[2024-01-24 13:01:26,560] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:26,562] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:26,562] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ff0ed8e-b721-4ee7-b47f-07786a76b5a1/dqc_reference
[2024-01-24 13:01:27,906] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:27,907] [INFO] Task started: Prodigal
[2024-01-24 13:01:27,907] [INFO] Running command: gunzip -c /var/lib/cwl/stg42f55e90-2e7b-4e3d-a247-5c4e07f548f2/GCF_008370495.1_ASM837049v1_genomic.fna.gz | prodigal -d GCF_008370495.1_ASM837049v1_genomic.fna/cds.fna -a GCF_008370495.1_ASM837049v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:42,643] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:42,643] [INFO] Task started: HMMsearch
[2024-01-24 13:01:42,643] [INFO] Running command: hmmsearch --tblout GCF_008370495.1_ASM837049v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ff0ed8e-b721-4ee7-b47f-07786a76b5a1/dqc_reference/reference_markers.hmm GCF_008370495.1_ASM837049v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:42,941] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:42,944] [INFO] Found 6/6 markers.
[2024-01-24 13:01:43,011] [INFO] Query marker FASTA was written to GCF_008370495.1_ASM837049v1_genomic.fna/markers.fasta
[2024-01-24 13:01:43,012] [INFO] Task started: Blastn
[2024-01-24 13:01:43,012] [INFO] Running command: blastn -query GCF_008370495.1_ASM837049v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ff0ed8e-b721-4ee7-b47f-07786a76b5a1/dqc_reference/reference_markers.fasta -out GCF_008370495.1_ASM837049v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:43,978] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:43,982] [INFO] Selected 19 target genomes.
[2024-01-24 13:01:43,982] [INFO] Target genome list was writen to GCF_008370495.1_ASM837049v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:44,025] [INFO] Task started: fastANI
[2024-01-24 13:01:44,025] [INFO] Running command: fastANI --query /var/lib/cwl/stg42f55e90-2e7b-4e3d-a247-5c4e07f548f2/GCF_008370495.1_ASM837049v1_genomic.fna.gz --refList GCF_008370495.1_ASM837049v1_genomic.fna/target_genomes.txt --output GCF_008370495.1_ASM837049v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:58,322] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:58,322] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ff0ed8e-b721-4ee7-b47f-07786a76b5a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:58,323] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ff0ed8e-b721-4ee7-b47f-07786a76b5a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:58,339] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:01:58,339] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:01:58,339] [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
Seongchinamella sediminis	strain=U0301	GCA_003457605.1	2283635	2283635	type	True	78.8811	528	1467	95	below_threshold
Pseudohalioglobus lutimaris	strain=HF004	GCA_002866825.1	1737061	1737061	type	True	78.6256	487	1467	95	below_threshold
Seongchinamella unica	strain=GH4-78	GCA_004354085.1	2547392	2547392	type	True	78.3131	480	1467	95	below_threshold
Parahaliea mediterranea	strain=DSM 21924	GCA_003402235.1	651086	651086	type	True	78.0864	332	1467	95	below_threshold
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	77.7646	313	1467	95	below_threshold
Haliea salexigens	strain=DSM 19537	GCA_000423125.1	287487	287487	type	True	77.762	197	1467	95	below_threshold
Halioglobus japonicus	strain=KCTC 23429	GCA_014652255.1	930805	930805	type	True	77.758	294	1467	95	below_threshold
Halioglobus japonicus	strain=S1-36	GCA_002869505.1	930805	930805	type	True	77.7213	299	1467	95	below_threshold
Halioglobus japonicus	strain=NBRC 107739	GCA_001983995.1	930805	930805	type	True	77.6982	299	1467	95	below_threshold
Parahaliea maris	strain=HSLHS9	GCA_008064665.1	2716870	2716870	type	True	77.6238	287	1467	95	below_threshold
Halioglobus maricola	strain=IMCC14385	GCA_009388985.1	2601894	2601894	type	True	77.393	295	1467	95	below_threshold
Spongiibacter thalassae	strain=KMU-166	GCA_012272835.1	2721624	2721624	type	True	76.3307	54	1467	95	below_threshold
Alcanivorax balearicus	strain=MACL04	GCA_025532145.1	413232	413232	type	True	76.2993	73	1467	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.2795	108	1467	95	below_threshold
Halomonas stenophila	strain=CECT 7744	GCA_014192275.1	795312	795312	type	True	76.2635	86	1467	95	below_threshold
Marinobacter bryozoorum	strain=DSM 15401	GCA_023156245.1	256324	256324	type	True	76.0715	72	1467	95	below_threshold
