[2023-03-18 04:24:34,129] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:24:34,131] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:24:34,131] [INFO] DQC Reference Directory: /var/lib/cwl/stge72fd983-36c8-4461-9c78-c5866f650823/dqc_reference
[2023-03-18 04:24:35,782] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:24:35,782] [INFO] Task started: Prodigal
[2023-03-18 04:24:35,783] [INFO] Running command: cat /var/lib/cwl/stg9ef81556-d7ec-4fdf-847a-7c3e05f2327a/OceanDNA-b10387.fa | prodigal -d OceanDNA-b10387/cds.fna -a OceanDNA-b10387/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:24:43,038] [INFO] Task succeeded: Prodigal
[2023-03-18 04:24:43,039] [INFO] Task started: HMMsearch
[2023-03-18 04:24:43,039] [INFO] Running command: hmmsearch --tblout OceanDNA-b10387/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge72fd983-36c8-4461-9c78-c5866f650823/dqc_reference/reference_markers.hmm OceanDNA-b10387/protein.faa > /dev/null
[2023-03-18 04:24:43,210] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:24:43,211] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9ef81556-d7ec-4fdf-847a-7c3e05f2327a/OceanDNA-b10387.fa]
[2023-03-18 04:24:43,230] [INFO] Query marker FASTA was written to OceanDNA-b10387/markers.fasta
[2023-03-18 04:24:43,230] [INFO] Task started: Blastn
[2023-03-18 04:24:43,230] [INFO] Running command: blastn -query OceanDNA-b10387/markers.fasta -db /var/lib/cwl/stge72fd983-36c8-4461-9c78-c5866f650823/dqc_reference/reference_markers.fasta -out OceanDNA-b10387/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:24:43,789] [INFO] Task succeeded: Blastn
[2023-03-18 04:24:43,792] [INFO] Selected 20 target genomes.
[2023-03-18 04:24:43,792] [INFO] Target genome list was writen to OceanDNA-b10387/target_genomes.txt
[2023-03-18 04:24:43,806] [INFO] Task started: fastANI
[2023-03-18 04:24:43,806] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ef81556-d7ec-4fdf-847a-7c3e05f2327a/OceanDNA-b10387.fa --refList OceanDNA-b10387/target_genomes.txt --output OceanDNA-b10387/fastani_result.tsv --threads 1
[2023-03-18 04:24:55,102] [INFO] Task succeeded: fastANI
[2023-03-18 04:24:55,103] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge72fd983-36c8-4461-9c78-c5866f650823/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:24:55,103] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge72fd983-36c8-4461-9c78-c5866f650823/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:24:55,103] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 04:24:55,103] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 04:24:55,103] [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
--------------------------------------------------------------------------------
[2023-03-18 04:24:55,106] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10387/tc_result.tsv
[2023-03-18 04:24:55,108] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:24:55,108] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:24:55,108] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge72fd983-36c8-4461-9c78-c5866f650823/dqc_reference/checkm_data
[2023-03-18 04:24:55,111] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:24:55,121] [INFO] Task started: CheckM
[2023-03-18 04:24:55,121] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10387/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10387/checkm_input OceanDNA-b10387/checkm_result
[2023-03-18 04:25:19,005] [INFO] Task succeeded: CheckM
[2023-03-18 04:25:19,005] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.66%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 04:25:19,168] [INFO] ===== Completeness check finished =====
[2023-03-18 04:25:19,168] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:25:19,168] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10387/markers.fasta)
[2023-03-18 04:25:19,169] [INFO] Task started: Blastn
[2023-03-18 04:25:19,169] [INFO] Running command: blastn -query OceanDNA-b10387/markers.fasta -db /var/lib/cwl/stge72fd983-36c8-4461-9c78-c5866f650823/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10387/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:25:20,118] [INFO] Task succeeded: Blastn
[2023-03-18 04:25:20,146] [INFO] Selected 8 target genomes.
[2023-03-18 04:25:20,146] [INFO] Target genome list was writen to OceanDNA-b10387/target_genomes_gtdb.txt
[2023-03-18 04:25:20,173] [INFO] Task started: fastANI
[2023-03-18 04:25:20,173] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ef81556-d7ec-4fdf-847a-7c3e05f2327a/OceanDNA-b10387.fa --refList OceanDNA-b10387/target_genomes_gtdb.txt --output OceanDNA-b10387/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:25:22,530] [INFO] Task succeeded: fastANI
[2023-03-18 04:25:22,535] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 04:25:22,535] [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_902595825.1	s__TMED96 sp902595825	98.128	255	368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TMED96	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902598305.1	s__TMED96 sp902598305	86.4631	327	368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TMED96	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902628605.1	s__TMED96 sp902628605	85.615	153	368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TMED96	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902593075.1	s__TMED96 sp902593075	85.5711	232	368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TMED96	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002728075.1	s__TMED96 sp002728075	84.8747	272	368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TMED96	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002171475.2	s__TMED96 sp002171475	84.7414	322	368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TMED96	95.0	99.27	99.27	0.93	0.93	2	-
GCA_902635965.1	s__TMED96 sp902635965	84.0189	290	368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TMED96	95.0	97.75	95.54	0.87	0.85	3	-
--------------------------------------------------------------------------------
[2023-03-18 04:25:22,544] [INFO] GTDB search result was written to OceanDNA-b10387/result_gtdb.tsv
[2023-03-18 04:25:22,559] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:25:22,569] [INFO] DFAST_QC result json was written to OceanDNA-b10387/dqc_result.json
[2023-03-18 04:25:22,569] [INFO] DFAST_QC completed!
[2023-03-18 04:25:22,569] [INFO] Total running time: 0h0m48s