[2024-01-24 15:02:24,322] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:24,330] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:24,331] [INFO] DQC Reference Directory: /var/lib/cwl/stg9615fed9-40b0-45f4-8c49-995cc6617319/dqc_reference
[2024-01-24 15:02:26,425] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:26,426] [INFO] Task started: Prodigal
[2024-01-24 15:02:26,426] [INFO] Running command: gunzip -c /var/lib/cwl/stgff40e2a3-9a81-4d04-9ea8-a51b1ed4c588/GCF_010669285.1_ASM1066928v1_genomic.fna.gz | prodigal -d GCF_010669285.1_ASM1066928v1_genomic.fna/cds.fna -a GCF_010669285.1_ASM1066928v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:41,709] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:41,709] [INFO] Task started: HMMsearch
[2024-01-24 15:02:41,709] [INFO] Running command: hmmsearch --tblout GCF_010669285.1_ASM1066928v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9615fed9-40b0-45f4-8c49-995cc6617319/dqc_reference/reference_markers.hmm GCF_010669285.1_ASM1066928v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:42,033] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:42,035] [INFO] Found 6/6 markers.
[2024-01-24 15:02:42,080] [INFO] Query marker FASTA was written to GCF_010669285.1_ASM1066928v1_genomic.fna/markers.fasta
[2024-01-24 15:02:42,081] [INFO] Task started: Blastn
[2024-01-24 15:02:42,081] [INFO] Running command: blastn -query GCF_010669285.1_ASM1066928v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9615fed9-40b0-45f4-8c49-995cc6617319/dqc_reference/reference_markers.fasta -out GCF_010669285.1_ASM1066928v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:43,075] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:43,080] [INFO] Selected 17 target genomes.
[2024-01-24 15:02:43,080] [INFO] Target genome list was writen to GCF_010669285.1_ASM1066928v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:43,093] [INFO] Task started: fastANI
[2024-01-24 15:02:43,093] [INFO] Running command: fastANI --query /var/lib/cwl/stgff40e2a3-9a81-4d04-9ea8-a51b1ed4c588/GCF_010669285.1_ASM1066928v1_genomic.fna.gz --refList GCF_010669285.1_ASM1066928v1_genomic.fna/target_genomes.txt --output GCF_010669285.1_ASM1066928v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:58,314] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:58,315] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9615fed9-40b0-45f4-8c49-995cc6617319/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:58,315] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9615fed9-40b0-45f4-8c49-995cc6617319/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:58,329] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:02:58,330] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:02:58,330] [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
Kineobactrum salinum	strain=M2	GCA_010669285.1	2708301	2708301	type	True	100.0	1549	1549	95	conclusive
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	78.5007	383	1549	95	below_threshold
Parahaliea mediterranea	strain=DSM 21924	GCA_003402235.1	651086	651086	type	True	78.37	437	1549	95	below_threshold
Parahaliea maris	strain=HSLHS9	GCA_008064665.1	2716870	2716870	type	True	78.3225	349	1549	95	below_threshold
Haliea salexigens	strain=DSM 19537	GCA_000423125.1	287487	287487	type	True	78.2966	355	1549	95	below_threshold
Kineobactrum sediminis	strain=F02	GCA_002868715.1	1905677	1905677	type	True	78.2221	364	1549	95	below_threshold
Haliea alexandrii	strain=LZ-16-2	GCA_003719295.1	2448162	2448162	type	True	78.0986	341	1549	95	below_threshold
Seongchinamella sediminis	strain=U0301	GCA_003457605.1	2283635	2283635	type	True	77.723	331	1549	95	below_threshold
Seongchinamella unica	strain=GH4-78	GCA_004354085.1	2547392	2547392	type	True	77.4722	248	1549	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	77.1471	116	1549	95	below_threshold
Halomonas ventosae	strain=CECT 5797	GCA_004363555.1	229007	229007	type	True	77.0756	129	1549	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.8574	186	1549	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.8295	100	1549	95	below_threshold
Halomonas alimentaria	strain=DSM 15356	GCA_009902005.1	147248	147248	type	True	76.704	129	1549	95	below_threshold
Marinobacterium arenosum	strain=CAU 1594	GCA_019795155.1	2862496	2862496	type	True	76.6961	107	1549	95	below_threshold
Halomonas zhangzhouensis	strain=MCCC 1A11036	GCA_021404465.1	2733481	2733481	type	True	76.2693	102	1549	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	76.1399	106	1549	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:58,331] [INFO] DFAST Taxonomy check result was written to GCF_010669285.1_ASM1066928v1_genomic.fna/tc_result.tsv
