[2024-01-24 12:06:24,605] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:24,607] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:24,607] [INFO] DQC Reference Directory: /var/lib/cwl/stg70a97938-02f7-4270-934a-11f33141b79c/dqc_reference
[2024-01-24 12:06:25,877] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:25,878] [INFO] Task started: Prodigal
[2024-01-24 12:06:25,879] [INFO] Running command: gunzip -c /var/lib/cwl/stg58d7ae33-a0ec-4961-ba39-e31c693415d8/GCF_018476645.1_ASM1847664v1_genomic.fna.gz | prodigal -d GCF_018476645.1_ASM1847664v1_genomic.fna/cds.fna -a GCF_018476645.1_ASM1847664v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:40,259] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:40,260] [INFO] Task started: HMMsearch
[2024-01-24 12:06:40,260] [INFO] Running command: hmmsearch --tblout GCF_018476645.1_ASM1847664v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70a97938-02f7-4270-934a-11f33141b79c/dqc_reference/reference_markers.hmm GCF_018476645.1_ASM1847664v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:40,505] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:40,507] [INFO] Found 6/6 markers.
[2024-01-24 12:06:40,537] [INFO] Query marker FASTA was written to GCF_018476645.1_ASM1847664v1_genomic.fna/markers.fasta
[2024-01-24 12:06:40,537] [INFO] Task started: Blastn
[2024-01-24 12:06:40,537] [INFO] Running command: blastn -query GCF_018476645.1_ASM1847664v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70a97938-02f7-4270-934a-11f33141b79c/dqc_reference/reference_markers.fasta -out GCF_018476645.1_ASM1847664v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:41,132] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:41,136] [INFO] Selected 19 target genomes.
[2024-01-24 12:06:41,136] [INFO] Target genome list was writen to GCF_018476645.1_ASM1847664v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:41,143] [INFO] Task started: fastANI
[2024-01-24 12:06:41,143] [INFO] Running command: fastANI --query /var/lib/cwl/stg58d7ae33-a0ec-4961-ba39-e31c693415d8/GCF_018476645.1_ASM1847664v1_genomic.fna.gz --refList GCF_018476645.1_ASM1847664v1_genomic.fna/target_genomes.txt --output GCF_018476645.1_ASM1847664v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:52,928] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:52,929] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg70a97938-02f7-4270-934a-11f33141b79c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:52,929] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg70a97938-02f7-4270-934a-11f33141b79c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:52,943] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:52,943] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:52,943] [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
Aequorivita echinoideorum	strain=JCM30378	GCA_018476645.1	1549647	1549647	type	True	100.0	966	966	95	conclusive
Aequorivita vladivostokensis	strain=KMM 3516	GCA_000952855.1	171194	171194	type	True	79.5108	345	966	95	below_threshold
Aequorivita iocasae	strain=KX20305	GCA_016757735.1	2803865	2803865	type	True	78.8625	386	966	95	below_threshold
Aequorivita soesokkakensis	strain=RSSK-12	GCA_001641085.1	1385699	1385699	type	True	78.7879	386	966	95	below_threshold
Aequorivita aquimaris	strain=D-24	GCA_001573155.1	1548749	1548749	type	True	78.514	358	966	95	below_threshold
Aequorivita lipolytica	strain=Y10-2	GCA_007997135.1	153267	153267	type	True	78.4402	311	966	95	below_threshold
Aequorivita antarctica	strain=SW49	GCA_007997155.1	153266	153266	type	True	78.3753	333	966	95	below_threshold
Aequorivita sublithincola	strain=DSM 14238	GCA_000265385.1	101385	101385	type	True	77.9282	303	966	95	below_threshold
Aequorivita capsosiphonis	strain=DSM 23843	GCA_000429125.1	487317	487317	type	True	77.8139	268	966	95	below_threshold
Aequorivita sinensis	strain=S1-10	GCA_006346335.1	1382458	1382458	type	True	77.6336	180	966	95	below_threshold
Aequorivita viscosa	strain=CGMCC 1.11023	GCA_900106795.1	797419	797419	type	True	77.4662	178	966	95	below_threshold
Aequorivita viscosa	strain=DSM 26349	GCA_900141955.1	797419	797419	type	True	77.3824	176	966	95	below_threshold
Ulvibacter antarcticus	strain=DSM 23424	GCA_003688405.1	442714	442714	type	True	77.1086	95	966	95	below_threshold
Marinirhabdus gelatinilytica	strain=DSM 101478	GCA_003353425.1	1703343	1703343	type	True	76.9988	102	966	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.963	50	966	95	below_threshold
