[2024-01-24 11:05:03,928] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:03,935] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:03,935] [INFO] DQC Reference Directory: /var/lib/cwl/stga508611d-7aad-490c-8328-d4220b257789/dqc_reference
[2024-01-24 11:05:05,814] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:05,815] [INFO] Task started: Prodigal
[2024-01-24 11:05:05,815] [INFO] Running command: gunzip -c /var/lib/cwl/stg8d03dd15-4459-48b9-930f-d9f383112fb4/GCF_024298885.1_ASM2429888v1_genomic.fna.gz | prodigal -d GCF_024298885.1_ASM2429888v1_genomic.fna/cds.fna -a GCF_024298885.1_ASM2429888v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:25,102] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:25,103] [INFO] Task started: HMMsearch
[2024-01-24 11:05:25,103] [INFO] Running command: hmmsearch --tblout GCF_024298885.1_ASM2429888v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga508611d-7aad-490c-8328-d4220b257789/dqc_reference/reference_markers.hmm GCF_024298885.1_ASM2429888v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:25,327] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:25,328] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg8d03dd15-4459-48b9-930f-d9f383112fb4/GCF_024298885.1_ASM2429888v1_genomic.fna.gz]
[2024-01-24 11:05:25,365] [INFO] Query marker FASTA was written to GCF_024298885.1_ASM2429888v1_genomic.fna/markers.fasta
[2024-01-24 11:05:25,365] [INFO] Task started: Blastn
[2024-01-24 11:05:25,365] [INFO] Running command: blastn -query GCF_024298885.1_ASM2429888v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga508611d-7aad-490c-8328-d4220b257789/dqc_reference/reference_markers.fasta -out GCF_024298885.1_ASM2429888v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:25,859] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:25,861] [INFO] Selected 9 target genomes.
[2024-01-24 11:05:25,861] [INFO] Target genome list was writen to GCF_024298885.1_ASM2429888v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:25,864] [INFO] Task started: fastANI
[2024-01-24 11:05:25,864] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d03dd15-4459-48b9-930f-d9f383112fb4/GCF_024298885.1_ASM2429888v1_genomic.fna.gz --refList GCF_024298885.1_ASM2429888v1_genomic.fna/target_genomes.txt --output GCF_024298885.1_ASM2429888v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:33,971] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:33,972] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga508611d-7aad-490c-8328-d4220b257789/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:33,972] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga508611d-7aad-490c-8328-d4220b257789/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:33,979] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:05:33,979] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:05:33,979] [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
Haloglomus irregulare	strain=F16-60	GCA_007421925.1	2234134	2234134	type	True	83.3122	821	1481	95	below_threshold
Salinirubellus salinus	strain=ZS-35-S2	GCA_025231485.1	1364945	1364945	type	True	79.1737	615	1481	95	below_threshold
Natronomonas salina	strain=YPL13	GCA_013391105.1	1710540	1710540	type	True	79.1481	534	1481	95	below_threshold
Halomarina salina	strain=ZS-57-S	GCA_023074835.1	1872699	1872699	type	True	78.5438	510	1481	95	below_threshold
Halorientalis marina	strain=GDY88	GCA_023028345.1	2931976	2931976	type	True	78.4629	534	1481	95	below_threshold
Natronomonas gomsonensis	strain=KCTC 4088	GCA_024300825.1	1046043	1046043	type	True	78.2549	437	1481	95	below_threshold
Natronomonas halophila	strain=C90	GCA_013391085.1	2747817	2747817	type	True	77.9957	416	1481	95	below_threshold
Halorientalis salina	strain=NEN8	GCA_005049285.1	2932266	2932266	type	True	77.9188	427	1481	95	below_threshold
Salinirussus salinus	strain=YGH44	GCA_009831455.1	1198300	1198300	type	True	77.7339	401	1481	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:33,981] [INFO] DFAST Taxonomy check result was written to GCF_024298885.1_ASM2429888v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:33,981] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:33,981] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:33,981] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga508611d-7aad-490c-8328-d4220b257789/dqc_reference/checkm_data
[2024-01-24 11:05:33,982] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:34,031] [INFO] Task started: CheckM
[2024-01-24 11:05:34,032] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024298885.1_ASM2429888v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024298885.1_ASM2429888v1_genomic.fna/checkm_input GCF_024298885.1_ASM2429888v1_genomic.fna/checkm_result
[2024-01-24 11:06:24,099] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:24,100] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:24,116] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:24,116] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:24,117] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024298885.1_ASM2429888v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:24,117] [INFO] Task started: Blastn
[2024-01-24 11:06:24,117] [INFO] Running command: blastn -query GCF_024298885.1_ASM2429888v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga508611d-7aad-490c-8328-d4220b257789/dqc_reference/reference_markers_gtdb.fasta -out GCF_024298885.1_ASM2429888v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:24,594] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:24,597] [INFO] Selected 9 target genomes.
[2024-01-24 11:06:24,597] [INFO] Target genome list was writen to GCF_024298885.1_ASM2429888v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:24,602] [INFO] Task started: fastANI
[2024-01-24 11:06:24,602] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d03dd15-4459-48b9-930f-d9f383112fb4/GCF_024298885.1_ASM2429888v1_genomic.fna.gz --refList GCF_024298885.1_ASM2429888v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024298885.1_ASM2429888v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:31,261] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:31,268] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:06:31,268] [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_003020985.1	s__Haloglomus sp003020985	84.7655	759	1481	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloglomus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007421925.1	s__Haloglomus irregulare	83.3249	820	1481	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloglomus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013391105.1	s__Natronomonas salina	79.1436	535	1481	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003022005.1	s__QS-5-70-15 sp003022005	78.4199	410	1481	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__QS-5-70-15	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009741925.1	s__Natronomonas sp009741925	78.3061	403	1481	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003021175.1	s__CBA1134 sp003021175	78.2726	398	1481	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__CBA1134	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013391085.1	s__Natronomonas halophila	78.0129	414	1481	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003020965.1	s__Natronomonas sp003020965	77.7876	449	1481	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009831455.1	s__Salinirussus salinus	77.725	403	1481	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Salinirussus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:31,269] [INFO] GTDB search result was written to GCF_024298885.1_ASM2429888v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:31,270] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:31,272] [INFO] DFAST_QC result json was written to GCF_024298885.1_ASM2429888v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:31,272] [INFO] DFAST_QC completed!
[2024-01-24 11:06:31,272] [INFO] Total running time: 0h1m27s