[2024-01-25 19:01:50,614] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:01:50,616] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:01:50,616] [INFO] DQC Reference Directory: /var/lib/cwl/stgd0504d62-6660-4b4c-814e-83023d0070a6/dqc_reference
[2024-01-25 19:01:51,708] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:01:51,709] [INFO] Task started: Prodigal
[2024-01-25 19:01:51,709] [INFO] Running command: gunzip -c /var/lib/cwl/stgf7cb3ccf-a284-49df-b824-a47649a14882/GCF_017873775.1_ASM1787377v1_genomic.fna.gz | prodigal -d GCF_017873775.1_ASM1787377v1_genomic.fna/cds.fna -a GCF_017873775.1_ASM1787377v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:02:02,461] [INFO] Task succeeded: Prodigal
[2024-01-25 19:02:02,461] [INFO] Task started: HMMsearch
[2024-01-25 19:02:02,461] [INFO] Running command: hmmsearch --tblout GCF_017873775.1_ASM1787377v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd0504d62-6660-4b4c-814e-83023d0070a6/dqc_reference/reference_markers.hmm GCF_017873775.1_ASM1787377v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:02:02,627] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:02:02,628] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgf7cb3ccf-a284-49df-b824-a47649a14882/GCF_017873775.1_ASM1787377v1_genomic.fna.gz]
[2024-01-25 19:02:02,651] [INFO] Query marker FASTA was written to GCF_017873775.1_ASM1787377v1_genomic.fna/markers.fasta
[2024-01-25 19:02:02,652] [INFO] Task started: Blastn
[2024-01-25 19:02:02,652] [INFO] Running command: blastn -query GCF_017873775.1_ASM1787377v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0504d62-6660-4b4c-814e-83023d0070a6/dqc_reference/reference_markers.fasta -out GCF_017873775.1_ASM1787377v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:02:03,139] [INFO] Task succeeded: Blastn
[2024-01-25 19:02:03,142] [INFO] Selected 5 target genomes.
[2024-01-25 19:02:03,142] [INFO] Target genome list was writen to GCF_017873775.1_ASM1787377v1_genomic.fna/target_genomes.txt
[2024-01-25 19:02:03,151] [INFO] Task started: fastANI
[2024-01-25 19:02:03,151] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7cb3ccf-a284-49df-b824-a47649a14882/GCF_017873775.1_ASM1787377v1_genomic.fna.gz --refList GCF_017873775.1_ASM1787377v1_genomic.fna/target_genomes.txt --output GCF_017873775.1_ASM1787377v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:02:07,281] [INFO] Task succeeded: fastANI
[2024-01-25 19:02:07,281] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd0504d62-6660-4b4c-814e-83023d0070a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:02:07,281] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd0504d62-6660-4b4c-814e-83023d0070a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:02:07,286] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:02:07,286] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:02:07,286] [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
Halarchaeum rubridurum	strain=DSM 22443	GCA_017873775.1	489911	489911	type	True	100.0	931	932	95	conclusive
Halarchaeum rubridurum	strain=JCM 16108	GCA_014647115.1	489911	489911	type	True	99.9931	923	932	95	conclusive
Halarchaeum acidiphilum	strain=JCM 16109	GCA_000474235.1	489138	489138	type	True	87.3152	613	932	95	below_threshold
Halarchaeum acidiphilum	strain=MH1-52-1	GCA_000400975.1	489138	489138	type	True	87.2621	412	932	95	below_threshold
Halarchaeum grantii	strain=JCM 19585	GCA_014647455.2	1193105	1193105	type	True	85.3303	650	932	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:02:07,288] [INFO] DFAST Taxonomy check result was written to GCF_017873775.1_ASM1787377v1_genomic.fna/tc_result.tsv
[2024-01-25 19:02:07,289] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:02:07,289] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:02:07,290] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd0504d62-6660-4b4c-814e-83023d0070a6/dqc_reference/checkm_data
[2024-01-25 19:02:07,290] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:02:07,319] [INFO] Task started: CheckM
[2024-01-25 19:02:07,319] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017873775.1_ASM1787377v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017873775.1_ASM1787377v1_genomic.fna/checkm_input GCF_017873775.1_ASM1787377v1_genomic.fna/checkm_result
[2024-01-25 19:02:38,920] [INFO] Task succeeded: CheckM
[2024-01-25 19:02:38,921] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:02:38,951] [INFO] ===== Completeness check finished =====
[2024-01-25 19:02:38,951] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:02:38,952] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017873775.1_ASM1787377v1_genomic.fna/markers.fasta)
[2024-01-25 19:02:38,952] [INFO] Task started: Blastn
[2024-01-25 19:02:38,952] [INFO] Running command: blastn -query GCF_017873775.1_ASM1787377v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0504d62-6660-4b4c-814e-83023d0070a6/dqc_reference/reference_markers_gtdb.fasta -out GCF_017873775.1_ASM1787377v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:02:39,473] [INFO] Task succeeded: Blastn
[2024-01-25 19:02:39,476] [INFO] Selected 6 target genomes.
[2024-01-25 19:02:39,476] [INFO] Target genome list was writen to GCF_017873775.1_ASM1787377v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:02:39,485] [INFO] Task started: fastANI
[2024-01-25 19:02:39,485] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7cb3ccf-a284-49df-b824-a47649a14882/GCF_017873775.1_ASM1787377v1_genomic.fna.gz --refList GCF_017873775.1_ASM1787377v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017873775.1_ASM1787377v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:02:45,051] [INFO] Task succeeded: fastANI
[2024-01-25 19:02:45,056] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:02:45,057] [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_014647115.1	s__Halarchaeum rubridurum	99.9931	923	932	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halobacteriaceae;g__Halarchaeum	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_014647155.1	s__Halarchaeum nitratireducens	90.1828	748	932	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halobacteriaceae;g__Halarchaeum	95.0	98.88	98.88	0.86	0.86	2	-
GCF_017874335.1	s__Halarchaeum salinum	88.9096	665	932	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halobacteriaceae;g__Halarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000474235.1	s__Halarchaeum acidiphilum	87.3122	614	932	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halobacteriaceae;g__Halarchaeum	95.0	99.69	99.69	0.96	0.96	2	-
GCF_014647455.2	s__Halarchaeum grantii	85.3773	647	932	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halobacteriaceae;g__Halarchaeum	95.0	95.76	95.76	0.83	0.83	2	-
GCF_014647475.1	s__Halocalculus aciditolerans	80.0448	536	932	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halobacteriaceae;g__Halocalculus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:02:45,058] [INFO] GTDB search result was written to GCF_017873775.1_ASM1787377v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:02:45,059] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:02:45,061] [INFO] DFAST_QC result json was written to GCF_017873775.1_ASM1787377v1_genomic.fna/dqc_result.json
[2024-01-25 19:02:45,061] [INFO] DFAST_QC completed!
[2024-01-25 19:02:45,061] [INFO] Total running time: 0h0m54s