[2024-01-24 13:55:14,904] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:14,906] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:14,906] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d72c170-7815-418d-8d1b-06fdd66efde8/dqc_reference
[2024-01-24 13:55:16,278] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:16,279] [INFO] Task started: Prodigal
[2024-01-24 13:55:16,279] [INFO] Running command: gunzip -c /var/lib/cwl/stgfe6fdde2-7b90-427f-a07c-238d4802a550/GCF_014652255.1_ASM1465225v1_genomic.fna.gz | prodigal -d GCF_014652255.1_ASM1465225v1_genomic.fna/cds.fna -a GCF_014652255.1_ASM1465225v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:28,601] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:28,601] [INFO] Task started: HMMsearch
[2024-01-24 13:55:28,602] [INFO] Running command: hmmsearch --tblout GCF_014652255.1_ASM1465225v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d72c170-7815-418d-8d1b-06fdd66efde8/dqc_reference/reference_markers.hmm GCF_014652255.1_ASM1465225v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:28,928] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:28,930] [INFO] Found 6/6 markers.
[2024-01-24 13:55:28,966] [INFO] Query marker FASTA was written to GCF_014652255.1_ASM1465225v1_genomic.fna/markers.fasta
[2024-01-24 13:55:28,966] [INFO] Task started: Blastn
[2024-01-24 13:55:28,967] [INFO] Running command: blastn -query GCF_014652255.1_ASM1465225v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d72c170-7815-418d-8d1b-06fdd66efde8/dqc_reference/reference_markers.fasta -out GCF_014652255.1_ASM1465225v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:29,768] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:29,771] [INFO] Selected 12 target genomes.
[2024-01-24 13:55:29,772] [INFO] Target genome list was writen to GCF_014652255.1_ASM1465225v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:29,777] [INFO] Task started: fastANI
[2024-01-24 13:55:29,777] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe6fdde2-7b90-427f-a07c-238d4802a550/GCF_014652255.1_ASM1465225v1_genomic.fna.gz --refList GCF_014652255.1_ASM1465225v1_genomic.fna/target_genomes.txt --output GCF_014652255.1_ASM1465225v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:55:39,354] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:39,355] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d72c170-7815-418d-8d1b-06fdd66efde8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:55:39,355] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d72c170-7815-418d-8d1b-06fdd66efde8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:55:39,366] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:55:39,366] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:55:39,367] [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
Halioglobus japonicus	strain=KCTC 23429	GCA_014652255.1	930805	930805	type	True	100.0	1342	1344	95	conclusive
Halioglobus japonicus	strain=S1-36	GCA_002869505.1	930805	930805	type	True	99.9968	1341	1344	95	conclusive
Halioglobus japonicus	strain=NBRC 107739	GCA_001983995.1	930805	930805	type	True	99.9895	1344	1344	95	conclusive
Halioglobus maricola	strain=IMCC14385	GCA_009388985.1	2601894	2601894	type	True	79.394	548	1344	95	below_threshold
Seongchinamella unica	strain=GH4-78	GCA_004354085.1	2547392	2547392	type	True	78.3748	356	1344	95	below_threshold
Seongchinamella sediminis	strain=U0301	GCA_003457605.1	2283635	2283635	type	True	78.3115	398	1344	95	below_threshold
Parahaliea mediterranea	strain=DSM 21924	GCA_003402235.1	651086	651086	type	True	77.9695	289	1344	95	below_threshold
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	77.7279	271	1344	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	77.0601	63	1344	95	below_threshold
Microbulbifer celer	strain=KCTC 12973	GCA_020991125.1	435905	435905	type	True	76.6401	90	1344	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.5912	96	1344	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:55:39,368] [INFO] DFAST Taxonomy check result was written to GCF_014652255.1_ASM1465225v1_genomic.fna/tc_result.tsv
[2024-01-24 13:55:39,369] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:55:39,369] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:55:39,369] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d72c170-7815-418d-8d1b-06fdd66efde8/dqc_reference/checkm_data
[2024-01-24 13:55:39,371] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:55:39,416] [INFO] Task started: CheckM
[2024-01-24 13:55:39,416] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014652255.1_ASM1465225v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014652255.1_ASM1465225v1_genomic.fna/checkm_input GCF_014652255.1_ASM1465225v1_genomic.fna/checkm_result
[2024-01-24 13:56:19,913] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:19,914] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:19,932] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:19,932] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:19,933] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014652255.1_ASM1465225v1_genomic.fna/markers.fasta)
[2024-01-24 13:56:19,933] [INFO] Task started: Blastn
[2024-01-24 13:56:19,933] [INFO] Running command: blastn -query GCF_014652255.1_ASM1465225v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d72c170-7815-418d-8d1b-06fdd66efde8/dqc_reference/reference_markers_gtdb.fasta -out GCF_014652255.1_ASM1465225v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:21,252] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:21,256] [INFO] Selected 14 target genomes.
[2024-01-24 13:56:21,256] [INFO] Target genome list was writen to GCF_014652255.1_ASM1465225v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:21,270] [INFO] Task started: fastANI
[2024-01-24 13:56:21,270] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe6fdde2-7b90-427f-a07c-238d4802a550/GCF_014652255.1_ASM1465225v1_genomic.fna.gz --refList GCF_014652255.1_ASM1465225v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014652255.1_ASM1465225v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:56:32,684] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:32,699] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:56:32,699] [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_001983995.1	s__Halioglobus japonicus	99.9895	1344	1344	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.41	98.25	0.97	0.92	4	conclusive
GCF_009388985.1	s__Halioglobus maricola	79.3942	548	1344	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004354085.1	s__Halioglobus sp004354085	78.3794	355	1344	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003457605.1	s__Halioglobus sediminis	78.3115	398	1344	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745945.1	s__Halioglobus sp004745945	77.9971	297	1344	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003402235.1	s__Parahaliea mediterranea	77.9576	290	1344	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	77.9344	261	1344	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255185.1	s__Parahaliea mediterranea_A	77.8321	266	1344	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008370495.1	s__Halioglobus sp008370495	77.7958	311	1344	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008064635.1	s__Parahaliea aestuarii	77.7156	272	1344	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002866825.1	s__Halioglobus lutimaris	77.5278	255	1344	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	98.98	98.98	0.91	0.91	2	-
GCA_009937575.1	s__Halioglobus sp009937575	77.4497	236	1344	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699145.1	s__Halioglobus sp002699145	77.0397	260	1344	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.96	99.96	0.98	0.98	2	-
GCA_002416125.1	s__Haliea sp002416125	76.776	161	1344	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	99.96	99.96	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:56:32,701] [INFO] GTDB search result was written to GCF_014652255.1_ASM1465225v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:56:32,702] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:56:32,708] [INFO] DFAST_QC result json was written to GCF_014652255.1_ASM1465225v1_genomic.fna/dqc_result.json
[2024-01-24 13:56:32,709] [INFO] DFAST_QC completed!
[2024-01-24 13:56:32,709] [INFO] Total running time: 0h1m18s