[2024-01-24 15:18:32,526] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:32,528] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:32,529] [INFO] DQC Reference Directory: /var/lib/cwl/stg935b00d6-9b81-473a-bdf0-a1e284de5c16/dqc_reference
[2024-01-24 15:18:34,813] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:34,814] [INFO] Task started: Prodigal
[2024-01-24 15:18:34,814] [INFO] Running command: gunzip -c /var/lib/cwl/stg910b7041-e50b-4b9a-9de8-de2d8a082dd1/GCF_003044065.1_ASM304406v1_genomic.fna.gz | prodigal -d GCF_003044065.1_ASM304406v1_genomic.fna/cds.fna -a GCF_003044065.1_ASM304406v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:42,383] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:42,383] [INFO] Task started: HMMsearch
[2024-01-24 15:18:42,384] [INFO] Running command: hmmsearch --tblout GCF_003044065.1_ASM304406v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg935b00d6-9b81-473a-bdf0-a1e284de5c16/dqc_reference/reference_markers.hmm GCF_003044065.1_ASM304406v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:42,603] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:42,604] [INFO] Found 6/6 markers.
[2024-01-24 15:18:42,633] [INFO] Query marker FASTA was written to GCF_003044065.1_ASM304406v1_genomic.fna/markers.fasta
[2024-01-24 15:18:42,633] [INFO] Task started: Blastn
[2024-01-24 15:18:42,634] [INFO] Running command: blastn -query GCF_003044065.1_ASM304406v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg935b00d6-9b81-473a-bdf0-a1e284de5c16/dqc_reference/reference_markers.fasta -out GCF_003044065.1_ASM304406v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:43,199] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:43,202] [INFO] Selected 23 target genomes.
[2024-01-24 15:18:43,203] [INFO] Target genome list was writen to GCF_003044065.1_ASM304406v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:43,369] [INFO] Task started: fastANI
[2024-01-24 15:18:43,370] [INFO] Running command: fastANI --query /var/lib/cwl/stg910b7041-e50b-4b9a-9de8-de2d8a082dd1/GCF_003044065.1_ASM304406v1_genomic.fna.gz --refList GCF_003044065.1_ASM304406v1_genomic.fna/target_genomes.txt --output GCF_003044065.1_ASM304406v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:57,782] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:57,782] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg935b00d6-9b81-473a-bdf0-a1e284de5c16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:57,783] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg935b00d6-9b81-473a-bdf0-a1e284de5c16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:57,791] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:18:57,791] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:18:57,791] [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
Alkalicoccus saliphilus	strain=6AG	GCA_003044065.1	200989	200989	type	True	100.0	1137	1140	95	conclusive
Alkalicoccus halolimnae	strain=BZ-SZ-XJ29	GCA_008014775.1	1667239	1667239	type	True	78.4048	306	1140	95	below_threshold
Paenalkalicoccus suaedae	strain=M4U3P1	GCA_006965545.2	2592382	2592382	type	True	77.7971	60	1140	95	below_threshold
Alteribacter natronophilus	strain=M30	GCA_006007885.1	2583810	2583810	type	True	77.6963	66	1140	95	below_threshold
Alkalicoccus daliensis	strain=CGMCC 1.10369	GCA_900103955.1	745820	745820	type	True	77.6544	194	1140	95	below_threshold
Salipaludibacillus keqinensis	strain=KQ-12	GCA_003226325.1	2045207	2045207	type	True	77.5232	59	1140	95	below_threshold
Alteribacter lacisalsi	strain=YSP-3	GCA_003226345.1	2045244	2045244	type	True	77.4488	64	1140	95	below_threshold
Alkalicoccus urumqiensis	strain=BZ-SZ-XJ18	GCA_002993335.1	1548213	1548213	type	True	77.4447	162	1140	95	below_threshold
Alkalicoccus chagannorensis	strain=DSM 18086	GCA_000429725.1	427072	427072	type	True	77.2503	112	1140	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:57,793] [INFO] DFAST Taxonomy check result was written to GCF_003044065.1_ASM304406v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:57,793] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:57,794] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:57,794] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg935b00d6-9b81-473a-bdf0-a1e284de5c16/dqc_reference/checkm_data
[2024-01-24 15:18:57,795] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:57,828] [INFO] Task started: CheckM
[2024-01-24 15:18:57,828] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003044065.1_ASM304406v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003044065.1_ASM304406v1_genomic.fna/checkm_input GCF_003044065.1_ASM304406v1_genomic.fna/checkm_result
[2024-01-24 15:19:24,638] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:24,639] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:24,657] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:24,657] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:24,657] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003044065.1_ASM304406v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:24,657] [INFO] Task started: Blastn
[2024-01-24 15:19:24,657] [INFO] Running command: blastn -query GCF_003044065.1_ASM304406v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg935b00d6-9b81-473a-bdf0-a1e284de5c16/dqc_reference/reference_markers_gtdb.fasta -out GCF_003044065.1_ASM304406v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:25,431] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:25,434] [INFO] Selected 13 target genomes.
[2024-01-24 15:19:25,434] [INFO] Target genome list was writen to GCF_003044065.1_ASM304406v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:25,474] [INFO] Task started: fastANI
[2024-01-24 15:19:25,474] [INFO] Running command: fastANI --query /var/lib/cwl/stg910b7041-e50b-4b9a-9de8-de2d8a082dd1/GCF_003044065.1_ASM304406v1_genomic.fna.gz --refList GCF_003044065.1_ASM304406v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003044065.1_ASM304406v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:35,265] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:35,273] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:35,273] [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_003044065.1	s__Alkalicoccus saliphilus	100.0	1137	1140	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alkalicoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003560495.1	s__Alkalicoccus sp003560495	92.6175	708	1140	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alkalicoccus	95.0	99.31	99.31	0.92	0.92	2	-
GCA_007692495.1	s__Alkalicoccus sp007692495	89.309	723	1140	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alkalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008014775.1	s__Alkalicoccus halolimnae	78.4771	297	1140	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alkalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006965545.2	s__Alkalicoccus sp006965545	77.8477	59	1140	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alkalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103955.1	s__Alkalicoccus daliensis	77.6694	194	1140	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alkalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012034335.1	s__Alkalicoccus luteus	77.6272	161	1140	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alkalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002993335.1	s__Alkalicoccus urumqiensis	77.4447	162	1140	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alkalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:35,274] [INFO] GTDB search result was written to GCF_003044065.1_ASM304406v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:35,275] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:35,278] [INFO] DFAST_QC result json was written to GCF_003044065.1_ASM304406v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:35,278] [INFO] DFAST_QC completed!
[2024-01-24 15:19:35,278] [INFO] Total running time: 0h1m3s