[2023-06-04 18:00:19,246] [INFO] DFAST_QC pipeline started.
[2023-06-04 18:00:19,248] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 18:00:19,248] [INFO] DQC Reference Directory: /var/lib/cwl/stga0516763-5d7f-4a37-b3c6-286aa935f4c8/dqc_reference
[2023-06-04 18:00:20,731] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 18:00:20,732] [INFO] Task started: Prodigal
[2023-06-04 18:00:20,732] [INFO] Running command: gunzip -c /var/lib/cwl/stg31fa5a49-4e52-47f6-9f3b-8bb15874ff8f/GCA_010028665.1_ASM1002866v1_genomic.fna.gz | prodigal -d GCA_010028665.1_ASM1002866v1_genomic.fna/cds.fna -a GCA_010028665.1_ASM1002866v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 18:00:22,701] [INFO] Task succeeded: Prodigal
[2023-06-04 18:00:22,702] [INFO] Task started: HMMsearch
[2023-06-04 18:00:22,702] [INFO] Running command: hmmsearch --tblout GCA_010028665.1_ASM1002866v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga0516763-5d7f-4a37-b3c6-286aa935f4c8/dqc_reference/reference_markers.hmm GCA_010028665.1_ASM1002866v1_genomic.fna/protein.faa > /dev/null
[2023-06-04 18:00:22,916] [INFO] Task succeeded: HMMsearch
[2023-06-04 18:00:22,917] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg31fa5a49-4e52-47f6-9f3b-8bb15874ff8f/GCA_010028665.1_ASM1002866v1_genomic.fna.gz]
[2023-06-04 18:00:22,931] [INFO] Query marker FASTA was written to GCA_010028665.1_ASM1002866v1_genomic.fna/markers.fasta
[2023-06-04 18:00:22,931] [INFO] Task started: Blastn
[2023-06-04 18:00:22,931] [INFO] Running command: blastn -query GCA_010028665.1_ASM1002866v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga0516763-5d7f-4a37-b3c6-286aa935f4c8/dqc_reference/reference_markers.fasta -out GCA_010028665.1_ASM1002866v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 18:00:23,574] [INFO] Task succeeded: Blastn
[2023-06-04 18:00:23,578] [INFO] Selected 22 target genomes.
[2023-06-04 18:00:23,578] [INFO] Target genome list was writen to GCA_010028665.1_ASM1002866v1_genomic.fna/target_genomes.txt
[2023-06-04 18:00:24,071] [INFO] Task started: fastANI
[2023-06-04 18:00:24,072] [INFO] Running command: fastANI --query /var/lib/cwl/stg31fa5a49-4e52-47f6-9f3b-8bb15874ff8f/GCA_010028665.1_ASM1002866v1_genomic.fna.gz --refList GCA_010028665.1_ASM1002866v1_genomic.fna/target_genomes.txt --output GCA_010028665.1_ASM1002866v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 18:00:32,944] [INFO] Task succeeded: fastANI
[2023-06-04 18:00:32,944] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga0516763-5d7f-4a37-b3c6-286aa935f4c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 18:00:32,944] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga0516763-5d7f-4a37-b3c6-286aa935f4c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 18:00:32,946] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 18:00:32,946] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 18:00:32,947] [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
--------------------------------------------------------------------------------
[2023-06-04 18:00:32,949] [INFO] DFAST Taxonomy check result was written to GCA_010028665.1_ASM1002866v1_genomic.fna/tc_result.tsv
[2023-06-04 18:00:32,950] [INFO] ===== Taxonomy check completed =====
[2023-06-04 18:00:32,950] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 18:00:32,951] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga0516763-5d7f-4a37-b3c6-286aa935f4c8/dqc_reference/checkm_data
[2023-06-04 18:00:32,954] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 18:00:32,970] [INFO] Task started: CheckM
[2023-06-04 18:00:32,970] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_010028665.1_ASM1002866v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_010028665.1_ASM1002866v1_genomic.fna/checkm_input GCA_010028665.1_ASM1002866v1_genomic.fna/checkm_result
[2023-06-04 18:00:49,222] [INFO] Task succeeded: CheckM
[2023-06-04 18:00:49,224] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.70%
Contamintation: 2.89%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 18:00:49,248] [INFO] ===== Completeness check finished =====
[2023-06-04 18:00:49,249] [INFO] ===== Start GTDB Search =====
[2023-06-04 18:00:49,249] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_010028665.1_ASM1002866v1_genomic.fna/markers.fasta)
[2023-06-04 18:00:49,250] [INFO] Task started: Blastn
[2023-06-04 18:00:49,250] [INFO] Running command: blastn -query GCA_010028665.1_ASM1002866v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga0516763-5d7f-4a37-b3c6-286aa935f4c8/dqc_reference/reference_markers_gtdb.fasta -out GCA_010028665.1_ASM1002866v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 18:00:50,065] [INFO] Task succeeded: Blastn
[2023-06-04 18:00:50,070] [INFO] Selected 12 target genomes.
[2023-06-04 18:00:50,070] [INFO] Target genome list was writen to GCA_010028665.1_ASM1002866v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 18:00:50,161] [INFO] Task started: fastANI
[2023-06-04 18:00:50,161] [INFO] Running command: fastANI --query /var/lib/cwl/stg31fa5a49-4e52-47f6-9f3b-8bb15874ff8f/GCA_010028665.1_ASM1002866v1_genomic.fna.gz --refList GCA_010028665.1_ASM1002866v1_genomic.fna/target_genomes_gtdb.txt --output GCA_010028665.1_ASM1002866v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 18:00:53,569] [INFO] Task succeeded: fastANI
[2023-06-04 18:00:53,579] [INFO] Found 8 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-04 18:00:53,579] [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_002688585.1	s__Fonsibacter ubiquis	97.8257	152	155	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Fonsibacter	95.0	97.79	97.41	0.98	0.94	23	inconclusive
GCA_016882185.1	s__Fonsibacter sp016882185	95.3874	106	155	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Fonsibacter	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_000371845.1	s__Fonsibacter sp000371845	85.9385	90	155	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Fonsibacter	95.0	95.54	95.54	0.55	0.55	2	-
GCA_018882565.1	s__Fonsibacter sp018882565	85.4427	130	155	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Fonsibacter	95.0	96.85	95.99	0.76	0.70	5	-
GCA_010021145.1	s__Fonsibacter lacus_A	85.1036	98	155	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Fonsibacter	95.0	99.30	99.10	0.81	0.79	3	-
GCA_009693745.1	s__Fonsibacter sp009693745	84.8589	129	155	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Fonsibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018658635.1	s__Fonsibacter sp018658635	84.7768	115	155	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Fonsibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000510845.1	s__Fonsibacter sp000510845	84.7463	107	155	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Fonsibacter	95.0	95.98	95.03	0.69	0.68	4	-
--------------------------------------------------------------------------------
[2023-06-04 18:00:53,581] [INFO] GTDB search result was written to GCA_010028665.1_ASM1002866v1_genomic.fna/result_gtdb.tsv
[2023-06-04 18:00:53,582] [INFO] ===== GTDB Search completed =====
[2023-06-04 18:00:53,584] [INFO] DFAST_QC result json was written to GCA_010028665.1_ASM1002866v1_genomic.fna/dqc_result.json
[2023-06-04 18:00:53,585] [INFO] DFAST_QC completed!
[2023-06-04 18:00:53,585] [INFO] Total running time: 0h0m34s