[2024-01-24 13:57:42,789] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:42,793] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:42,794] [INFO] DQC Reference Directory: /var/lib/cwl/stg45b27b1b-e003-446c-913d-55d95ff70f50/dqc_reference
[2024-01-24 13:57:44,172] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:44,174] [INFO] Task started: Prodigal
[2024-01-24 13:57:44,174] [INFO] Running command: gunzip -c /var/lib/cwl/stgdb8c6b74-fbde-462c-8188-62610d9eb783/GCF_003096655.1_ASM309665v1_genomic.fna.gz | prodigal -d GCF_003096655.1_ASM309665v1_genomic.fna/cds.fna -a GCF_003096655.1_ASM309665v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:54,895] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:54,895] [INFO] Task started: HMMsearch
[2024-01-24 13:57:54,896] [INFO] Running command: hmmsearch --tblout GCF_003096655.1_ASM309665v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg45b27b1b-e003-446c-913d-55d95ff70f50/dqc_reference/reference_markers.hmm GCF_003096655.1_ASM309665v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:55,208] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:55,210] [INFO] Found 6/6 markers.
[2024-01-24 13:57:55,248] [INFO] Query marker FASTA was written to GCF_003096655.1_ASM309665v1_genomic.fna/markers.fasta
[2024-01-24 13:57:55,249] [INFO] Task started: Blastn
[2024-01-24 13:57:55,249] [INFO] Running command: blastn -query GCF_003096655.1_ASM309665v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45b27b1b-e003-446c-913d-55d95ff70f50/dqc_reference/reference_markers.fasta -out GCF_003096655.1_ASM309665v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:56,249] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:56,252] [INFO] Selected 18 target genomes.
[2024-01-24 13:57:56,253] [INFO] Target genome list was writen to GCF_003096655.1_ASM309665v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:56,259] [INFO] Task started: fastANI
[2024-01-24 13:57:56,260] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb8c6b74-fbde-462c-8188-62610d9eb783/GCF_003096655.1_ASM309665v1_genomic.fna.gz --refList GCF_003096655.1_ASM309665v1_genomic.fna/target_genomes.txt --output GCF_003096655.1_ASM309665v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:09,497] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:09,497] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg45b27b1b-e003-446c-913d-55d95ff70f50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:09,498] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg45b27b1b-e003-446c-913d-55d95ff70f50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:09,523] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:58:09,523] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:09,524] [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
Tamilnaduibacter salinus	strain=DSM 28688	GCA_003096655.1	1484056	1484056	type	True	100.0	1120	1120	95	conclusive
Tamilnaduibacter salinus	strain=Mi-7	GCA_002287355.1	1484056	1484056	type	True	98.8172	975	1120	95	conclusive
Marinobacter bohaiensis	strain=T17	GCA_003258515.1	2201898	2201898	type	True	78.3446	393	1120	95	below_threshold
Marinobacter halodurans	strain=YJ-S3-2	GCA_004327985.1	2528979	2528979	type	True	78.2468	377	1120	95	below_threshold
Marinobacter mangrovi	strain=CHFG3-1-5	GCA_016798325.1	2803918	2803918	type	True	78.0637	382	1120	95	below_threshold
Marinobacter persicus	strain=IBRC-M 10445	GCA_900114155.1	930118	930118	type	True	77.671	223	1120	95	below_threshold
Marinobacter persicus	strain=KCTC 23561	GCA_014652295.1	930118	930118	type	True	77.6634	224	1120	95	below_threshold
Marinobacter zhanjiangensis	strain=KCTC 22280	GCA_014651935.1	578215	578215	type	True	77.6002	269	1120	95	below_threshold
Marinobacter segnicrescens	strain=CGMCC 1.6489	GCA_900111555.1	430453	430453	type	True	77.4945	225	1120	95	below_threshold
Marinobacter daqiaonensis	strain=YCSA40	GCA_012070355.1	650891	650891	type	True	77.4882	229	1120	95	below_threshold
Marinobacter daqiaonensis	strain=CGMCC 1.9167	GCA_900115285.1	650891	650891	type	True	77.4265	229	1120	95	below_threshold
Marinobacter maroccanus	strain=N4	GCA_002933275.1	2055143	2055143	type	True	77.2955	240	1120	95	below_threshold
Marinobacter litoralis	strain=Sw-45	GCA_003336705.1	187981	187981	type	True	76.7676	139	1120	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	76.7094	124	1120	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	76.5461	111	1120	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	76.4845	125	1120	95	below_threshold
Halomonas zhangzhouensis	strain=MCCC 1A11036	GCA_021404465.1	2733481	2733481	type	True	76.3399	102	1120	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:09,525] [INFO] DFAST Taxonomy check result was written to GCF_003096655.1_ASM309665v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:09,527] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:09,528] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:09,528] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg45b27b1b-e003-446c-913d-55d95ff70f50/dqc_reference/checkm_data
