[2023-03-18 04:39:10,900] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:39:10,900] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:39:10,900] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb89c69c-9dff-4067-99ec-d384d9c5aab4/dqc_reference
[2023-03-18 04:39:12,071] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:39:12,072] [INFO] Task started: Prodigal
[2023-03-18 04:39:12,072] [INFO] Running command: cat /var/lib/cwl/stg4aa43846-cc4a-49cf-8aab-92a3f5c28743/OceanDNA-b20998.fa | prodigal -d OceanDNA-b20998/cds.fna -a OceanDNA-b20998/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:39:28,041] [INFO] Task succeeded: Prodigal
[2023-03-18 04:39:28,041] [INFO] Task started: HMMsearch
[2023-03-18 04:39:28,041] [INFO] Running command: hmmsearch --tblout OceanDNA-b20998/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb89c69c-9dff-4067-99ec-d384d9c5aab4/dqc_reference/reference_markers.hmm OceanDNA-b20998/protein.faa > /dev/null
[2023-03-18 04:39:28,289] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:39:28,289] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4aa43846-cc4a-49cf-8aab-92a3f5c28743/OceanDNA-b20998.fa]
[2023-03-18 04:39:28,317] [INFO] Query marker FASTA was written to OceanDNA-b20998/markers.fasta
[2023-03-18 04:39:28,318] [INFO] Task started: Blastn
[2023-03-18 04:39:28,318] [INFO] Running command: blastn -query OceanDNA-b20998/markers.fasta -db /var/lib/cwl/stgbb89c69c-9dff-4067-99ec-d384d9c5aab4/dqc_reference/reference_markers.fasta -out OceanDNA-b20998/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:39:28,942] [INFO] Task succeeded: Blastn
[2023-03-18 04:39:28,944] [INFO] Selected 28 target genomes.
[2023-03-18 04:39:28,944] [INFO] Target genome list was writen to OceanDNA-b20998/target_genomes.txt
[2023-03-18 04:39:28,955] [INFO] Task started: fastANI
[2023-03-18 04:39:28,955] [INFO] Running command: fastANI --query /var/lib/cwl/stg4aa43846-cc4a-49cf-8aab-92a3f5c28743/OceanDNA-b20998.fa --refList OceanDNA-b20998/target_genomes.txt --output OceanDNA-b20998/fastani_result.tsv --threads 1
[2023-03-18 04:39:50,185] [INFO] Task succeeded: fastANI
[2023-03-18 04:39:50,185] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb89c69c-9dff-4067-99ec-d384d9c5aab4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:39:50,186] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb89c69c-9dff-4067-99ec-d384d9c5aab4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:39:50,189] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 04:39:50,189] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 04:39:50,189] [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
Haliangium ochraceum	strain=DSM 14365	GCA_000024805.1	80816	80816	type	True	74.788	68	522	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 04:39:50,189] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20998/tc_result.tsv
[2023-03-18 04:39:50,189] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:39:50,189] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:39:50,189] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb89c69c-9dff-4067-99ec-d384d9c5aab4/dqc_reference/checkm_data
[2023-03-18 04:39:50,190] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:39:50,197] [INFO] Task started: CheckM
[2023-03-18 04:39:50,197] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20998/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20998/checkm_input OceanDNA-b20998/checkm_result
[2023-03-18 04:40:31,470] [INFO] Task succeeded: CheckM
[2023-03-18 04:40:31,470] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.60%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 04:40:31,473] [INFO] ===== Completeness check finished =====
[2023-03-18 04:40:31,473] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:40:31,473] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20998/markers.fasta)
[2023-03-18 04:40:31,474] [INFO] Task started: Blastn
[2023-03-18 04:40:31,474] [INFO] Running command: blastn -query OceanDNA-b20998/markers.fasta -db /var/lib/cwl/stgbb89c69c-9dff-4067-99ec-d384d9c5aab4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20998/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:40:32,266] [INFO] Task succeeded: Blastn
[2023-03-18 04:40:32,267] [INFO] Selected 34 target genomes.
[2023-03-18 04:40:32,267] [INFO] Target genome list was writen to OceanDNA-b20998/target_genomes_gtdb.txt
[2023-03-18 04:40:32,387] [INFO] Task started: fastANI
[2023-03-18 04:40:32,387] [INFO] Running command: fastANI --query /var/lib/cwl/stg4aa43846-cc4a-49cf-8aab-92a3f5c28743/OceanDNA-b20998.fa --refList OceanDNA-b20998/target_genomes_gtdb.txt --output OceanDNA-b20998/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:40:56,304] [INFO] Task succeeded: fastANI
[2023-03-18 04:40:56,308] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 04:40:56,308] [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_903869075.1	s__CAIYBN01 sp903869075	76.1165	52	522	d__Bacteria;p__Myxococcota;c__UBA9042;o__UBA9042;f__UBA9042;g__CAIYBN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005777155.1	s__SXNM01 sp005777155	75.571	74	522	d__Bacteria;p__Myxococcota;c__UBA9042;o__UBA9042;f__UBA9042;g__SXNM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903955385.1	s__CAJBNH01 sp903955385	75.5622	58	522	d__Bacteria;p__Myxococcota;c__UBA9042;o__UBA9042;f__UBA9042;g__CAJBNH01	95.0	99.88	99.77	0.96	0.95	7	-
GCA_903929795.1	s__CAIYBN01 sp903929795	75.5166	52	522	d__Bacteria;p__Myxococcota;c__UBA9042;o__UBA9042;f__UBA9042;g__CAIYBN01	95.0	99.55	99.37	0.95	0.92	7	-
--------------------------------------------------------------------------------
[2023-03-18 04:40:56,308] [INFO] GTDB search result was written to OceanDNA-b20998/result_gtdb.tsv
[2023-03-18 04:40:56,308] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:40:56,309] [INFO] DFAST_QC result json was written to OceanDNA-b20998/dqc_result.json
[2023-03-18 04:40:56,309] [INFO] DFAST_QC completed!
[2023-03-18 04:40:56,309] [INFO] Total running time: 0h1m45s