Luteirhabdus pelagi	strain=A3-108	GCA_016827595.1	2792783	2792783	type	True	76.6593	66	966	95	below_threshold
Halomarinibacterium sedimenti	strain=CAU 1614	GCA_019312585.1	2857106	2857106	type	True	76.6474	100	966	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	76.4927	50	966	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:52,945] [INFO] DFAST Taxonomy check result was written to GCF_018476645.1_ASM1847664v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:52,946] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:52,946] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:52,946] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70a97938-02f7-4270-934a-11f33141b79c/dqc_reference/checkm_data
[2024-01-24 12:06:52,947] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:52,977] [INFO] Task started: CheckM
[2024-01-24 12:06:52,978] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018476645.1_ASM1847664v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018476645.1_ASM1847664v1_genomic.fna/checkm_input GCF_018476645.1_ASM1847664v1_genomic.fna/checkm_result
[2024-01-24 12:07:33,481] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:33,483] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:33,500] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:33,500] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:33,500] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018476645.1_ASM1847664v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:33,501] [INFO] Task started: Blastn
[2024-01-24 12:07:33,501] [INFO] Running command: blastn -query GCF_018476645.1_ASM1847664v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70a97938-02f7-4270-934a-11f33141b79c/dqc_reference/reference_markers_gtdb.fasta -out GCF_018476645.1_ASM1847664v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:34,330] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:34,334] [INFO] Selected 14 target genomes.
[2024-01-24 12:07:34,334] [INFO] Target genome list was writen to GCF_018476645.1_ASM1847664v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:34,343] [INFO] Task started: fastANI
[2024-01-24 12:07:34,344] [INFO] Running command: fastANI --query /var/lib/cwl/stg58d7ae33-a0ec-4961-ba39-e31c693415d8/GCF_018476645.1_ASM1847664v1_genomic.fna.gz --refList GCF_018476645.1_ASM1847664v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018476645.1_ASM1847664v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:42,339] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:42,350] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:42,351] [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_018476645.1	s__Aequorivita echinoideorum	100.0	966	966	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000952855.1	s__Aequorivita vladivostokensis	79.4957	346	966	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	98.24	98.00	0.93	0.90	7	-
GCA_002733915.1	s__Aequorivita sp002733915	79.0778	352	966	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002715485.1	s__Aequorivita sp002715485	79.039	300	966	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.49	99.49	0.87	0.87	2	-
GCF_016757735.1	s__Aequorivita sp016757735	78.8843	384	966	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001641085.1	s__Aequorivita soesokkakensis	78.7879	386	966	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	97.26	97.26	0.92	0.92	2	-
GCA_002364215.1	s__Aequorivita sp002364215	78.5619	364	966	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.66	98.55	0.97	0.89	12	-
GCF_001573155.1	s__Aequorivita aquimaris	78.514	358	966	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997135.1	s__Aequorivita lipolytica	78.4394	311	966	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900489465.1	s__Aequorivita sp900489465	78.2536	341	966	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016649715.1	s__Aequorivita sp016649715	78.0683	305	966	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265385.1	s__Aequorivita sublithincola	77.9399	302	966	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106795.1	s__Aequorivita viscosa	77.4496	179	966	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:42,352] [INFO] GTDB search result was written to GCF_018476645.1_ASM1847664v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:42,353] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:42,356] [INFO] DFAST_QC result json was written to GCF_018476645.1_ASM1847664v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:42,357] [INFO] DFAST_QC completed!
[2024-01-24 12:07:42,357] [INFO] Total running time: 0h1m18s