[2024-01-25 20:25:50,486] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:25:50,487] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:25:50,487] [INFO] DQC Reference Directory: /var/lib/cwl/stg332a09da-db79-442c-bd31-76f0396836a5/dqc_reference
[2024-01-25 20:25:51,719] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:25:51,719] [INFO] Task started: Prodigal
[2024-01-25 20:25:51,720] [INFO] Running command: gunzip -c /var/lib/cwl/stg2666f24f-c859-423a-abab-2bee3fa4a310/GCF_000153125.2_ASM15312v2_genomic.fna.gz | prodigal -d GCF_000153125.2_ASM15312v2_genomic.fna/cds.fna -a GCF_000153125.2_ASM15312v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:26:03,673] [INFO] Task succeeded: Prodigal
[2024-01-25 20:26:03,673] [INFO] Task started: HMMsearch
[2024-01-25 20:26:03,673] [INFO] Running command: hmmsearch --tblout GCF_000153125.2_ASM15312v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg332a09da-db79-442c-bd31-76f0396836a5/dqc_reference/reference_markers.hmm GCF_000153125.2_ASM15312v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:26:03,941] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:26:03,942] [INFO] Found 6/6 markers.
[2024-01-25 20:26:03,978] [INFO] Query marker FASTA was written to GCF_000153125.2_ASM15312v2_genomic.fna/markers.fasta
[2024-01-25 20:26:03,978] [INFO] Task started: Blastn
[2024-01-25 20:26:03,979] [INFO] Running command: blastn -query GCF_000153125.2_ASM15312v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg332a09da-db79-442c-bd31-76f0396836a5/dqc_reference/reference_markers.fasta -out GCF_000153125.2_ASM15312v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:26:04,585] [INFO] Task succeeded: Blastn
[2024-01-25 20:26:04,588] [INFO] Selected 40 target genomes.
[2024-01-25 20:26:04,589] [INFO] Target genome list was writen to GCF_000153125.2_ASM15312v2_genomic.fna/target_genomes.txt
[2024-01-25 20:26:04,639] [INFO] Task started: fastANI
[2024-01-25 20:26:04,640] [INFO] Running command: fastANI --query /var/lib/cwl/stg2666f24f-c859-423a-abab-2bee3fa4a310/GCF_000153125.2_ASM15312v2_genomic.fna.gz --refList GCF_000153125.2_ASM15312v2_genomic.fna/target_genomes.txt --output GCF_000153125.2_ASM15312v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:26:32,780] [INFO] Task succeeded: fastANI
[2024-01-25 20:26:32,781] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg332a09da-db79-442c-bd31-76f0396836a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:26:32,781] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg332a09da-db79-442c-bd31-76f0396836a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:26:32,790] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:26:32,790] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:26:32,790] [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
Congregibacter litoralis	strain=KT71	GCA_000153125.2	393662	393662	type	True	100.0	1450	1450	95	conclusive
Seongchinamella unica	strain=GH4-78	GCA_004354085.1	2547392	2547392	type	True	78.6769	124	1450	95	below_threshold
Halioglobus maricola	strain=IMCC14385	GCA_009388985.1	2601894	2601894	type	True	77.0744	85	1450	95	below_threshold
Halioglobus japonicus	strain=NBRC 107739	GCA_001983995.1	930805	930805	type	True	76.9977	92	1450	95	below_threshold
Parahaliea mediterranea	strain=DSM 21924	GCA_003402235.1	651086	651086	type	True	76.9398	165	1450	95	below_threshold
Halioglobus pacificus	strain=KCTC 23430	GCA_014652275.1	930806	930806	type	True	76.7416	92	1450	95	below_threshold
Seongchinamella sediminis	strain=U0301	GCA_003457605.1	2283635	2283635	type	True	76.7287	130	1450	95	below_threshold
Pseudohaliea rubra	strain=DSM 19751	GCA_000764025.1	475795	475795	type	True	76.7063	137	1450	95	below_threshold
Microbulbifer taiwanensis	strain=LMG 26125	GCA_014904815.1	986746	986746	type	True	76.7058	53	1450	95	below_threshold
Pseudohalioglobus lutimaris	strain=HF004	GCA_002866825.1	1737061	1737061	type	True	76.5548	93	1450	95	below_threshold
Halioglobus japonicus	strain=KCTC 23429	GCA_014652255.1	930805	930805	type	True	76.4734	88	1450	95	below_threshold
Halioglobus japonicus	strain=S1-36	GCA_002869505.1	930805	930805	type	True	76.4061	91	1450	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	75.893	56	1450	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:26:32,792] [INFO] DFAST Taxonomy check result was written to GCF_000153125.2_ASM15312v2_genomic.fna/tc_result.tsv
[2024-01-25 20:26:32,792] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:26:32,792] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:26:32,793] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg332a09da-db79-442c-bd31-76f0396836a5/dqc_reference/checkm_data
