[2023-03-18 10:15:15,036] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:15:15,036] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:15:15,036] [INFO] DQC Reference Directory: /var/lib/cwl/stgb3f8f6ea-7d0f-4579-9537-edd47fb8aac3/dqc_reference
[2023-03-18 10:15:16,171] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:15:16,172] [INFO] Task started: Prodigal
[2023-03-18 10:15:16,172] [INFO] Running command: cat /var/lib/cwl/stg556c2af3-7d7f-4b53-a006-8930289ac731/OceanDNA-b4534.fa | prodigal -d OceanDNA-b4534/cds.fna -a OceanDNA-b4534/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:15:27,867] [INFO] Task succeeded: Prodigal
[2023-03-18 10:15:27,867] [INFO] Task started: HMMsearch
[2023-03-18 10:15:27,867] [INFO] Running command: hmmsearch --tblout OceanDNA-b4534/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb3f8f6ea-7d0f-4579-9537-edd47fb8aac3/dqc_reference/reference_markers.hmm OceanDNA-b4534/protein.faa > /dev/null
[2023-03-18 10:15:28,035] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:15:28,035] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg556c2af3-7d7f-4b53-a006-8930289ac731/OceanDNA-b4534.fa]
[2023-03-18 10:15:28,050] [INFO] Query marker FASTA was written to OceanDNA-b4534/markers.fasta
[2023-03-18 10:15:28,051] [INFO] Task started: Blastn
[2023-03-18 10:15:28,051] [INFO] Running command: blastn -query OceanDNA-b4534/markers.fasta -db /var/lib/cwl/stgb3f8f6ea-7d0f-4579-9537-edd47fb8aac3/dqc_reference/reference_markers.fasta -out OceanDNA-b4534/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:15:28,563] [INFO] Task succeeded: Blastn
[2023-03-18 10:15:28,564] [INFO] Selected 25 target genomes.
[2023-03-18 10:15:28,564] [INFO] Target genome list was writen to OceanDNA-b4534/target_genomes.txt
[2023-03-18 10:15:28,631] [INFO] Task started: fastANI
[2023-03-18 10:15:28,631] [INFO] Running command: fastANI --query /var/lib/cwl/stg556c2af3-7d7f-4b53-a006-8930289ac731/OceanDNA-b4534.fa --refList OceanDNA-b4534/target_genomes.txt --output OceanDNA-b4534/fastani_result.tsv --threads 1
[2023-03-18 10:15:43,614] [INFO] Task succeeded: fastANI
[2023-03-18 10:15:43,615] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb3f8f6ea-7d0f-4579-9537-edd47fb8aac3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:15:43,615] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb3f8f6ea-7d0f-4579-9537-edd47fb8aac3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:15:43,615] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:15:43,615] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 10:15:43,615] [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 10:15:43,615] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4534/tc_result.tsv
[2023-03-18 10:15:43,616] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:15:43,616] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:15:43,616] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb3f8f6ea-7d0f-4579-9537-edd47fb8aac3/dqc_reference/checkm_data
[2023-03-18 10:15:43,619] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:15:43,622] [INFO] Task started: CheckM
[2023-03-18 10:15:43,622] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4534/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4534/checkm_input OceanDNA-b4534/checkm_result
[2023-03-18 10:16:17,562] [INFO] Task succeeded: CheckM
[2023-03-18 10:16:17,562] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 10:16:17,576] [INFO] ===== Completeness check finished =====
[2023-03-18 10:16:17,576] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:16:17,576] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4534/markers.fasta)
[2023-03-18 10:16:17,577] [INFO] Task started: Blastn
[2023-03-18 10:16:17,577] [INFO] Running command: blastn -query OceanDNA-b4534/markers.fasta -db /var/lib/cwl/stgb3f8f6ea-7d0f-4579-9537-edd47fb8aac3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4534/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:16:18,304] [INFO] Task succeeded: Blastn
[2023-03-18 10:16:18,305] [INFO] Selected 24 target genomes.
[2023-03-18 10:16:18,305] [INFO] Target genome list was writen to OceanDNA-b4534/target_genomes_gtdb.txt
[2023-03-18 10:16:18,335] [INFO] Task started: fastANI
[2023-03-18 10:16:18,336] [INFO] Running command: fastANI --query /var/lib/cwl/stg556c2af3-7d7f-4b53-a006-8930289ac731/OceanDNA-b4534.fa --refList OceanDNA-b4534/target_genomes_gtdb.txt --output OceanDNA-b4534/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:16:31,072] [INFO] Task succeeded: fastANI
[2023-03-18 10:16:31,075] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 10:16:31,076] [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_905479105.1	s__SHAN690 sp002390775	93.7188	457	477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Salibacteraceae;g__SHAN690	95.0	99.12	98.21	0.92	0.80	5	-
GCA_002389645.1	s__SHAN690 sp002389645	79.5268	235	477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Salibacteraceae;g__SHAN690	95.0	99.96	99.93	0.94	0.94	3	-
GCA_018401875.1	s__SHAN690 sp018401875	78.5211	124	477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Salibacteraceae;g__SHAN690	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 10:16:31,078] [INFO] GTDB search result was written to OceanDNA-b4534/result_gtdb.tsv
[2023-03-18 10:16:31,085] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:16:31,091] [INFO] DFAST_QC result json was written to OceanDNA-b4534/dqc_result.json
[2023-03-18 10:16:31,091] [INFO] DFAST_QC completed!
[2023-03-18 10:16:31,091] [INFO] Total running time: 0h1m16s