[2023-03-19 04:43:18,628] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:43:18,628] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:43:18,628] [INFO] DQC Reference Directory: /var/lib/cwl/stg1ba34690-5ed0-4c67-911a-5a8f95e713b5/dqc_reference
[2023-03-19 04:43:19,777] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:43:19,777] [INFO] Task started: Prodigal
[2023-03-19 04:43:19,777] [INFO] Running command: cat /var/lib/cwl/stgda8a0629-479b-47b4-9cfd-cd86f3b527a4/OceanDNA-b43084.fa | prodigal -d OceanDNA-b43084/cds.fna -a OceanDNA-b43084/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:43:23,544] [INFO] Task succeeded: Prodigal
[2023-03-19 04:43:23,545] [INFO] Task started: HMMsearch
[2023-03-19 04:43:23,545] [INFO] Running command: hmmsearch --tblout OceanDNA-b43084/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1ba34690-5ed0-4c67-911a-5a8f95e713b5/dqc_reference/reference_markers.hmm OceanDNA-b43084/protein.faa > /dev/null
[2023-03-19 04:43:23,691] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:43:23,691] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgda8a0629-479b-47b4-9cfd-cd86f3b527a4/OceanDNA-b43084.fa]
[2023-03-19 04:43:23,700] [INFO] Query marker FASTA was written to OceanDNA-b43084/markers.fasta
[2023-03-19 04:43:23,700] [INFO] Task started: Blastn
[2023-03-19 04:43:23,700] [INFO] Running command: blastn -query OceanDNA-b43084/markers.fasta -db /var/lib/cwl/stg1ba34690-5ed0-4c67-911a-5a8f95e713b5/dqc_reference/reference_markers.fasta -out OceanDNA-b43084/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:43:24,204] [INFO] Task succeeded: Blastn
[2023-03-19 04:43:24,205] [INFO] Selected 22 target genomes.
[2023-03-19 04:43:24,205] [INFO] Target genome list was writen to OceanDNA-b43084/target_genomes.txt
[2023-03-19 04:43:24,219] [INFO] Task started: fastANI
[2023-03-19 04:43:24,220] [INFO] Running command: fastANI --query /var/lib/cwl/stgda8a0629-479b-47b4-9cfd-cd86f3b527a4/OceanDNA-b43084.fa --refList OceanDNA-b43084/target_genomes.txt --output OceanDNA-b43084/fastani_result.tsv --threads 1
[2023-03-19 04:43:34,671] [INFO] Task succeeded: fastANI
[2023-03-19 04:43:34,672] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1ba34690-5ed0-4c67-911a-5a8f95e713b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:43:34,672] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1ba34690-5ed0-4c67-911a-5a8f95e713b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:43:34,672] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:43:34,672] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 04:43:34,672] [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
--------------------------------------------------------------------------------
[2023-03-19 04:43:34,672] [INFO] DFAST Taxonomy check result was written to OceanDNA-b43084/tc_result.tsv
[2023-03-19 04:43:34,673] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:43:34,673] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:43:34,673] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1ba34690-5ed0-4c67-911a-5a8f95e713b5/dqc_reference/checkm_data
[2023-03-19 04:43:34,676] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:43:34,699] [INFO] Task started: CheckM
[2023-03-19 04:43:34,699] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b43084/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b43084/checkm_input OceanDNA-b43084/checkm_result
[2023-03-19 04:43:50,743] [INFO] Task succeeded: CheckM
[2023-03-19 04:43:50,744] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.53%
Contamintation: 0.93%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:43:50,745] [INFO] ===== Completeness check finished =====
[2023-03-19 04:43:50,745] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:43:50,746] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b43084/markers.fasta)
[2023-03-19 04:43:50,747] [INFO] Task started: Blastn
[2023-03-19 04:43:50,747] [INFO] Running command: blastn -query OceanDNA-b43084/markers.fasta -db /var/lib/cwl/stg1ba34690-5ed0-4c67-911a-5a8f95e713b5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b43084/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:43:51,444] [INFO] Task succeeded: Blastn
[2023-03-19 04:43:51,445] [INFO] Selected 13 target genomes.
[2023-03-19 04:43:51,445] [INFO] Target genome list was writen to OceanDNA-b43084/target_genomes_gtdb.txt
[2023-03-19 04:43:51,519] [INFO] Task started: fastANI
[2023-03-19 04:43:51,520] [INFO] Running command: fastANI --query /var/lib/cwl/stgda8a0629-479b-47b4-9cfd-cd86f3b527a4/OceanDNA-b43084.fa --refList OceanDNA-b43084/target_genomes_gtdb.txt --output OceanDNA-b43084/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:43:54,286] [INFO] Task succeeded: fastANI
[2023-03-19 04:43:54,292] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 04:43:54,292] [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_002698045.1	s__Pseudothioglobus sp002698045	95.19	100	228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	95.47	95.47	0.68	0.68	2	conclusive
GCA_905620445.1	s__Pseudothioglobus sp905620445	79.3203	64	228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905618925.1	s__Pseudothioglobus sp905618925	79.1052	99	228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	95.58	95.58	0.66	0.66	2	-
GCA_014384565.1	s__Pseudothioglobus aerophilus	78.9859	105	228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	99.14	98.97	0.83	0.77	11	-
GCA_905612405.1	s__Pseudothioglobus sp905612405	78.9521	83	228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182815.1	s__Pseudothioglobus sp905182815	78.7895	107	228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003326015.1	s__Pseudothioglobus singularis_A	78.5836	139	228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902513495.1	s__Pseudothioglobus sp902513495	78.5166	74	228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	97.65	97.05	0.53	0.51	3	-
--------------------------------------------------------------------------------
[2023-03-19 04:43:54,292] [INFO] GTDB search result was written to OceanDNA-b43084/result_gtdb.tsv
[2023-03-19 04:43:54,292] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:43:54,293] [INFO] DFAST_QC result json was written to OceanDNA-b43084/dqc_result.json
[2023-03-19 04:43:54,293] [INFO] DFAST_QC completed!
[2023-03-19 04:43:54,293] [INFO] Total running time: 0h0m36s