[2023-06-27 00:13:21,499] [INFO] DFAST_QC pipeline started.
[2023-06-27 00:13:21,536] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 00:13:21,536] [INFO] DQC Reference Directory: /var/lib/cwl/stg88f9ac6a-5363-4cdf-96a9-d499f44430f0/dqc_reference
[2023-06-27 00:13:23,981] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 00:13:23,982] [INFO] Task started: Prodigal
[2023-06-27 00:13:23,983] [INFO] Running command: gunzip -c /var/lib/cwl/stgd8b48fee-dc76-4a16-9db8-6f673c2c2974/GCA_002360435.1_ASM236043v1_genomic.fna.gz | prodigal -d GCA_002360435.1_ASM236043v1_genomic.fna/cds.fna -a GCA_002360435.1_ASM236043v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 00:13:30,469] [INFO] Task succeeded: Prodigal
[2023-06-27 00:13:30,470] [INFO] Task started: HMMsearch
[2023-06-27 00:13:30,470] [INFO] Running command: hmmsearch --tblout GCA_002360435.1_ASM236043v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg88f9ac6a-5363-4cdf-96a9-d499f44430f0/dqc_reference/reference_markers.hmm GCA_002360435.1_ASM236043v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 00:13:30,751] [INFO] Task succeeded: HMMsearch
[2023-06-27 00:13:30,754] [INFO] Found 6/6 markers.
[2023-06-27 00:13:30,800] [INFO] Query marker FASTA was written to GCA_002360435.1_ASM236043v1_genomic.fna/markers.fasta
[2023-06-27 00:13:30,801] [INFO] Task started: Blastn
[2023-06-27 00:13:30,801] [INFO] Running command: blastn -query GCA_002360435.1_ASM236043v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg88f9ac6a-5363-4cdf-96a9-d499f44430f0/dqc_reference/reference_markers.fasta -out GCA_002360435.1_ASM236043v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 00:13:31,494] [INFO] Task succeeded: Blastn
[2023-06-27 00:13:31,498] [INFO] Selected 17 target genomes.
[2023-06-27 00:13:31,498] [INFO] Target genome list was writen to GCA_002360435.1_ASM236043v1_genomic.fna/target_genomes.txt
[2023-06-27 00:13:31,505] [INFO] Task started: fastANI
[2023-06-27 00:13:31,505] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8b48fee-dc76-4a16-9db8-6f673c2c2974/GCA_002360435.1_ASM236043v1_genomic.fna.gz --refList GCA_002360435.1_ASM236043v1_genomic.fna/target_genomes.txt --output GCA_002360435.1_ASM236043v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 00:13:40,892] [INFO] Task succeeded: fastANI
[2023-06-27 00:13:40,892] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg88f9ac6a-5363-4cdf-96a9-d499f44430f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 00:13:40,892] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg88f9ac6a-5363-4cdf-96a9-d499f44430f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 00:13:40,901] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2023-06-27 00:13:40,901] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-27 00:13:40,901] [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
Idiomarina abyssalis	strain=KMM 227	GCA_900116625.1	86102	86102	type	True	97.6629	795	910	95	conclusive
Idiomarina abyssalis	strain=KMM 227	GCA_001294685.1	86102	86102	type	True	97.6593	795	910	95	conclusive
Idiomarina ramblicola	strain=R22	GCA_003987255.1	263724	263724	type	True	85.6601	686	910	95	below_threshold
Idiomarina loihiensis	strain=L2TR	GCA_000008465.1	135577	135577	type	True	84.6831	646	910	95	below_threshold
Idiomarina zobellii	strain=KMM 231	GCA_900100855.1	86103	86103	type	True	81.6917	420	910	95	below_threshold
Idiomarina zobellii	strain=KMM 231	GCA_001294745.1	86103	86103	type	True	81.5927	416	910	95	below_threshold
Idiomarina piscisalsi	strain=TPS4-2	GCA_003987095.1	1096243	1096243	type	True	80.7191	417	910	95	below_threshold
Idiomarina fontislapidosi	strain=F23	GCA_003987025.1	263723	263723	type	True	78.4376	118	910	95	below_threshold
