[2024-01-24 12:30:19,535] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:19,537] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:19,537] [INFO] DQC Reference Directory: /var/lib/cwl/stg41494df6-6696-47ee-bc0a-e3caf890abc5/dqc_reference
[2024-01-24 12:30:20,797] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:20,798] [INFO] Task started: Prodigal
[2024-01-24 12:30:20,798] [INFO] Running command: gunzip -c /var/lib/cwl/stg38cefc1c-b144-4b4a-9eb9-05a4d57bc289/GCF_024508235.1_ASM2450823v1_genomic.fna.gz | prodigal -d GCF_024508235.1_ASM2450823v1_genomic.fna/cds.fna -a GCF_024508235.1_ASM2450823v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:30:34,849] [INFO] Task succeeded: Prodigal
[2024-01-24 12:30:34,850] [INFO] Task started: HMMsearch
[2024-01-24 12:30:34,850] [INFO] Running command: hmmsearch --tblout GCF_024508235.1_ASM2450823v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg41494df6-6696-47ee-bc0a-e3caf890abc5/dqc_reference/reference_markers.hmm GCF_024508235.1_ASM2450823v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:30:35,084] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:30:35,086] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg38cefc1c-b144-4b4a-9eb9-05a4d57bc289/GCF_024508235.1_ASM2450823v1_genomic.fna.gz]
[2024-01-24 12:30:35,116] [INFO] Query marker FASTA was written to GCF_024508235.1_ASM2450823v1_genomic.fna/markers.fasta
[2024-01-24 12:30:35,116] [INFO] Task started: Blastn
[2024-01-24 12:30:35,117] [INFO] Running command: blastn -query GCF_024508235.1_ASM2450823v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41494df6-6696-47ee-bc0a-e3caf890abc5/dqc_reference/reference_markers.fasta -out GCF_024508235.1_ASM2450823v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:35,690] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:35,694] [INFO] Selected 5 target genomes.
[2024-01-24 12:30:35,694] [INFO] Target genome list was writen to GCF_024508235.1_ASM2450823v1_genomic.fna/target_genomes.txt
[2024-01-24 12:30:35,698] [INFO] Task started: fastANI
[2024-01-24 12:30:35,698] [INFO] Running command: fastANI --query /var/lib/cwl/stg38cefc1c-b144-4b4a-9eb9-05a4d57bc289/GCF_024508235.1_ASM2450823v1_genomic.fna.gz --refList GCF_024508235.1_ASM2450823v1_genomic.fna/target_genomes.txt --output GCF_024508235.1_ASM2450823v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:40,296] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:40,297] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg41494df6-6696-47ee-bc0a-e3caf890abc5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:40,298] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg41494df6-6696-47ee-bc0a-e3caf890abc5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:40,309] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:30:40,310] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:40,310] [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
Halococcus qingdaonensis	strain=CGMCC 1.4243	GCA_024508235.1	224402	224402	type	True	100.0	901	901	95	conclusive
Halococcus thailandensis	strain=JCM 13552	GCA_000336715.1	335952	335952	type	True	93.8008	792	901	95	below_threshold
Halococcus morrhuae	strain=DSM 1307	GCA_000336695.1	2250	2250	type	True	93.0565	759	901	95	below_threshold
Halococcus dombrowskii	strain=H4	GCA_022870485.1	179637	179637	type	True	93.0245	811	901	95	below_threshold
Halococcus sediminicola	strain=CBA1101	GCA_000755245.1	1264579	1264579	type	True	86.1791	727	901	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:40,312] [INFO] DFAST Taxonomy check result was written to GCF_024508235.1_ASM2450823v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:40,313] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:40,313] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:40,314] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg41494df6-6696-47ee-bc0a-e3caf890abc5/dqc_reference/checkm_data
[2024-01-24 12:30:40,316] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:40,347] [INFO] Task started: CheckM
[2024-01-24 12:30:40,348] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024508235.1_ASM2450823v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024508235.1_ASM2450823v1_genomic.fna/checkm_input GCF_024508235.1_ASM2450823v1_genomic.fna/checkm_result
[2024-01-24 12:31:22,699] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:22,700] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:22,718] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:22,719] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:22,719] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024508235.1_ASM2450823v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:22,719] [INFO] Task started: Blastn
[2024-01-24 12:31:22,719] [INFO] Running command: blastn -query GCF_024508235.1_ASM2450823v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41494df6-6696-47ee-bc0a-e3caf890abc5/dqc_reference/reference_markers_gtdb.fasta -out GCF_024508235.1_ASM2450823v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:23,260] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:23,263] [INFO] Selected 8 target genomes.
[2024-01-24 12:31:23,263] [INFO] Target genome list was writen to GCF_024508235.1_ASM2450823v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:23,285] [INFO] Task started: fastANI
[2024-01-24 12:31:23,285] [INFO] Running command: fastANI --query /var/lib/cwl/stg38cefc1c-b144-4b4a-9eb9-05a4d57bc289/GCF_024508235.1_ASM2450823v1_genomic.fna.gz --refList GCF_024508235.1_ASM2450823v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024508235.1_ASM2450823v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:29,716] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:29,724] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:31:29,725] [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_000336715.1	s__Halococcus thailandensis	93.8044	792	901	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halococcaceae;g__Halococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000336695.1	s__Halococcus morrhuae	93.0684	758	901	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halococcaceae;g__Halococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000755245.1	s__Halococcus sediminicola	86.1767	728	901	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halococcaceae;g__Halococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000334895.1	s__Halococcus agarilyticus	80.6586	562	901	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halococcaceae;g__Halococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000336915.1	s__Halococcus saccharolyticus	80.3216	550	901	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halococcaceae;g__Halococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000336675.1	s__Halococcus hamelinensis	80.284	520	901	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halococcaceae;g__Halococcus	95.0	99.96	99.96	0.98	0.98	2	-
GCF_009900715.1	s__Halococcus salsus	80.1789	529	901	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halococcaceae;g__Halococcus	95.0	95.85	95.85	0.78	0.78	2	-
GCA_003022685.1	s__Halococcus sp003022685	80.1217	408	901	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halococcaceae;g__Halococcus	95.0	95.70	95.70	0.79	0.79	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:29,731] [INFO] GTDB search result was written to GCF_024508235.1_ASM2450823v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:29,733] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:29,737] [INFO] DFAST_QC result json was written to GCF_024508235.1_ASM2450823v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:29,737] [INFO] DFAST_QC completed!
[2024-01-24 12:31:29,737] [INFO] Total running time: 0h1m10s