[2023-03-17 07:01:51,101] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:01:51,101] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:01:51,101] [INFO] DQC Reference Directory: /var/lib/cwl/stge505a0ba-6236-4d78-b230-aacbe29b9c3b/dqc_reference
[2023-03-17 07:01:52,270] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:01:52,270] [INFO] Task started: Prodigal
[2023-03-17 07:01:52,270] [INFO] Running command: cat /var/lib/cwl/stg163f0526-50db-4436-bb75-234608b6d60a/OceanDNA-b25394.fa | prodigal -d OceanDNA-b25394/cds.fna -a OceanDNA-b25394/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:01:57,819] [INFO] Task succeeded: Prodigal
[2023-03-17 07:01:57,819] [INFO] Task started: HMMsearch
[2023-03-17 07:01:57,819] [INFO] Running command: hmmsearch --tblout OceanDNA-b25394/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge505a0ba-6236-4d78-b230-aacbe29b9c3b/dqc_reference/reference_markers.hmm OceanDNA-b25394/protein.faa > /dev/null
[2023-03-17 07:01:57,982] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:01:57,983] [INFO] Found 6/6 markers.
[2023-03-17 07:01:57,990] [INFO] Query marker FASTA was written to OceanDNA-b25394/markers.fasta
[2023-03-17 07:01:57,990] [INFO] Task started: Blastn
[2023-03-17 07:01:57,990] [INFO] Running command: blastn -query OceanDNA-b25394/markers.fasta -db /var/lib/cwl/stge505a0ba-6236-4d78-b230-aacbe29b9c3b/dqc_reference/reference_markers.fasta -out OceanDNA-b25394/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:01:58,503] [INFO] Task succeeded: Blastn
[2023-03-17 07:01:58,504] [INFO] Selected 16 target genomes.
[2023-03-17 07:01:58,504] [INFO] Target genome list was writen to OceanDNA-b25394/target_genomes.txt
[2023-03-17 07:01:58,512] [INFO] Task started: fastANI
[2023-03-17 07:01:58,512] [INFO] Running command: fastANI --query /var/lib/cwl/stg163f0526-50db-4436-bb75-234608b6d60a/OceanDNA-b25394.fa --refList OceanDNA-b25394/target_genomes.txt --output OceanDNA-b25394/fastani_result.tsv --threads 1
[2023-03-17 07:02:04,491] [INFO] Task succeeded: fastANI
[2023-03-17 07:02:04,491] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge505a0ba-6236-4d78-b230-aacbe29b9c3b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:02:04,491] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge505a0ba-6236-4d78-b230-aacbe29b9c3b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:02:04,494] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:02:04,494] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 07:02:04,494] [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
Candidatus Pelagibacter ubique	strain=HTCC1062	GCA_000012345.1	198252	198252	suspected-type	True	75.8573	54	294	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 07:02:04,494] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25394/tc_result.tsv
[2023-03-17 07:02:04,494] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:02:04,494] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:02:04,494] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge505a0ba-6236-4d78-b230-aacbe29b9c3b/dqc_reference/checkm_data
[2023-03-17 07:02:04,495] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:02:04,497] [INFO] Task started: CheckM
[2023-03-17 07:02:04,497] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25394/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25394/checkm_input OceanDNA-b25394/checkm_result
[2023-03-17 07:02:24,089] [INFO] Task succeeded: CheckM
[2023-03-17 07:02:24,089] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 07:02:24,091] [INFO] ===== Completeness check finished =====
[2023-03-17 07:02:24,091] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:02:24,091] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25394/markers.fasta)
[2023-03-17 07:02:24,091] [INFO] Task started: Blastn
[2023-03-17 07:02:24,091] [INFO] Running command: blastn -query OceanDNA-b25394/markers.fasta -db /var/lib/cwl/stge505a0ba-6236-4d78-b230-aacbe29b9c3b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25394/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:02:24,871] [INFO] Task succeeded: Blastn
[2023-03-17 07:02:24,872] [INFO] Selected 12 target genomes.
[2023-03-17 07:02:24,872] [INFO] Target genome list was writen to OceanDNA-b25394/target_genomes_gtdb.txt
[2023-03-17 07:02:25,027] [INFO] Task started: fastANI
[2023-03-17 07:02:25,027] [INFO] Running command: fastANI --query /var/lib/cwl/stg163f0526-50db-4436-bb75-234608b6d60a/OceanDNA-b25394.fa --refList OceanDNA-b25394/target_genomes_gtdb.txt --output OceanDNA-b25394/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:02:27,534] [INFO] Task succeeded: fastANI
[2023-03-17 07:02:27,541] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 07:02:27,541] [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_002690285.1	s__AAA240-E13 sp002690285	99.5989	188	294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AAA240-E13	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000513075.1	s__AAA240-E13 sp000513075	88.5082	148	294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AAA240-E13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003211695.1	s__AAA240-E13 sp003211695	85.91	200	294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AAA240-E13	95.0	100.00	100.00	1.00	1.00	2	-
GCA_000504605.1	s__AAA240-E13 sp000504605	84.6428	127	294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AAA240-E13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000513055.1	s__AAA240-E13 sp000513055	84.2389	150	294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AAA240-E13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000504625.1	s__AAA240-E13 sp000504625	81.9851	195	294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AAA240-E13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003209225.1	s__AAA240-E13 sp003209225	78.8623	125	294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AAA240-E13	95.0	100.00	100.00	0.99	0.99	2	-
GCA_016764285.1	s__AG-414-E02 sp016764285	78.7268	83	294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902594235.1	s__Pelagibacter sp902594235	76.0369	56	294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902540275.1	s__Pelagibacter sp902540275	75.979	52	294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 07:02:27,541] [INFO] GTDB search result was written to OceanDNA-b25394/result_gtdb.tsv
[2023-03-17 07:02:27,541] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:02:27,542] [INFO] DFAST_QC result json was written to OceanDNA-b25394/dqc_result.json
[2023-03-17 07:02:27,542] [INFO] DFAST_QC completed!
[2023-03-17 07:02:27,543] [INFO] Total running time: 0h0m36s