[2023-03-16 23:35:13,188] [INFO] DFAST_QC pipeline started.
[2023-03-16 23:35:13,188] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 23:35:13,188] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe1ff0b0-241b-4542-b7d0-e5be0dcbdc2b/dqc_reference
[2023-03-16 23:35:14,948] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 23:35:14,948] [INFO] Task started: Prodigal
[2023-03-16 23:35:14,948] [INFO] Running command: cat /var/lib/cwl/stgb745eecc-56bc-437e-9298-fc5b99f852d6/OceanDNA-b22159.fa | prodigal -d OceanDNA-b22159/cds.fna -a OceanDNA-b22159/protein.faa -g 11 -q > /dev/null
[2023-03-16 23:35:24,958] [INFO] Task succeeded: Prodigal
[2023-03-16 23:35:24,958] [INFO] Task started: HMMsearch
[2023-03-16 23:35:24,958] [INFO] Running command: hmmsearch --tblout OceanDNA-b22159/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe1ff0b0-241b-4542-b7d0-e5be0dcbdc2b/dqc_reference/reference_markers.hmm OceanDNA-b22159/protein.faa > /dev/null
[2023-03-16 23:35:25,131] [INFO] Task succeeded: HMMsearch
[2023-03-16 23:35:25,131] [INFO] Found 6/6 markers.
[2023-03-16 23:35:25,142] [INFO] Query marker FASTA was written to OceanDNA-b22159/markers.fasta
[2023-03-16 23:35:25,142] [INFO] Task started: Blastn
[2023-03-16 23:35:25,142] [INFO] Running command: blastn -query OceanDNA-b22159/markers.fasta -db /var/lib/cwl/stgbe1ff0b0-241b-4542-b7d0-e5be0dcbdc2b/dqc_reference/reference_markers.fasta -out OceanDNA-b22159/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:35:25,632] [INFO] Task succeeded: Blastn
[2023-03-16 23:35:25,633] [INFO] Selected 19 target genomes.
[2023-03-16 23:35:25,633] [INFO] Target genome list was writen to OceanDNA-b22159/target_genomes.txt
[2023-03-16 23:35:25,644] [INFO] Task started: fastANI
[2023-03-16 23:35:25,644] [INFO] Running command: fastANI --query /var/lib/cwl/stgb745eecc-56bc-437e-9298-fc5b99f852d6/OceanDNA-b22159.fa --refList OceanDNA-b22159/target_genomes.txt --output OceanDNA-b22159/fastani_result.tsv --threads 1
[2023-03-16 23:35:33,351] [INFO] Task succeeded: fastANI
[2023-03-16 23:35:33,351] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe1ff0b0-241b-4542-b7d0-e5be0dcbdc2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 23:35:33,351] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe1ff0b0-241b-4542-b7d0-e5be0dcbdc2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 23:35:33,351] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 23:35:33,351] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 23:35:33,352] [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
--------------------------------------------------------------------------------
[2023-03-16 23:35:33,352] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22159/tc_result.tsv
[2023-03-16 23:35:33,352] [INFO] ===== Taxonomy check completed =====
[2023-03-16 23:35:33,352] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 23:35:33,352] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe1ff0b0-241b-4542-b7d0-e5be0dcbdc2b/dqc_reference/checkm_data
[2023-03-16 23:35:33,354] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 23:35:33,360] [INFO] Task started: CheckM
[2023-03-16 23:35:33,360] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22159/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22159/checkm_input OceanDNA-b22159/checkm_result
[2023-03-16 23:36:02,686] [INFO] Task succeeded: CheckM
[2023-03-16 23:36:02,686] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 23:36:02,688] [INFO] ===== Completeness check finished =====
[2023-03-16 23:36:02,688] [INFO] ===== Start GTDB Search =====
[2023-03-16 23:36:02,688] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22159/markers.fasta)
[2023-03-16 23:36:02,690] [INFO] Task started: Blastn
[2023-03-16 23:36:02,690] [INFO] Running command: blastn -query OceanDNA-b22159/markers.fasta -db /var/lib/cwl/stgbe1ff0b0-241b-4542-b7d0-e5be0dcbdc2b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22159/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:36:03,361] [INFO] Task succeeded: Blastn
[2023-03-16 23:36:03,362] [INFO] Selected 21 target genomes.
[2023-03-16 23:36:03,362] [INFO] Target genome list was writen to OceanDNA-b22159/target_genomes_gtdb.txt
[2023-03-16 23:36:03,794] [INFO] Task started: fastANI
[2023-03-16 23:36:03,794] [INFO] Running command: fastANI --query /var/lib/cwl/stgb745eecc-56bc-437e-9298-fc5b99f852d6/OceanDNA-b22159.fa --refList OceanDNA-b22159/target_genomes_gtdb.txt --output OceanDNA-b22159/fastani_result_gtdb.tsv --threads 1
[2023-03-16 23:36:09,445] [INFO] Task succeeded: fastANI
[2023-03-16 23:36:09,451] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 23:36:09,452] [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_018665385.1	s__GCA-002718515 sp018665385	97.1813	429	543	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002718515	95.0	99.09	99.03	0.85	0.83	4	conclusive
GCA_018701395.1	s__GCA-002718515 sp018701395	78.8144	101	543	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002718515	95.0	99.63	99.41	0.94	0.92	4	-
GCA_018657585.1	s__GCA-002718515 sp018657585	77.6114	138	543	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002718515	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014238785.1	s__GCA-002718515 sp014238785	77.3178	99	543	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002718515	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002689385.1	s__GCA-002718515 sp002689385	77.2818	102	543	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002718515	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014381555.1	s__GCA-002718515 sp014381555	77.0036	79	543	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002718515	95.0	99.84	99.84	0.86	0.86	2	-
GCA_018656645.1	s__GCA-002718515 sp018656645	76.8373	62	543	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002718515	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014381385.1	s__GCA-002718515 sp014381385	76.7233	60	543	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002718515	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014238125.1	s__GCA-002718515 sp014238125	76.4713	67	543	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002718515	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014381305.1	s__GCA-002718515 sp014381305	76.4632	55	543	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002718515	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 23:36:09,452] [INFO] GTDB search result was written to OceanDNA-b22159/result_gtdb.tsv
[2023-03-16 23:36:09,452] [INFO] ===== GTDB Search completed =====
[2023-03-16 23:36:09,453] [INFO] DFAST_QC result json was written to OceanDNA-b22159/dqc_result.json
[2023-03-16 23:36:09,453] [INFO] DFAST_QC completed!
[2023-03-16 23:36:09,453] [INFO] Total running time: 0h0m56s