Pseudomonas aeruginosa	strain=CCUG 551	GCA_008801675.1	287	287	type	True	76.0222	111	1467	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_900167195.1	287	287	type	True	75.8069	117	1467	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	75.8008	80	1467	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:58,342] [INFO] DFAST Taxonomy check result was written to GCF_008370495.1_ASM837049v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:58,343] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:58,343] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:58,343] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ff0ed8e-b721-4ee7-b47f-07786a76b5a1/dqc_reference/checkm_data
[2024-01-24 13:01:58,345] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:58,395] [INFO] Task started: CheckM
[2024-01-24 13:01:58,395] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008370495.1_ASM837049v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008370495.1_ASM837049v1_genomic.fna/checkm_input GCF_008370495.1_ASM837049v1_genomic.fna/checkm_result
[2024-01-24 13:02:40,388] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:40,389] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:40,410] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:40,410] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:40,411] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008370495.1_ASM837049v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:40,411] [INFO] Task started: Blastn
[2024-01-24 13:02:40,411] [INFO] Running command: blastn -query GCF_008370495.1_ASM837049v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ff0ed8e-b721-4ee7-b47f-07786a76b5a1/dqc_reference/reference_markers_gtdb.fasta -out GCF_008370495.1_ASM837049v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:41,749] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:41,752] [INFO] Selected 14 target genomes.
[2024-01-24 13:02:41,752] [INFO] Target genome list was writen to GCF_008370495.1_ASM837049v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:41,776] [INFO] Task started: fastANI
[2024-01-24 13:02:41,777] [INFO] Running command: fastANI --query /var/lib/cwl/stg42f55e90-2e7b-4e3d-a247-5c4e07f548f2/GCF_008370495.1_ASM837049v1_genomic.fna.gz --refList GCF_008370495.1_ASM837049v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008370495.1_ASM837049v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:53,971] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:53,989] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:53,989] [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_008370495.1	s__Halioglobus sp008370495	100.0	1466	1467	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003457605.1	s__Halioglobus sediminis	78.8811	528	1467	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002866825.1	s__Halioglobus lutimaris	78.6175	488	1467	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	98.98	98.98	0.91	0.91	2	-
GCA_004354085.1	s__Halioglobus sp004354085	78.3211	479	1467	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	78.296	367	1467	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	78.054	335	1467	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699145.1	s__Halioglobus sp002699145	77.9209	379	1467	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.96	99.96	0.98	0.98	2	-
GCF_017255185.1	s__Parahaliea mediterranea_A	77.8876	353	1467	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937575.1	s__Halioglobus sp009937575	77.8754	339	1467	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423125.1	s__Haliea salexigens	77.744	199	1467	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	96.91	96.59	0.87	0.83	15	-
GCF_001983995.1	s__Halioglobus japonicus	77.6963	300	1467	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.41	98.25	0.97	0.92	4	-
GCF_008064665.1	s__Parahaliea maris	77.6221	288	1467	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002414665.1	s__Haliea sp002414665	77.4946	204	1467	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	99.89	99.89	0.97	0.97	2	-
GCF_009388985.1	s__Halioglobus maricola	77.3927	295	1467	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 13:02:53,991] [INFO] GTDB search result was written to GCF_008370495.1_ASM837049v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:53,992] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:54,000] [INFO] DFAST_QC result json was written to GCF_008370495.1_ASM837049v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:54,000] [INFO] DFAST_QC completed!
[2024-01-24 13:02:54,000] [INFO] Total running time: 0h1m27s