[2024-01-24 13:27:31,850] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:31,851] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:31,852] [INFO] DQC Reference Directory: /var/lib/cwl/stg64f2a043-ba53-425d-a407-2aab7ac1bf59/dqc_reference
[2024-01-24 13:27:33,251] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:33,252] [INFO] Task started: Prodigal
[2024-01-24 13:27:33,253] [INFO] Running command: gunzip -c /var/lib/cwl/stg6c0fe4a4-ca3b-4f9a-9f09-f8a874abb197/GCF_000337495.1_ASM33749v1_genomic.fna.gz | prodigal -d GCF_000337495.1_ASM33749v1_genomic.fna/cds.fna -a GCF_000337495.1_ASM33749v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:27:54,533] [INFO] Task succeeded: Prodigal
[2024-01-24 13:27:54,534] [INFO] Task started: HMMsearch
[2024-01-24 13:27:54,534] [INFO] Running command: hmmsearch --tblout GCF_000337495.1_ASM33749v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg64f2a043-ba53-425d-a407-2aab7ac1bf59/dqc_reference/reference_markers.hmm GCF_000337495.1_ASM33749v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:27:54,820] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:27:54,822] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg6c0fe4a4-ca3b-4f9a-9f09-f8a874abb197/GCF_000337495.1_ASM33749v1_genomic.fna.gz]
[2024-01-24 13:27:54,868] [INFO] Query marker FASTA was written to GCF_000337495.1_ASM33749v1_genomic.fna/markers.fasta
[2024-01-24 13:27:54,868] [INFO] Task started: Blastn
[2024-01-24 13:27:54,868] [INFO] Running command: blastn -query GCF_000337495.1_ASM33749v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg64f2a043-ba53-425d-a407-2aab7ac1bf59/dqc_reference/reference_markers.fasta -out GCF_000337495.1_ASM33749v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:55,419] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:55,422] [INFO] Selected 7 target genomes.
[2024-01-24 13:27:55,422] [INFO] Target genome list was writen to GCF_000337495.1_ASM33749v1_genomic.fna/target_genomes.txt
[2024-01-24 13:27:55,431] [INFO] Task started: fastANI
[2024-01-24 13:27:55,431] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c0fe4a4-ca3b-4f9a-9f09-f8a874abb197/GCF_000337495.1_ASM33749v1_genomic.fna.gz --refList GCF_000337495.1_ASM33749v1_genomic.fna/target_genomes.txt --output GCF_000337495.1_ASM33749v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:04,752] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:04,752] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg64f2a043-ba53-425d-a407-2aab7ac1bf59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:04,752] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg64f2a043-ba53-425d-a407-2aab7ac1bf59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:04,759] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:04,759] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:04,760] [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
Haloterrigena salina	strain=JCM 13891	GCA_000337495.1	504937	504937	type	True	100.0	1577	1580	95	conclusive
Haloterrigena salifodinae	strain=ZY19	GCA_003977755.1	2675099	2675099	type	True	94.8745	1410	1580	95	below_threshold
Haloterrigena turkmenica	strain=DSM 5511	GCA_000025325.1	62320	62320	type	True	92.4089	1331	1580	95	below_threshold
Haloterrigena alkaliphila	strain=KZCA68	GCA_017352155.2	2816475	2816475	type	True	85.8532	1007	1580	95	below_threshold
Halopiger aswanensis	strain=DSM 13151	GCA_003610195.1	148449	148449	type	True	82.6475	954	1580	95	below_threshold
Natronorubrum halalkaliphilum	strain=JWXQ-INN-674	GCA_009834785.1	2691917	2691917	type	True	82.0163	887	1580	95	below_threshold
Natronobacterium gregoryi	strain=SP2	GCA_900114025.1	44930	44930	type	True	80.0348	592	1580	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:04,761] [INFO] DFAST Taxonomy check result was written to GCF_000337495.1_ASM33749v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:04,762] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:04,762] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:04,762] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg64f2a043-ba53-425d-a407-2aab7ac1bf59/dqc_reference/checkm_data
[2024-01-24 13:28:04,763] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:04,808] [INFO] Task started: CheckM
[2024-01-24 13:28:04,808] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000337495.1_ASM33749v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000337495.1_ASM33749v1_genomic.fna/checkm_input GCF_000337495.1_ASM33749v1_genomic.fna/checkm_result
[2024-01-24 13:28:59,964] [INFO] Task succeeded: CheckM
[2024-01-24 13:28:59,966] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:28:59,991] [INFO] ===== Completeness check finished =====
[2024-01-24 13:28:59,992] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:28:59,992] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000337495.1_ASM33749v1_genomic.fna/markers.fasta)
[2024-01-24 13:28:59,992] [INFO] Task started: Blastn
[2024-01-24 13:28:59,993] [INFO] Running command: blastn -query GCF_000337495.1_ASM33749v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg64f2a043-ba53-425d-a407-2aab7ac1bf59/dqc_reference/reference_markers_gtdb.fasta -out GCF_000337495.1_ASM33749v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:00,490] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:00,494] [INFO] Selected 6 target genomes.
[2024-01-24 13:29:00,494] [INFO] Target genome list was writen to GCF_000337495.1_ASM33749v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:00,517] [INFO] Task started: fastANI
[2024-01-24 13:29:00,517] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c0fe4a4-ca3b-4f9a-9f09-f8a874abb197/GCF_000337495.1_ASM33749v1_genomic.fna.gz --refList GCF_000337495.1_ASM33749v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000337495.1_ASM33749v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:08,893] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:08,900] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:08,900] [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_000337495.1	s__Haloterrigena salina	100.0	1577	1580	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003977755.1	s__Haloterrigena salifodinae	94.8745	1410	1580	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	98.23	98.23	0.92	0.92	2	-
GCF_013342135.1	s__Haloterrigena sp013342135	94.7657	1418	1580	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	99.13	99.13	0.91	0.91	2	-
GCF_000025325.1	s__Haloterrigena turkmenica	92.3991	1332	1580	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017352155.1	s__Haloterrigena sp017352155	85.9292	953	1580	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337215.1	s__Natronolimnohabitans innermongolicus	83.0117	895	1580	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronolimnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:08,902] [INFO] GTDB search result was written to GCF_000337495.1_ASM33749v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:08,903] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:08,905] [INFO] DFAST_QC result json was written to GCF_000337495.1_ASM33749v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:08,906] [INFO] DFAST_QC completed!
[2024-01-24 13:29:08,906] [INFO] Total running time: 0h1m37s