Aliidiomarina halalkaliphila	strain=IM 1326	GCA_007096385.1	2593535	2593535	type	True	76.9423	52	910	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 00:13:40,908] [INFO] DFAST Taxonomy check result was written to GCA_002360435.1_ASM236043v1_genomic.fna/tc_result.tsv
[2023-06-27 00:13:40,908] [INFO] ===== Taxonomy check completed =====
[2023-06-27 00:13:40,909] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 00:13:40,909] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg88f9ac6a-5363-4cdf-96a9-d499f44430f0/dqc_reference/checkm_data
[2023-06-27 00:13:40,911] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 00:13:40,942] [INFO] Task started: CheckM
[2023-06-27 00:13:40,943] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002360435.1_ASM236043v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002360435.1_ASM236043v1_genomic.fna/checkm_input GCA_002360435.1_ASM236043v1_genomic.fna/checkm_result
[2023-06-27 00:14:06,368] [INFO] Task succeeded: CheckM
[2023-06-27 00:14:06,370] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 00:14:06,405] [INFO] ===== Completeness check finished =====
[2023-06-27 00:14:06,406] [INFO] ===== Start GTDB Search =====
[2023-06-27 00:14:06,406] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002360435.1_ASM236043v1_genomic.fna/markers.fasta)
[2023-06-27 00:14:06,407] [INFO] Task started: Blastn
[2023-06-27 00:14:06,407] [INFO] Running command: blastn -query GCA_002360435.1_ASM236043v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg88f9ac6a-5363-4cdf-96a9-d499f44430f0/dqc_reference/reference_markers_gtdb.fasta -out GCA_002360435.1_ASM236043v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 00:14:07,426] [INFO] Task succeeded: Blastn
[2023-06-27 00:14:07,433] [INFO] Selected 14 target genomes.
[2023-06-27 00:14:07,433] [INFO] Target genome list was writen to GCA_002360435.1_ASM236043v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 00:14:07,447] [INFO] Task started: fastANI
[2023-06-27 00:14:07,447] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8b48fee-dc76-4a16-9db8-6f673c2c2974/GCA_002360435.1_ASM236043v1_genomic.fna.gz --refList GCA_002360435.1_ASM236043v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002360435.1_ASM236043v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 00:14:16,285] [INFO] Task succeeded: fastANI
[2023-06-27 00:14:16,301] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 00:14:16,301] [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_900116625.1	s__Idiomarina abyssalis	97.6629	795	910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	97.70	97.34	0.91	0.79	25	conclusive
GCF_003987255.1	s__Idiomarina ramblicola	85.6601	686	910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000008465.1	s__Idiomarina loihiensis	84.673	646	910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	96.95	95.80	0.91	0.86	17	-
GCF_900100855.1	s__Idiomarina zobellii	81.6746	421	910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	96.93	96.27	0.89	0.85	9	-
GCF_002808045.1	s__Idiomarina sp002808045	80.9087	402	910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	96.72	96.72	0.95	0.95	2	-
GCF_003987095.1	s__Idiomarina piscisalsi	80.7191	417	910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362895.1	s__Idiomarina sp002729675	79.7219	227	910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	97.61	97.37	0.88	0.80	5	-
GCF_003226255.1	s__Idiomarina fontislapidosi	78.2803	119	910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-27 00:14:16,318] [INFO] GTDB search result was written to GCA_002360435.1_ASM236043v1_genomic.fna/result_gtdb.tsv
[2023-06-27 00:14:16,319] [INFO] ===== GTDB Search completed =====
[2023-06-27 00:14:16,331] [INFO] DFAST_QC result json was written to GCA_002360435.1_ASM236043v1_genomic.fna/dqc_result.json
[2023-06-27 00:14:16,331] [INFO] DFAST_QC completed!
[2023-06-27 00:14:16,331] [INFO] Total running time: 0h0m55s