[2024-01-24 15:02:58,332] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:58,332] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:58,332] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9615fed9-40b0-45f4-8c49-995cc6617319/dqc_reference/checkm_data
[2024-01-24 15:02:58,334] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:58,380] [INFO] Task started: CheckM
[2024-01-24 15:02:58,381] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010669285.1_ASM1066928v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010669285.1_ASM1066928v1_genomic.fna/checkm_input GCF_010669285.1_ASM1066928v1_genomic.fna/checkm_result
[2024-01-24 15:03:43,512] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:43,513] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:43,536] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:43,536] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:43,537] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010669285.1_ASM1066928v1_genomic.fna/markers.fasta)
[2024-01-24 15:03:43,537] [INFO] Task started: Blastn
[2024-01-24 15:03:43,537] [INFO] Running command: blastn -query GCF_010669285.1_ASM1066928v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9615fed9-40b0-45f4-8c49-995cc6617319/dqc_reference/reference_markers_gtdb.fasta -out GCF_010669285.1_ASM1066928v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:45,063] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:45,067] [INFO] Selected 14 target genomes.
[2024-01-24 15:03:45,067] [INFO] Target genome list was writen to GCF_010669285.1_ASM1066928v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:45,097] [INFO] Task started: fastANI
[2024-01-24 15:03:45,097] [INFO] Running command: fastANI --query /var/lib/cwl/stgff40e2a3-9a81-4d04-9ea8-a51b1ed4c588/GCF_010669285.1_ASM1066928v1_genomic.fna.gz --refList GCF_010669285.1_ASM1066928v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010669285.1_ASM1066928v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:03:58,376] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:58,388] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:03:58,389] [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_010669285.1	s__Kineobactrum salinum	100.0	1549	1549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Kineobactrum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017255185.1	s__Parahaliea mediterranea_A	78.8302	464	1549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002692965.1	s__NZNC01 sp002692965	78.5193	378	1549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__NZNC01	95.0	98.60	97.22	0.91	0.84	3	-
GCF_008064635.1	s__Parahaliea aestuarii	78.49	384	1549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003402235.1	s__Parahaliea mediterranea	78.3463	439	1549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008064665.1	s__Parahaliea maris	78.3291	349	1549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423125.1	s__Haliea salexigens	78.3196	354	1549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	96.91	96.59	0.87	0.83	15	-
GCA_002416125.1	s__Haliea sp002416125	78.2605	336	1549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	99.96	99.96	0.96	0.96	2	-
GCF_002868715.1	s__Kineobactrum sediminis	78.2338	364	1549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Kineobactrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745945.1	s__Halioglobus sp004745945	78.1154	309	1549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003719295.1	s__Haliea alexandrii	78.0986	341	1549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699145.1	s__Halioglobus sp002699145	78.0428	328	1549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.96	99.96	0.98	0.98	2	-
GCA_002414665.1	s__Haliea sp002414665	77.8671	336	1549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	99.89	99.89	0.97	0.97	2	-
GCA_009937575.1	s__Halioglobus sp009937575	77.8429	249	1549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:03:58,390] [INFO] GTDB search result was written to GCF_010669285.1_ASM1066928v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:03:58,391] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:03:58,397] [INFO] DFAST_QC result json was written to GCF_010669285.1_ASM1066928v1_genomic.fna/dqc_result.json
[2024-01-24 15:03:58,398] [INFO] DFAST_QC completed!
[2024-01-24 15:03:58,398] [INFO] Total running time: 0h1m34s