[2024-01-24 13:58:09,529] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:09,574] [INFO] Task started: CheckM
[2024-01-24 13:58:09,574] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003096655.1_ASM309665v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003096655.1_ASM309665v1_genomic.fna/checkm_input GCF_003096655.1_ASM309665v1_genomic.fna/checkm_result
[2024-01-24 13:58:45,306] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:45,308] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:45,339] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:45,340] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:45,340] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003096655.1_ASM309665v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:45,340] [INFO] Task started: Blastn
[2024-01-24 13:58:45,340] [INFO] Running command: blastn -query GCF_003096655.1_ASM309665v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45b27b1b-e003-446c-913d-55d95ff70f50/dqc_reference/reference_markers_gtdb.fasta -out GCF_003096655.1_ASM309665v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:46,882] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:46,886] [INFO] Selected 19 target genomes.
[2024-01-24 13:58:46,886] [INFO] Target genome list was writen to GCF_003096655.1_ASM309665v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:46,908] [INFO] Task started: fastANI
[2024-01-24 13:58:46,908] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb8c6b74-fbde-462c-8188-62610d9eb783/GCF_003096655.1_ASM309665v1_genomic.fna.gz --refList GCF_003096655.1_ASM309665v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003096655.1_ASM309665v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:00,684] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:00,700] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:00,700] [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_003096655.1	s__Tamilnaduibacter salinus	100.0	1120	1120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Tamilnaduibacter	95.0	98.82	98.82	0.93	0.93	2	conclusive
GCF_003258515.1	s__Marinobacter_A bohaiensis	78.3544	392	1120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	98.52	98.52	0.96	0.96	2	-
GCF_004327985.1	s__Marinobacter_A halodurans	78.2638	376	1120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003789045.1	s__Marinobacter_A sp003789045	78.1737	374	1120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	97.70	97.70	0.91	0.91	2	-
GCF_002934325.1	s__Marinobacter persicus_A	77.9977	237	1120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.99	99.99	0.99	0.99	3	-
GCF_003315345.1	s__Marinobacter pelagius_A	77.9934	274	1120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114155.1	s__Marinobacter persicus	77.6849	222	1120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.98	99.98	1.00	1.00	2	-
GCF_900115175.1	s__Marinobacter gudaonensis	77.6611	265	1120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651935.1	s__Marinobacter zhanjiangensis	77.6084	269	1120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018424605.1	s__Marinobacter lipolyticus_B	77.6017	268	1120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114925.1	s__Marinobacter pelagius	77.5871	285	1120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002744715.1	s__Marinobacter profundi	77.5467	260	1120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.28	99.28	0.94	0.94	2	-
GCF_900111555.1	s__Marinobacter segnicrescens	77.4945	225	1120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115285.1	s__Marinobacter daqiaonensis	77.4135	230	1120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002258215.1	s__Marinobacter vinifirmus	77.3746	256	1120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	96.96	96.78	0.87	0.84	7	-
GCA_018623515.1	s__Marinobacter sp018623515	77.3695	230	1120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762755.1	s__Marinobacter sp014762755	77.0903	189	1120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002879645.1	s__Halomonas heilongjiangensis	76.6471	117	1120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.98	99.98	1.00	1.00	2	-
GCA_002726615.1	s__Marinobacter sp002726615	76.5961	151	1120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.52	98.30	0.75	0.64	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:00,702] [INFO] GTDB search result was written to GCF_003096655.1_ASM309665v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:00,703] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:00,707] [INFO] DFAST_QC result json was written to GCF_003096655.1_ASM309665v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:00,708] [INFO] DFAST_QC completed!
[2024-01-24 13:59:00,708] [INFO] Total running time: 0h1m18s