[2023-03-18 02:02:52,817] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:02:52,817] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:02:52,817] [INFO] DQC Reference Directory: /var/lib/cwl/stgda888e9a-5b22-4834-837d-cd287456fd2b/dqc_reference
[2023-03-18 02:02:53,934] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:02:53,934] [INFO] Task started: Prodigal
[2023-03-18 02:02:53,934] [INFO] Running command: cat /var/lib/cwl/stgab9e8d54-366e-4492-82ab-d7a20287819a/OceanDNA-b17731.fa | prodigal -d OceanDNA-b17731/cds.fna -a OceanDNA-b17731/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:03:17,024] [INFO] Task succeeded: Prodigal
[2023-03-18 02:03:17,024] [INFO] Task started: HMMsearch
[2023-03-18 02:03:17,024] [INFO] Running command: hmmsearch --tblout OceanDNA-b17731/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgda888e9a-5b22-4834-837d-cd287456fd2b/dqc_reference/reference_markers.hmm OceanDNA-b17731/protein.faa > /dev/null
[2023-03-18 02:03:17,247] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:03:17,247] [INFO] Found 6/6 markers.
[2023-03-18 02:03:17,275] [INFO] Query marker FASTA was written to OceanDNA-b17731/markers.fasta
[2023-03-18 02:03:17,276] [INFO] Task started: Blastn
[2023-03-18 02:03:17,276] [INFO] Running command: blastn -query OceanDNA-b17731/markers.fasta -db /var/lib/cwl/stgda888e9a-5b22-4834-837d-cd287456fd2b/dqc_reference/reference_markers.fasta -out OceanDNA-b17731/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:03:17,831] [INFO] Task succeeded: Blastn
[2023-03-18 02:03:17,833] [INFO] Selected 36 target genomes.
[2023-03-18 02:03:17,834] [INFO] Target genome list was writen to OceanDNA-b17731/target_genomes.txt
[2023-03-18 02:03:17,855] [INFO] Task started: fastANI
[2023-03-18 02:03:17,855] [INFO] Running command: fastANI --query /var/lib/cwl/stgab9e8d54-366e-4492-82ab-d7a20287819a/OceanDNA-b17731.fa --refList OceanDNA-b17731/target_genomes.txt --output OceanDNA-b17731/fastani_result.tsv --threads 1
[2023-03-18 02:03:45,850] [INFO] Task succeeded: fastANI
[2023-03-18 02:03:45,851] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgda888e9a-5b22-4834-837d-cd287456fd2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:03:45,851] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgda888e9a-5b22-4834-837d-cd287456fd2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:03:45,854] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:03:45,854] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 02:03:45,854] [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
Archangium violaceum	strain=Cb vi76	GCA_000733295.1	83451	83451	type	True	74.9466	57	1301	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 02:03:45,855] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17731/tc_result.tsv
[2023-03-18 02:03:45,855] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:03:45,855] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:03:45,855] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgda888e9a-5b22-4834-837d-cd287456fd2b/dqc_reference/checkm_data
[2023-03-18 02:03:45,856] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:03:45,862] [INFO] Task started: CheckM
[2023-03-18 02:03:45,862] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17731/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17731/checkm_input OceanDNA-b17731/checkm_result
[2023-03-18 02:04:42,864] [INFO] Task succeeded: CheckM
[2023-03-18 02:04:42,864] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 02:04:42,867] [INFO] ===== Completeness check finished =====
[2023-03-18 02:04:42,867] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:04:42,867] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17731/markers.fasta)
[2023-03-18 02:04:42,869] [INFO] Task started: Blastn
[2023-03-18 02:04:42,869] [INFO] Running command: blastn -query OceanDNA-b17731/markers.fasta -db /var/lib/cwl/stgda888e9a-5b22-4834-837d-cd287456fd2b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17731/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:04:43,719] [INFO] Task succeeded: Blastn
[2023-03-18 02:04:43,720] [INFO] Selected 31 target genomes.
[2023-03-18 02:04:43,720] [INFO] Target genome list was writen to OceanDNA-b17731/target_genomes_gtdb.txt
[2023-03-18 02:04:43,747] [INFO] Task started: fastANI
[2023-03-18 02:04:43,748] [INFO] Running command: fastANI --query /var/lib/cwl/stgab9e8d54-366e-4492-82ab-d7a20287819a/OceanDNA-b17731.fa --refList OceanDNA-b17731/target_genomes_gtdb.txt --output OceanDNA-b17731/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:05:03,892] [INFO] Task succeeded: fastANI
[2023-03-18 02:05:03,898] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 02:05:03,898] [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_002725915.1	s__GCA-2725915 sp002725915	96.5286	806	1301	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2725915	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016867395.1	s__SICG01 sp016867395	76.4184	146	1301	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__SICG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002712305.1	s__UBA12574 sp002712305	76.1319	73	1301	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__UBA12574	95.0	98.27	97.81	0.83	0.79	3	-
GCA_009691525.1	s__SICG01 sp009691525	76.0814	106	1301	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__SICG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018673255.1	s__UBA12574 sp018673255	75.8979	82	1301	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__UBA12574	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002726335.1	s__UBA8231 sp002726335	75.8865	129	1301	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__UBA8231	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002724215.1	s__GCA-2724215 sp002724215	75.7609	119	1301	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903893785.1	s__CAITNQ01 sp903893785	75.6033	88	1301	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__CAITNQ01	95.0	99.57	99.57	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-03-18 02:05:03,898] [INFO] GTDB search result was written to OceanDNA-b17731/result_gtdb.tsv
[2023-03-18 02:05:03,898] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:05:03,899] [INFO] DFAST_QC result json was written to OceanDNA-b17731/dqc_result.json
[2023-03-18 02:05:03,899] [INFO] DFAST_QC completed!
[2023-03-18 02:05:03,899] [INFO] Total running time: 0h2m11s