[2023-03-19 05:19:33,805] [INFO] DFAST_QC pipeline started.
[2023-03-19 05:19:33,805] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 05:19:33,805] [INFO] DQC Reference Directory: /var/lib/cwl/stg7be3aadc-3d06-4b99-9cde-66564ccb8f5c/dqc_reference
[2023-03-19 05:19:35,406] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 05:19:35,406] [INFO] Task started: Prodigal
[2023-03-19 05:19:35,406] [INFO] Running command: cat /var/lib/cwl/stg126caf24-80a8-412f-9268-e17dfb4ab7fd/OceanDNA-b18171.fa | prodigal -d OceanDNA-b18171/cds.fna -a OceanDNA-b18171/protein.faa -g 11 -q > /dev/null
[2023-03-19 05:19:38,141] [INFO] Task succeeded: Prodigal
[2023-03-19 05:19:38,141] [INFO] Task started: HMMsearch
[2023-03-19 05:19:38,141] [INFO] Running command: hmmsearch --tblout OceanDNA-b18171/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7be3aadc-3d06-4b99-9cde-66564ccb8f5c/dqc_reference/reference_markers.hmm OceanDNA-b18171/protein.faa > /dev/null
[2023-03-19 05:19:38,381] [INFO] Task succeeded: HMMsearch
[2023-03-19 05:19:38,381] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg126caf24-80a8-412f-9268-e17dfb4ab7fd/OceanDNA-b18171.fa]
[2023-03-19 05:19:38,387] [INFO] Query marker FASTA was written to OceanDNA-b18171/markers.fasta
[2023-03-19 05:19:38,388] [INFO] Task started: Blastn
[2023-03-19 05:19:38,388] [INFO] Running command: blastn -query OceanDNA-b18171/markers.fasta -db /var/lib/cwl/stg7be3aadc-3d06-4b99-9cde-66564ccb8f5c/dqc_reference/reference_markers.fasta -out OceanDNA-b18171/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:19:38,928] [INFO] Task succeeded: Blastn
[2023-03-19 05:19:38,929] [INFO] Selected 15 target genomes.
[2023-03-19 05:19:38,929] [INFO] Target genome list was writen to OceanDNA-b18171/target_genomes.txt
[2023-03-19 05:19:38,937] [INFO] Task started: fastANI
[2023-03-19 05:19:38,937] [INFO] Running command: fastANI --query /var/lib/cwl/stg126caf24-80a8-412f-9268-e17dfb4ab7fd/OceanDNA-b18171.fa --refList OceanDNA-b18171/target_genomes.txt --output OceanDNA-b18171/fastani_result.tsv --threads 1
[2023-03-19 05:19:45,478] [INFO] Task succeeded: fastANI
[2023-03-19 05:19:45,479] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7be3aadc-3d06-4b99-9cde-66564ccb8f5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 05:19:45,479] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7be3aadc-3d06-4b99-9cde-66564ccb8f5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 05:19:45,479] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 05:19:45,479] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 05:19:45,479] [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 05:19:45,479] [INFO] DFAST Taxonomy check result was written to OceanDNA-b18171/tc_result.tsv
[2023-03-19 05:19:45,479] [INFO] ===== Taxonomy check completed =====
[2023-03-19 05:19:45,480] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 05:19:45,480] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7be3aadc-3d06-4b99-9cde-66564ccb8f5c/dqc_reference/checkm_data
[2023-03-19 05:19:45,482] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 05:19:45,485] [INFO] Task started: CheckM
[2023-03-19 05:19:45,485] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b18171/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b18171/checkm_input OceanDNA-b18171/checkm_result
[2023-03-19 05:19:59,294] [INFO] Task succeeded: CheckM
[2023-03-19 05:19:59,295] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.05%
Contamintation: 3.01%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 05:19:59,301] [INFO] ===== Completeness check finished =====
[2023-03-19 05:19:59,301] [INFO] ===== Start GTDB Search =====
[2023-03-19 05:19:59,302] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b18171/markers.fasta)
[2023-03-19 05:19:59,302] [INFO] Task started: Blastn
[2023-03-19 05:19:59,302] [INFO] Running command: blastn -query OceanDNA-b18171/markers.fasta -db /var/lib/cwl/stg7be3aadc-3d06-4b99-9cde-66564ccb8f5c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b18171/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:19:59,980] [INFO] Task succeeded: Blastn
[2023-03-19 05:19:59,986] [INFO] Selected 7 target genomes.
[2023-03-19 05:19:59,986] [INFO] Target genome list was writen to OceanDNA-b18171/target_genomes_gtdb.txt
[2023-03-19 05:19:59,995] [INFO] Task started: fastANI
[2023-03-19 05:19:59,996] [INFO] Running command: fastANI --query /var/lib/cwl/stg126caf24-80a8-412f-9268-e17dfb4ab7fd/OceanDNA-b18171.fa --refList OceanDNA-b18171/target_genomes_gtdb.txt --output OceanDNA-b18171/fastani_result_gtdb.tsv --threads 1
[2023-03-19 05:20:01,171] [INFO] Task succeeded: fastANI
[2023-03-19 05:20:01,177] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 05:20:01,177] [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_902624275.1	s__Marinisoma sp902624275	88.1056	123	146	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902599655.1	s__Marinisoma sp902599655	84.9331	100	146	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	97.53	97.28	0.66	0.66	3	-
GCA_016777965.1	s__Marinisoma sp016777965	84.9212	57	146	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902576865.1	s__Marinisoma sp902576865	84.3879	92	146	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	96.64	96.64	0.80	0.80	2	-
GCA_902525615.1	s__Marinisoma sp902525615	84.1886	111	146	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902538565.1	s__Marinisoma sp902538565	83.9533	133	146	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	99.07	99.04	0.96	0.96	3	-
GCA_000402655.1	s__Marinisoma sp000402655	82.9244	132	146	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	96.42	95.83	0.93	0.92	4	-
--------------------------------------------------------------------------------
[2023-03-19 05:20:01,177] [INFO] GTDB search result was written to OceanDNA-b18171/result_gtdb.tsv
[2023-03-19 05:20:01,177] [INFO] ===== GTDB Search completed =====
[2023-03-19 05:20:01,178] [INFO] DFAST_QC result json was written to OceanDNA-b18171/dqc_result.json
[2023-03-19 05:20:01,178] [INFO] DFAST_QC completed!
[2023-03-19 05:20:01,178] [INFO] Total running time: 0h0m27s