[2024-01-24 11:51:06,961] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:06,963] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:06,963] [INFO] DQC Reference Directory: /var/lib/cwl/stg35e0a302-55e1-4e47-bdae-77126880a6a6/dqc_reference
[2024-01-24 11:51:08,200] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:08,200] [INFO] Task started: Prodigal
[2024-01-24 11:51:08,201] [INFO] Running command: gunzip -c /var/lib/cwl/stg6c115e8b-63fd-4616-aa74-af3e51770281/GCF_009901955.1_ASM990195v1_genomic.fna.gz | prodigal -d GCF_009901955.1_ASM990195v1_genomic.fna/cds.fna -a GCF_009901955.1_ASM990195v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:18,800] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:18,801] [INFO] Task started: HMMsearch
[2024-01-24 11:51:18,801] [INFO] Running command: hmmsearch --tblout GCF_009901955.1_ASM990195v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg35e0a302-55e1-4e47-bdae-77126880a6a6/dqc_reference/reference_markers.hmm GCF_009901955.1_ASM990195v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:19,111] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:19,112] [INFO] Found 6/6 markers.
[2024-01-24 11:51:19,145] [INFO] Query marker FASTA was written to GCF_009901955.1_ASM990195v1_genomic.fna/markers.fasta
[2024-01-24 11:51:19,145] [INFO] Task started: Blastn
[2024-01-24 11:51:19,145] [INFO] Running command: blastn -query GCF_009901955.1_ASM990195v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35e0a302-55e1-4e47-bdae-77126880a6a6/dqc_reference/reference_markers.fasta -out GCF_009901955.1_ASM990195v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:20,083] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:20,087] [INFO] Selected 15 target genomes.
[2024-01-24 11:51:20,087] [INFO] Target genome list was writen to GCF_009901955.1_ASM990195v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:20,093] [INFO] Task started: fastANI
[2024-01-24 11:51:20,094] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c115e8b-63fd-4616-aa74-af3e51770281/GCF_009901955.1_ASM990195v1_genomic.fna.gz --refList GCF_009901955.1_ASM990195v1_genomic.fna/target_genomes.txt --output GCF_009901955.1_ASM990195v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:32,790] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:32,790] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg35e0a302-55e1-4e47-bdae-77126880a6a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:32,791] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg35e0a302-55e1-4e47-bdae-77126880a6a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:32,808] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:32,808] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:32,808] [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
Halomonas icarae	strain=D1-1	GCA_009901955.1	2691040	2691040	type	True	100.0	1158	1158	95	conclusive
Halomonas halodenitrificans	strain=DSM 735	GCA_000620045.1	28252	28252	type	True	86.1681	834	1158	95	below_threshold
Halomonas alimentaria	strain=DSM 15356	GCA_009902005.1	147248	147248	type	True	86.1449	835	1158	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	85.2473	824	1158	95	below_threshold
Halomonas campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	83.3407	755	1158	95	below_threshold
Halomonas ventosae	strain=CECT 5797	GCA_004363555.1	229007	229007	type	True	83.3148	771	1158	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	82.989	781	1158	95	below_threshold
Halomonas heilongjiangensis	strain=DSM 26881	GCA_002879645.1	1387883	1387883	type	True	82.2765	704	1158	95	below_threshold
Halomonas heilongjiangensis	strain=9-2	GCA_003202165.1	1387883	1387883	type	True	82.2337	720	1158	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	81.8631	691	1158	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	81.7276	704	1158	95	below_threshold
Halomonas daqiaonensis	strain=CGMCC 1.9150	GCA_900109725.1	650850	650850	type	True	81.6002	686	1158	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	81.318	661	1158	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	80.6121	640	1158	95	below_threshold
Halomonas zhangzhouensis	strain=MCCC 1A11036	GCA_021404465.1	2733481	2733481	type	True	80.6007	579	1158	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:32,810] [INFO] DFAST Taxonomy check result was written to GCF_009901955.1_ASM990195v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:32,810] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:32,810] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:32,810] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg35e0a302-55e1-4e47-bdae-77126880a6a6/dqc_reference/checkm_data
[2024-01-24 11:51:32,811] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:32,846] [INFO] Task started: CheckM
[2024-01-24 11:51:32,846] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009901955.1_ASM990195v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009901955.1_ASM990195v1_genomic.fna/checkm_input GCF_009901955.1_ASM990195v1_genomic.fna/checkm_result
[2024-01-24 11:52:07,886] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:07,887] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:07,912] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:07,913] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:07,913] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009901955.1_ASM990195v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:07,914] [INFO] Task started: Blastn
[2024-01-24 11:52:07,914] [INFO] Running command: blastn -query GCF_009901955.1_ASM990195v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35e0a302-55e1-4e47-bdae-77126880a6a6/dqc_reference/reference_markers_gtdb.fasta -out GCF_009901955.1_ASM990195v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:09,650] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:09,663] [INFO] Selected 8 target genomes.
[2024-01-24 11:52:09,663] [INFO] Target genome list was writen to GCF_009901955.1_ASM990195v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:09,674] [INFO] Task started: fastANI
[2024-01-24 11:52:09,674] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c115e8b-63fd-4616-aa74-af3e51770281/GCF_009901955.1_ASM990195v1_genomic.fna.gz --refList GCF_009901955.1_ASM990195v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009901955.1_ASM990195v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:16,607] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:16,622] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:16,623] [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_009901955.1	s__Halomonas icarae	100.0	1158	1158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.73	97.73	0.87	0.87	2	conclusive
GCF_015595025.1	s__Halomonas sp015595025	93.6822	959	1158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401555.1	s__Halomonas sp018401555	86.2737	755	1158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620045.1	s__Halomonas halodenitrificans	86.1572	835	1158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.15	97.15	0.89	0.89	2	-
GCF_009902005.1	s__Halomonas alimentaria	86.1449	835	1158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104135.1	s__Halomonas shengliensis	85.2271	826	1158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.66	95.66	0.79	0.79	2	-
GCF_014193375.1	s__Halomonas campaniensis	83.3503	755	1158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363755.1	s__Halomonas sp009363755	82.9557	756	1158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:16,625] [INFO] GTDB search result was written to GCF_009901955.1_ASM990195v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:16,625] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:16,631] [INFO] DFAST_QC result json was written to GCF_009901955.1_ASM990195v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:16,631] [INFO] DFAST_QC completed!
[2024-01-24 11:52:16,631] [INFO] Total running time: 0h1m10s