[2024-01-24 12:36:57,472] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:57,474] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:57,474] [INFO] DQC Reference Directory: /var/lib/cwl/stgb0598330-8b30-42c2-ab9f-853ad6b0ef69/dqc_reference
[2024-01-24 12:36:58,916] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:58,917] [INFO] Task started: Prodigal
[2024-01-24 12:36:58,917] [INFO] Running command: gunzip -c /var/lib/cwl/stgbef2eecd-fb8e-479e-a5bb-5f92d7e16f33/GCF_014652055.1_ASM1465205v1_genomic.fna.gz | prodigal -d GCF_014652055.1_ASM1465205v1_genomic.fna/cds.fna -a GCF_014652055.1_ASM1465205v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:09,168] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:09,169] [INFO] Task started: HMMsearch
[2024-01-24 12:37:09,169] [INFO] Running command: hmmsearch --tblout GCF_014652055.1_ASM1465205v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb0598330-8b30-42c2-ab9f-853ad6b0ef69/dqc_reference/reference_markers.hmm GCF_014652055.1_ASM1465205v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:09,472] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:09,473] [INFO] Found 6/6 markers.
[2024-01-24 12:37:09,508] [INFO] Query marker FASTA was written to GCF_014652055.1_ASM1465205v1_genomic.fna/markers.fasta
[2024-01-24 12:37:09,508] [INFO] Task started: Blastn
[2024-01-24 12:37:09,508] [INFO] Running command: blastn -query GCF_014652055.1_ASM1465205v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0598330-8b30-42c2-ab9f-853ad6b0ef69/dqc_reference/reference_markers.fasta -out GCF_014652055.1_ASM1465205v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:10,471] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:10,474] [INFO] Selected 13 target genomes.
[2024-01-24 12:37:10,474] [INFO] Target genome list was writen to GCF_014652055.1_ASM1465205v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:10,485] [INFO] Task started: fastANI
[2024-01-24 12:37:10,486] [INFO] Running command: fastANI --query /var/lib/cwl/stgbef2eecd-fb8e-479e-a5bb-5f92d7e16f33/GCF_014652055.1_ASM1465205v1_genomic.fna.gz --refList GCF_014652055.1_ASM1465205v1_genomic.fna/target_genomes.txt --output GCF_014652055.1_ASM1465205v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:22,726] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:22,726] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb0598330-8b30-42c2-ab9f-853ad6b0ef69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:22,727] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb0598330-8b30-42c2-ab9f-853ad6b0ef69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:22,739] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:37:22,739] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:22,739] [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
Oceanisphaera arctica	strain=KCTC 23013	GCA_014652055.1	641510	641510	type	True	100.0	1158	1161	95	conclusive
Oceanisphaera arctica	strain=V1-41	GCA_002936955.1	641510	641510	type	True	99.9483	1103	1161	95	conclusive
Oceanisphaera litoralis	strain=DSM 15406	GCA_016907015.1	225144	225144	type	True	89.8141	842	1161	95	below_threshold
Oceanisphaera psychrotolerans	strain=LAM-WHM-ZC	GCA_001870485.1	1414654	1414654	type	True	87.4629	904	1161	95	below_threshold
Zobellella endophytica	strain=59N8	GCA_003012775.1	2116700	2116700	type	True	82.5402	746	1161	95	below_threshold
Zobellella denitrificans	strain=ZD1	GCA_002237365.1	347534	347534	type	True	82.5078	727	1161	95	below_threshold
Oceanisphaera marina	strain=CGMCC 1.15923	GCA_014643915.1	2017550	2017550	type	True	81.7022	691	1161	95	below_threshold
Oceanimonas smirnovii	strain=ATCC BAA-899	GCA_000381965.1	264574	264574	type	True	80.4207	577	1161	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	76.3937	121	1161	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	76.3687	116	1161	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.3639	145	1161	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.1876	119	1161	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	75.9234	101	1161	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:22,741] [INFO] DFAST Taxonomy check result was written to GCF_014652055.1_ASM1465205v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:22,742] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:22,742] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:22,742] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb0598330-8b30-42c2-ab9f-853ad6b0ef69/dqc_reference/checkm_data
[2024-01-24 12:37:22,744] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:22,781] [INFO] Task started: CheckM
[2024-01-24 12:37:22,782] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014652055.1_ASM1465205v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014652055.1_ASM1465205v1_genomic.fna/checkm_input GCF_014652055.1_ASM1465205v1_genomic.fna/checkm_result
[2024-01-24 12:37:59,189] [INFO] Task succeeded: CheckM
[2024-01-24 12:37:59,190] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.75%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:37:59,210] [INFO] ===== Completeness check finished =====
[2024-01-24 12:37:59,211] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:37:59,211] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014652055.1_ASM1465205v1_genomic.fna/markers.fasta)
[2024-01-24 12:37:59,212] [INFO] Task started: Blastn
[2024-01-24 12:37:59,212] [INFO] Running command: blastn -query GCF_014652055.1_ASM1465205v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0598330-8b30-42c2-ab9f-853ad6b0ef69/dqc_reference/reference_markers_gtdb.fasta -out GCF_014652055.1_ASM1465205v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:00,685] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:00,688] [INFO] Selected 8 target genomes.
[2024-01-24 12:38:00,688] [INFO] Target genome list was writen to GCF_014652055.1_ASM1465205v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:00,701] [INFO] Task started: fastANI
[2024-01-24 12:38:00,701] [INFO] Running command: fastANI --query /var/lib/cwl/stgbef2eecd-fb8e-479e-a5bb-5f92d7e16f33/GCF_014652055.1_ASM1465205v1_genomic.fna.gz --refList GCF_014652055.1_ASM1465205v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014652055.1_ASM1465205v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:09,062] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:09,069] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:09,070] [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_002936955.1	s__Oceanisphaera arctica	99.9483	1103	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanisphaera	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_016907015.1	s__Oceanisphaera litoralis	89.8141	842	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222825.1	s__Oceanisphaera sp018222825	87.6802	685	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001870485.1	s__Oceanisphaera psychrotolerans	87.4629	904	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016746085.1	s__CGMCC-1-18722 sp016746085	82.5795	784	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__CGMCC-1-18722	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003012775.1	s__Zobellella_C endophytica	82.517	749	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Zobellella_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002237365.1	s__Zobellella denitrificans	82.4979	728	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Zobellella	95.0	98.78	98.78	0.93	0.93	2	-
GCF_014643915.1	s__Oceanisphaera marina	81.6805	694	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanisphaera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:09,071] [INFO] GTDB search result was written to GCF_014652055.1_ASM1465205v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:09,072] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:09,075] [INFO] DFAST_QC result json was written to GCF_014652055.1_ASM1465205v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:09,076] [INFO] DFAST_QC completed!
[2024-01-24 12:38:09,076] [INFO] Total running time: 0h1m12s