[2023-03-18 00:10:22,967] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:10:22,968] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:10:22,968] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd39329c-9933-4744-aab4-1cca85800e0a/dqc_reference
[2023-03-18 00:10:24,045] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:10:24,046] [INFO] Task started: Prodigal
[2023-03-18 00:10:24,046] [INFO] Running command: cat /var/lib/cwl/stge66ae12c-3660-48df-ab18-51a56491e2ec/OceanDNA-b4709.fa | prodigal -d OceanDNA-b4709/cds.fna -a OceanDNA-b4709/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:10:42,909] [INFO] Task succeeded: Prodigal
[2023-03-18 00:10:42,909] [INFO] Task started: HMMsearch
[2023-03-18 00:10:42,909] [INFO] Running command: hmmsearch --tblout OceanDNA-b4709/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd39329c-9933-4744-aab4-1cca85800e0a/dqc_reference/reference_markers.hmm OceanDNA-b4709/protein.faa > /dev/null
[2023-03-18 00:10:43,095] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:10:43,096] [INFO] Found 6/6 markers.
[2023-03-18 00:10:43,113] [INFO] Query marker FASTA was written to OceanDNA-b4709/markers.fasta
[2023-03-18 00:10:43,115] [INFO] Task started: Blastn
[2023-03-18 00:10:43,115] [INFO] Running command: blastn -query OceanDNA-b4709/markers.fasta -db /var/lib/cwl/stgbd39329c-9933-4744-aab4-1cca85800e0a/dqc_reference/reference_markers.fasta -out OceanDNA-b4709/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:10:43,723] [INFO] Task succeeded: Blastn
[2023-03-18 00:10:43,724] [INFO] Selected 32 target genomes.
[2023-03-18 00:10:43,724] [INFO] Target genome list was writen to OceanDNA-b4709/target_genomes.txt
[2023-03-18 00:10:43,741] [INFO] Task started: fastANI
[2023-03-18 00:10:43,741] [INFO] Running command: fastANI --query /var/lib/cwl/stge66ae12c-3660-48df-ab18-51a56491e2ec/OceanDNA-b4709.fa --refList OceanDNA-b4709/target_genomes.txt --output OceanDNA-b4709/fastani_result.tsv --threads 1
[2023-03-18 00:11:02,396] [INFO] Task succeeded: fastANI
[2023-03-18 00:11:02,396] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd39329c-9933-4744-aab4-1cca85800e0a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:11:02,396] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd39329c-9933-4744-aab4-1cca85800e0a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:11:02,396] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:11:02,396] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 00:11:02,396] [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 00:11:02,397] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4709/tc_result.tsv
[2023-03-18 00:11:02,397] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:11:02,397] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:11:02,397] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd39329c-9933-4744-aab4-1cca85800e0a/dqc_reference/checkm_data
[2023-03-18 00:11:02,400] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:11:02,405] [INFO] Task started: CheckM
[2023-03-18 00:11:02,405] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4709/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4709/checkm_input OceanDNA-b4709/checkm_result
[2023-03-18 00:11:51,037] [INFO] Task succeeded: CheckM
[2023-03-18 00:11:51,037] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:11:51,039] [INFO] ===== Completeness check finished =====
[2023-03-18 00:11:51,039] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:11:51,040] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4709/markers.fasta)
[2023-03-18 00:11:51,052] [INFO] Task started: Blastn
[2023-03-18 00:11:51,052] [INFO] Running command: blastn -query OceanDNA-b4709/markers.fasta -db /var/lib/cwl/stgbd39329c-9933-4744-aab4-1cca85800e0a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4709/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:11:51,770] [INFO] Task succeeded: Blastn
[2023-03-18 00:11:51,770] [INFO] Selected 23 target genomes.
[2023-03-18 00:11:51,771] [INFO] Target genome list was writen to OceanDNA-b4709/target_genomes_gtdb.txt
[2023-03-18 00:11:51,819] [INFO] Task started: fastANI
[2023-03-18 00:11:51,819] [INFO] Running command: fastANI --query /var/lib/cwl/stge66ae12c-3660-48df-ab18-51a56491e2ec/OceanDNA-b4709.fa --refList OceanDNA-b4709/target_genomes_gtdb.txt --output OceanDNA-b4709/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:12:04,917] [INFO] Task succeeded: fastANI
[2023-03-18 00:12:04,920] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 00:12:04,920] [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_002707155.1	s__UBA6770 sp002707155	99.3067	876	928	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Salibacteraceae;g__UBA6770	95.0	99.26	99.24	0.93	0.88	4	conclusive
GCA_905181875.1	s__UBA6770 sp905181875	79.8767	482	928	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Salibacteraceae;g__UBA6770	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002453255.1	s__UBA6770 sp002453255	79.6042	526	928	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Salibacteraceae;g__UBA6770	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002713215.1	s__UBA2108 sp002713215	77.5767	62	928	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Salibacteraceae;g__UBA2108	95.0	99.97	99.97	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2023-03-18 00:12:04,920] [INFO] GTDB search result was written to OceanDNA-b4709/result_gtdb.tsv
[2023-03-18 00:12:04,920] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:12:04,921] [INFO] DFAST_QC result json was written to OceanDNA-b4709/dqc_result.json
[2023-03-18 00:12:04,921] [INFO] DFAST_QC completed!
[2023-03-18 00:12:04,921] [INFO] Total running time: 0h1m42s