[2024-01-25 20:26:32,793] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:26:32,834] [INFO] Task started: CheckM
[2024-01-25 20:26:32,834] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000153125.2_ASM15312v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000153125.2_ASM15312v2_genomic.fna/checkm_input GCF_000153125.2_ASM15312v2_genomic.fna/checkm_result
[2024-01-25 20:27:09,627] [INFO] Task succeeded: CheckM
[2024-01-25 20:27:09,628] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:27:09,644] [INFO] ===== Completeness check finished =====
[2024-01-25 20:27:09,644] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:27:09,644] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000153125.2_ASM15312v2_genomic.fna/markers.fasta)
[2024-01-25 20:27:09,645] [INFO] Task started: Blastn
[2024-01-25 20:27:09,645] [INFO] Running command: blastn -query GCF_000153125.2_ASM15312v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg332a09da-db79-442c-bd31-76f0396836a5/dqc_reference/reference_markers_gtdb.fasta -out GCF_000153125.2_ASM15312v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:27:10,561] [INFO] Task succeeded: Blastn
[2024-01-25 20:27:10,564] [INFO] Selected 30 target genomes.
[2024-01-25 20:27:10,564] [INFO] Target genome list was writen to GCF_000153125.2_ASM15312v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:27:10,598] [INFO] Task started: fastANI
[2024-01-25 20:27:10,598] [INFO] Running command: fastANI --query /var/lib/cwl/stg2666f24f-c859-423a-abab-2bee3fa4a310/GCF_000153125.2_ASM15312v2_genomic.fna.gz --refList GCF_000153125.2_ASM15312v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000153125.2_ASM15312v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:27:33,898] [INFO] Task succeeded: fastANI
[2024-01-25 20:27:33,909] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:27:33,910] [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_000153125.2	s__Congregibacter litoralis	100.0	1450	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Congregibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000423125.1	s__Haliea salexigens	79.0279	124	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	96.91	96.59	0.87	0.83	15	-
GCA_000158155.1	s__Congregibacter sp000158155	78.7345	463	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Congregibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004354085.1	s__Halioglobus sp004354085	78.6769	124	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010669285.1	s__Kineobactrum salinum	77.3106	96	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Kineobactrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009903625.1	s__Microbulbifer sp009903625	77.1122	51	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002428935.1	s__Congregibacter sp002428935	77.0859	169	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Congregibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001983995.1	s__Halioglobus japonicus	77.0664	93	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.41	98.25	0.97	0.92	4	-
GCF_009189165.1	s__Pseudomonas sp009189165	77.0371	53	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003402235.1	s__Parahaliea mediterranea	76.9398	165	1450	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	76.7727	104	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255185.1	s__Parahaliea mediterranea_A	76.7669	137	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003457605.1	s__Halioglobus sediminis	76.7287	130	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000764025.1	s__Pseudohaliea rubra	76.7063	137	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Pseudohaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904815.1	s__Microbulbifer taiwanensis	76.6638	54	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002866825.1	s__Halioglobus lutimaris	76.5314	94	1450	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	76.3432	85	1450	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	76.2817	130	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:27:33,911] [INFO] GTDB search result was written to GCF_000153125.2_ASM15312v2_genomic.fna/result_gtdb.tsv
[2024-01-25 20:27:33,911] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:27:33,914] [INFO] DFAST_QC result json was written to GCF_000153125.2_ASM15312v2_genomic.fna/dqc_result.json
[2024-01-25 20:27:33,914] [INFO] DFAST_QC completed!
[2024-01-25 20:27:33,914] [INFO] Total running time: 0h1m43s