[2024-01-25 19:55:05,834] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:55:05,835] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:55:05,835] [INFO] DQC Reference Directory: /var/lib/cwl/stg48d22747-003e-4d30-b5f5-9c7acbc74da7/dqc_reference
[2024-01-25 19:55:07,055] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:55:07,056] [INFO] Task started: Prodigal
[2024-01-25 19:55:07,056] [INFO] Running command: gunzip -c /var/lib/cwl/stg1f82cc66-8426-4ae7-935a-f57e9691ba97/GCF_002295105.1_ASM229510v1_genomic.fna.gz | prodigal -d GCF_002295105.1_ASM229510v1_genomic.fna/cds.fna -a GCF_002295105.1_ASM229510v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:55:12,399] [INFO] Task succeeded: Prodigal
[2024-01-25 19:55:12,399] [INFO] Task started: HMMsearch
[2024-01-25 19:55:12,399] [INFO] Running command: hmmsearch --tblout GCF_002295105.1_ASM229510v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg48d22747-003e-4d30-b5f5-9c7acbc74da7/dqc_reference/reference_markers.hmm GCF_002295105.1_ASM229510v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:55:12,633] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:55:12,634] [INFO] Found 6/6 markers.
[2024-01-25 19:55:12,668] [INFO] Query marker FASTA was written to GCF_002295105.1_ASM229510v1_genomic.fna/markers.fasta
[2024-01-25 19:55:12,669] [INFO] Task started: Blastn
[2024-01-25 19:55:12,669] [INFO] Running command: blastn -query GCF_002295105.1_ASM229510v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg48d22747-003e-4d30-b5f5-9c7acbc74da7/dqc_reference/reference_markers.fasta -out GCF_002295105.1_ASM229510v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:55:13,208] [INFO] Task succeeded: Blastn
[2024-01-25 19:55:13,211] [INFO] Selected 13 target genomes.
[2024-01-25 19:55:13,211] [INFO] Target genome list was writen to GCF_002295105.1_ASM229510v1_genomic.fna/target_genomes.txt
[2024-01-25 19:55:13,232] [INFO] Task started: fastANI
[2024-01-25 19:55:13,232] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f82cc66-8426-4ae7-935a-f57e9691ba97/GCF_002295105.1_ASM229510v1_genomic.fna.gz --refList GCF_002295105.1_ASM229510v1_genomic.fna/target_genomes.txt --output GCF_002295105.1_ASM229510v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:55:20,407] [INFO] Task succeeded: fastANI
[2024-01-25 19:55:20,408] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg48d22747-003e-4d30-b5f5-9c7acbc74da7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:55:20,408] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg48d22747-003e-4d30-b5f5-9c7acbc74da7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:55:20,413] [INFO] Found 6 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 19:55:20,414] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 19:55:20,414] [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
Salimicrobium humidisoli	strain=WN024	GCA_002295105.1	2029857	2029857	type	True	100.0	838	843	95	inconclusive
Salimicrobium jeotgali	strain=MJ3	GCA_000299295.2	1230341	1230341	type	True	95.3054	758	843	95	inconclusive
Salimicrobium jeotgali	strain=MJ3	GCA_001685435.3	1230341	1230341	type	True	95.2542	763	843	95	inconclusive
Salimicrobium halophilum	strain=DSM 4771	GCA_900100295.1	86666	86666	type	True	78.4805	274	843	95	below_threshold
Salimicrobium flavidum	strain=DSM 23127	GCA_900156645.1	570947	570947	type	True	78.4241	328	843	95	below_threshold
Halobacillus halophilus	strain=type strain: DSM 2266	GCA_000284515.1	1570	1570	type	True	77.1482	56	843	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:55:20,415] [INFO] DFAST Taxonomy check result was written to GCF_002295105.1_ASM229510v1_genomic.fna/tc_result.tsv
[2024-01-25 19:55:20,416] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:55:20,416] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:55:20,416] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg48d22747-003e-4d30-b5f5-9c7acbc74da7/dqc_reference/checkm_data
[2024-01-25 19:55:20,417] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:55:20,443] [INFO] Task started: CheckM
[2024-01-25 19:55:20,444] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002295105.1_ASM229510v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002295105.1_ASM229510v1_genomic.fna/checkm_input GCF_002295105.1_ASM229510v1_genomic.fna/checkm_result
[2024-01-25 19:55:41,187] [INFO] Task succeeded: CheckM
[2024-01-25 19:55:41,188] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:55:41,202] [INFO] ===== Completeness check finished =====
[2024-01-25 19:55:41,203] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:55:41,203] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002295105.1_ASM229510v1_genomic.fna/markers.fasta)
[2024-01-25 19:55:41,203] [INFO] Task started: Blastn
[2024-01-25 19:55:41,203] [INFO] Running command: blastn -query GCF_002295105.1_ASM229510v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg48d22747-003e-4d30-b5f5-9c7acbc74da7/dqc_reference/reference_markers_gtdb.fasta -out GCF_002295105.1_ASM229510v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:55:41,947] [INFO] Task succeeded: Blastn
[2024-01-25 19:55:41,949] [INFO] Selected 19 target genomes.
[2024-01-25 19:55:41,950] [INFO] Target genome list was writen to GCF_002295105.1_ASM229510v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:55:41,969] [INFO] Task started: fastANI
[2024-01-25 19:55:41,969] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f82cc66-8426-4ae7-935a-f57e9691ba97/GCF_002295105.1_ASM229510v1_genomic.fna.gz --refList GCF_002295105.1_ASM229510v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002295105.1_ASM229510v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:55:53,611] [INFO] Task succeeded: fastANI
[2024-01-25 19:55:53,618] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:55:53,618] [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_002295105.1	s__Salimicrobium sp002295105	100.0	838	843	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Salimicrobium	95.0	98.33	98.33	0.92	0.92	2	conclusive
GCF_900107115.1	s__Salimicrobium album	94.6157	772	843	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Salimicrobium	95.0	97.70	97.32	0.90	0.88	5	-
GCF_900100295.1	s__Salimicrobium halophilum	78.5013	272	843	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Salimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156645.1	s__Salimicrobium flavidum	78.4241	328	843	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Salimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009856445.1	s__Halobacillus litoralis	77.1645	56	843	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	95.88	95.88	0.90	0.90	2	-
GCF_000469135.2	s__Halobacillus sp001592845	76.8237	61	843	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	99.23	99.19	0.95	0.95	3	-
GCF_004684905.1	s__Halobacillus salinus	76.8061	58	843	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	98.08	98.08	0.93	0.93	2	-
GCA_004078665.1	s__Halobacillus sp004078665	76.7376	70	843	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007991335.1	s__Halobacillus faecis	76.5183	63	843	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:55:53,619] [INFO] GTDB search result was written to GCF_002295105.1_ASM229510v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:55:53,620] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:55:53,622] [INFO] DFAST_QC result json was written to GCF_002295105.1_ASM229510v1_genomic.fna/dqc_result.json
[2024-01-25 19:55:53,623] [INFO] DFAST_QC completed!
[2024-01-25 19:55:53,623] [INFO] Total running time: 0h0m48s