[2023-03-15 21:57:40,316] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:57:40,319] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:57:40,319] [INFO] DQC Reference Directory: /var/lib/cwl/stgeecdf562-099b-44cf-8fb5-000d71af8ade/dqc_reference
[2023-03-15 21:57:41,425] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:57:41,426] [INFO] Task started: Prodigal
[2023-03-15 21:57:41,426] [INFO] Running command: cat /var/lib/cwl/stg37b5af05-c65a-4b18-ba26-739e8fbb1e4b/OceanDNA-b19387.fa | prodigal -d OceanDNA-b19387/cds.fna -a OceanDNA-b19387/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:57:47,138] [INFO] Task succeeded: Prodigal
[2023-03-15 21:57:47,138] [INFO] Task started: HMMsearch
[2023-03-15 21:57:47,138] [INFO] Running command: hmmsearch --tblout OceanDNA-b19387/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeecdf562-099b-44cf-8fb5-000d71af8ade/dqc_reference/reference_markers.hmm OceanDNA-b19387/protein.faa > /dev/null
[2023-03-15 21:57:47,308] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:57:47,309] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg37b5af05-c65a-4b18-ba26-739e8fbb1e4b/OceanDNA-b19387.fa]
[2023-03-15 21:57:47,423] [INFO] Query marker FASTA was written to OceanDNA-b19387/markers.fasta
[2023-03-15 21:57:47,423] [INFO] Task started: Blastn
[2023-03-15 21:57:47,423] [INFO] Running command: blastn -query OceanDNA-b19387/markers.fasta -db /var/lib/cwl/stgeecdf562-099b-44cf-8fb5-000d71af8ade/dqc_reference/reference_markers.fasta -out OceanDNA-b19387/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:57:47,939] [INFO] Task succeeded: Blastn
[2023-03-15 21:57:47,981] [INFO] Selected 12 target genomes.
[2023-03-15 21:57:47,982] [INFO] Target genome list was writen to OceanDNA-b19387/target_genomes.txt
[2023-03-15 21:57:47,988] [INFO] Task started: fastANI
[2023-03-15 21:57:47,989] [INFO] Running command: fastANI --query /var/lib/cwl/stg37b5af05-c65a-4b18-ba26-739e8fbb1e4b/OceanDNA-b19387.fa --refList OceanDNA-b19387/target_genomes.txt --output OceanDNA-b19387/fastani_result.tsv --threads 1
[2023-03-15 21:57:54,170] [INFO] Task succeeded: fastANI
[2023-03-15 21:57:54,170] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeecdf562-099b-44cf-8fb5-000d71af8ade/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:57:54,171] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeecdf562-099b-44cf-8fb5-000d71af8ade/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:57:54,171] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:57:54,171] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 21:57:54,171] [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
--------------------------------------------------------------------------------
[2023-03-15 21:57:54,188] [INFO] DFAST Taxonomy check result was written to OceanDNA-b19387/tc_result.tsv
[2023-03-15 21:57:54,210] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:57:54,211] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:57:54,211] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeecdf562-099b-44cf-8fb5-000d71af8ade/dqc_reference/checkm_data
[2023-03-15 21:57:54,214] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:57:54,219] [INFO] Task started: CheckM
[2023-03-15 21:57:54,219] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b19387/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b19387/checkm_input OceanDNA-b19387/checkm_result
[2023-03-15 21:58:14,783] [INFO] Task succeeded: CheckM
[2023-03-15 21:58:14,783] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.12%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 21:58:14,843] [INFO] ===== Completeness check finished =====
[2023-03-15 21:58:14,843] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:58:14,843] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b19387/markers.fasta)
[2023-03-15 21:58:14,844] [INFO] Task started: Blastn
[2023-03-15 21:58:14,844] [INFO] Running command: blastn -query OceanDNA-b19387/markers.fasta -db /var/lib/cwl/stgeecdf562-099b-44cf-8fb5-000d71af8ade/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b19387/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:58:15,537] [INFO] Task succeeded: Blastn
[2023-03-15 21:58:15,582] [INFO] Selected 18 target genomes.
[2023-03-15 21:58:15,582] [INFO] Target genome list was writen to OceanDNA-b19387/target_genomes_gtdb.txt
[2023-03-15 21:58:15,793] [INFO] Task started: fastANI
[2023-03-15 21:58:15,793] [INFO] Running command: fastANI --query /var/lib/cwl/stg37b5af05-c65a-4b18-ba26-739e8fbb1e4b/OceanDNA-b19387.fa --refList OceanDNA-b19387/target_genomes_gtdb.txt --output OceanDNA-b19387/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:58:21,121] [INFO] Task succeeded: fastANI
[2023-03-15 21:58:21,125] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 21:58:21,125] [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_002712245.1	s__TMED108 sp002712245	98.4714	220	364	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TMED108	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002725545.1	s__TMED108 sp002725545	92.4517	243	364	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TMED108	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002724475.1	s__TMED108 sp002724475	76.6874	73	364	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TMED108	95.0	97.60	97.08	0.73	0.61	4	-
--------------------------------------------------------------------------------
[2023-03-15 21:58:21,137] [INFO] GTDB search result was written to OceanDNA-b19387/result_gtdb.tsv
[2023-03-15 21:58:21,168] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:58:21,184] [INFO] DFAST_QC result json was written to OceanDNA-b19387/dqc_result.json
[2023-03-15 21:58:21,184] [INFO] DFAST_QC completed!
[2023-03-15 21:58:21,184] [INFO] Total running time: 0h0m41s