomic.fna/checkm_result
[2024-01-24 13:35:35,554] [INFO] Task succeeded: CheckM
[2024-01-24 13:35:35,556] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:35:35,580] [INFO] ===== Completeness check finished =====
[2024-01-24 13:35:35,580] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:35:35,581] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004361965.1_ASM436196v1_genomic.fna/markers.fasta)
[2024-01-24 13:35:35,581] [INFO] Task started: Blastn
[2024-01-24 13:35:35,581] [INFO] Running command: blastn -query GCF_004361965.1_ASM436196v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg574ff35b-6bd2-43e9-8101-5ffe5536746e/dqc_reference/reference_markers_gtdb.fasta -out GCF_004361965.1_ASM436196v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:35:37,450] [INFO] Task succeeded: Blastn
[2024-01-24 13:35:37,454] [INFO] Selected 8 target genomes.
[2024-01-24 13:35:37,455] [INFO] Target genome list was writen to GCF_004361965.1_ASM436196v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:35:37,498] [INFO] Task started: fastANI
[2024-01-24 13:35:37,498] [INFO] Running command: fastANI --query /var/lib/cwl/stgec8f04d8-312a-47b6-9adb-cce9a8f968dd/GCF_004361965.1_ASM436196v1_genomic.fna.gz --refList GCF_004361965.1_ASM436196v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004361965.1_ASM436196v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:35:54,915] [INFO] Task succeeded: fastANI
[2024-01-24 13:35:54,922] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:35:54,923] [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_003945385.1	s__Pseudonocardia autotrophica	99.9917	2508	2522	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	100.00	100.00	1.00	1.00	4	conclusive
GCF_017876315.1	s__Pseudonocardia parietis	84.8063	1560	2522	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	84.723	1524	2522	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001420995.1	s__Pseudonocardia sp001420995	84.4051	1492	2522	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	99.03	98.66	0.91	0.86	8	-
GCF_014267175.1	s__Pseudonocardia sp014267175	84.0741	1333	2522	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	83.9591	1442	2522	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	97.52	96.72	0.89	0.85	6	-
GCF_001698125.1	s__Pseudonocardia sp001698125	83.7278	1349	2522	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001294645.1	s__Pseudonocardia sp001294645	83.7179	1390	2522	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	96.56	96.19	0.82	0.80	7	-
--------------------------------------------------------------------------------
[2024-01-24 13:35:54,925] [INFO] GTDB search result was written to GCF_004361965.1_ASM436196v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:35:54,925] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:35:54,928] [INFO] DFAST_QC result json was written to GCF_004361965.1_ASM436196v1_genomic.fna/dqc_result.json
[2024-01-24 13:35:54,928] [INFO] DFAST_QC completed!
[2024-01-24 13:35:54,928] [INFO] Total running time: 0h3m20s