[2023-03-19 00:15:41,732] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:15:41,735] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:15:41,735] [INFO] DQC Reference Directory: /var/lib/cwl/stg60c04700-e395-464f-8344-aff31b0ee1ea/dqc_reference
[2023-03-19 00:15:43,440] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:15:43,440] [INFO] Task started: Prodigal
[2023-03-19 00:15:43,440] [INFO] Running command: cat /var/lib/cwl/stgac6a01e8-7557-4ae7-a9a3-52bd15d8ed18/OceanDNA-b34234.fa | prodigal -d OceanDNA-b34234/cds.fna -a OceanDNA-b34234/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:15:58,480] [INFO] Task succeeded: Prodigal
[2023-03-19 00:15:58,480] [INFO] Task started: HMMsearch
[2023-03-19 00:15:58,480] [INFO] Running command: hmmsearch --tblout OceanDNA-b34234/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg60c04700-e395-464f-8344-aff31b0ee1ea/dqc_reference/reference_markers.hmm OceanDNA-b34234/protein.faa > /dev/null
[2023-03-19 00:15:58,694] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:15:58,695] [INFO] Found 6/6 markers.
[2023-03-19 00:15:58,711] [INFO] Query marker FASTA was written to OceanDNA-b34234/markers.fasta
[2023-03-19 00:15:58,712] [INFO] Task started: Blastn
[2023-03-19 00:15:58,712] [INFO] Running command: blastn -query OceanDNA-b34234/markers.fasta -db /var/lib/cwl/stg60c04700-e395-464f-8344-aff31b0ee1ea/dqc_reference/reference_markers.fasta -out OceanDNA-b34234/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:15:59,311] [INFO] Task succeeded: Blastn
[2023-03-19 00:15:59,312] [INFO] Selected 28 target genomes.
[2023-03-19 00:15:59,312] [INFO] Target genome list was writen to OceanDNA-b34234/target_genomes.txt
[2023-03-19 00:15:59,330] [INFO] Task started: fastANI
[2023-03-19 00:15:59,330] [INFO] Running command: fastANI --query /var/lib/cwl/stgac6a01e8-7557-4ae7-a9a3-52bd15d8ed18/OceanDNA-b34234.fa --refList OceanDNA-b34234/target_genomes.txt --output OceanDNA-b34234/fastani_result.tsv --threads 1
[2023-03-19 00:16:16,677] [INFO] Task succeeded: fastANI
[2023-03-19 00:16:16,677] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg60c04700-e395-464f-8344-aff31b0ee1ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:16:16,678] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg60c04700-e395-464f-8344-aff31b0ee1ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:16:16,682] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:16:16,682] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 00:16:16,682] [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
Sedimenticola thiotaurini	strain=SIP-G1	GCA_001007875.1	1543721	1543721	type	True	76.4129	63	849	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:16:16,683] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34234/tc_result.tsv
[2023-03-19 00:16:16,683] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:16:16,683] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:16:16,683] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg60c04700-e395-464f-8344-aff31b0ee1ea/dqc_reference/checkm_data
[2023-03-19 00:16:16,685] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:16:16,766] [INFO] Task started: CheckM
[2023-03-19 00:16:16,766] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34234/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34234/checkm_input OceanDNA-b34234/checkm_result
[2023-03-19 00:16:55,829] [INFO] Task succeeded: CheckM
[2023-03-19 00:16:55,829] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.35%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:16:55,831] [INFO] ===== Completeness check finished =====
[2023-03-19 00:16:55,831] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:16:55,832] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34234/markers.fasta)
[2023-03-19 00:16:55,833] [INFO] Task started: Blastn
[2023-03-19 00:16:55,833] [INFO] Running command: blastn -query OceanDNA-b34234/markers.fasta -db /var/lib/cwl/stg60c04700-e395-464f-8344-aff31b0ee1ea/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34234/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:16:56,804] [INFO] Task succeeded: Blastn
[2023-03-19 00:16:56,805] [INFO] Selected 32 target genomes.
[2023-03-19 00:16:56,806] [INFO] Target genome list was writen to OceanDNA-b34234/target_genomes_gtdb.txt
[2023-03-19 00:16:56,834] [INFO] Task started: fastANI
[2023-03-19 00:16:56,834] [INFO] Running command: fastANI --query /var/lib/cwl/stgac6a01e8-7557-4ae7-a9a3-52bd15d8ed18/OceanDNA-b34234.fa --refList OceanDNA-b34234/target_genomes_gtdb.txt --output OceanDNA-b34234/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:17:13,421] [INFO] Task succeeded: fastANI
[2023-03-19 00:17:13,425] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 00:17:13,426] [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
GCA_015490795.1	s__DRKS01 sp015490795	76.479	51	849	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__DRKS01	95.0	99.53	99.46	0.94	0.93	5	-
GCA_003676145.1	s__Thiodiazotropha endolucinida	76.4339	50	849	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	97.91	96.39	0.93	0.89	26	-
GCF_001007875.1	s__Sedimenticola thiotaurini	76.4129	63	849	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Sedimenticola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003062205.1	s__Sedimenticola_A endophacoides	76.1824	51	849	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Sedimenticola_A	95.0	99.88	99.76	0.97	0.95	6	-
GCF_007625115.1	s__Sedimenticola selenatireducens_A	76.1162	51	849	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Sedimenticola	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002869585.1	s__BM503 sp002869585	76.0293	63	849	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__BM503	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:17:13,426] [INFO] GTDB search result was written to OceanDNA-b34234/result_gtdb.tsv
[2023-03-19 00:17:13,426] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:17:13,427] [INFO] DFAST_QC result json was written to OceanDNA-b34234/dqc_result.json
[2023-03-19 00:17:13,428] [INFO] DFAST_QC completed!
[2023-03-19 00:17:13,428] [INFO] Total running time: 0h1m32s