[2023-03-14 11:14:12,763] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:14:12,764] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:14:12,764] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b45b088-4f3e-4a75-b9fe-b04c3b173983/dqc_reference
[2023-03-14 11:14:14,203] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:14:14,204] [INFO] Task started: Prodigal
[2023-03-14 11:14:14,204] [INFO] Running command: cat /var/lib/cwl/stgce1eb492-27b1-4e4e-81bc-11f940a81ea9/OceanDNA-b20820.fa | prodigal -d OceanDNA-b20820/cds.fna -a OceanDNA-b20820/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:14:28,497] [INFO] Task succeeded: Prodigal
[2023-03-14 11:14:28,498] [INFO] Task started: HMMsearch
[2023-03-14 11:14:28,498] [INFO] Running command: hmmsearch --tblout OceanDNA-b20820/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b45b088-4f3e-4a75-b9fe-b04c3b173983/dqc_reference/reference_markers.hmm OceanDNA-b20820/protein.faa > /dev/null
[2023-03-14 11:14:28,675] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:14:28,675] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgce1eb492-27b1-4e4e-81bc-11f940a81ea9/OceanDNA-b20820.fa]
[2023-03-14 11:14:28,691] [INFO] Query marker FASTA was written to OceanDNA-b20820/markers.fasta
[2023-03-14 11:14:28,691] [INFO] Task started: Blastn
[2023-03-14 11:14:28,691] [INFO] Running command: blastn -query OceanDNA-b20820/markers.fasta -db /var/lib/cwl/stg7b45b088-4f3e-4a75-b9fe-b04c3b173983/dqc_reference/reference_markers.fasta -out OceanDNA-b20820/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:14:29,205] [INFO] Task succeeded: Blastn
[2023-03-14 11:14:29,205] [INFO] Selected 13 target genomes.
[2023-03-14 11:14:29,205] [INFO] Target genome list was writen to OceanDNA-b20820/target_genomes.txt
[2023-03-14 11:14:29,215] [INFO] Task started: fastANI
[2023-03-14 11:14:29,216] [INFO] Running command: fastANI --query /var/lib/cwl/stgce1eb492-27b1-4e4e-81bc-11f940a81ea9/OceanDNA-b20820.fa --refList OceanDNA-b20820/target_genomes.txt --output OceanDNA-b20820/fastani_result.tsv --threads 1
[2023-03-14 11:14:36,338] [INFO] Task succeeded: fastANI
[2023-03-14 11:14:36,338] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b45b088-4f3e-4a75-b9fe-b04c3b173983/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:14:36,338] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b45b088-4f3e-4a75-b9fe-b04c3b173983/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:14:36,339] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:14:36,339] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 11:14:36,339] [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
--------------------------------------------------------------------------------
[2023-03-14 11:14:36,339] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20820/tc_result.tsv
[2023-03-14 11:14:36,339] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:14:36,339] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:14:36,339] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b45b088-4f3e-4a75-b9fe-b04c3b173983/dqc_reference/checkm_data
[2023-03-14 11:14:36,342] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:14:36,346] [INFO] Task started: CheckM
[2023-03-14 11:14:36,347] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20820/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20820/checkm_input OceanDNA-b20820/checkm_result
[2023-03-14 11:15:15,807] [INFO] Task succeeded: CheckM
[2023-03-14 11:15:15,808] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.35%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:15:15,810] [INFO] ===== Completeness check finished =====
[2023-03-14 11:15:15,810] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:15:15,810] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20820/markers.fasta)
[2023-03-14 11:15:15,811] [INFO] Task started: Blastn
[2023-03-14 11:15:15,812] [INFO] Running command: blastn -query OceanDNA-b20820/markers.fasta -db /var/lib/cwl/stg7b45b088-4f3e-4a75-b9fe-b04c3b173983/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20820/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:15:16,604] [INFO] Task succeeded: Blastn
[2023-03-14 11:15:16,605] [INFO] Selected 16 target genomes.
[2023-03-14 11:15:16,605] [INFO] Target genome list was writen to OceanDNA-b20820/target_genomes_gtdb.txt
[2023-03-14 11:15:16,626] [INFO] Task started: fastANI
[2023-03-14 11:15:16,626] [INFO] Running command: fastANI --query /var/lib/cwl/stgce1eb492-27b1-4e4e-81bc-11f940a81ea9/OceanDNA-b20820.fa --refList OceanDNA-b20820/target_genomes_gtdb.txt --output OceanDNA-b20820/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:15:24,965] [INFO] Task succeeded: fastANI
[2023-03-14 11:15:24,971] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:15:24,971] [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_013202385.1	s__JABMPR01 sp013202385	94.4939	537	821	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016844955.1	s__JABMPR01 sp016844955	77.1067	142	821	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018650795.1	s__JABMPR01 sp018650795	77.0498	137	821	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	99.79	99.56	0.89	0.81	14	-
GCA_018673925.1	s__JABMPR01 sp018673925	76.9354	140	821	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	99.95	99.91	0.96	0.94	16	-
GCA_016845065.1	s__JABMPR01 sp016845065	76.9304	127	821	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018650445.1	s__JABMPR01 sp018650445	76.7898	138	821	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	99.76	99.61	0.86	0.82	5	-
GCA_016844945.1	s__JABMPR01 sp016844945	76.6726	138	821	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016784545.1	s__JABMPR01 sp016784545	76.6567	154	821	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:15:24,971] [INFO] GTDB search result was written to OceanDNA-b20820/result_gtdb.tsv
[2023-03-14 11:15:24,971] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:15:24,972] [INFO] DFAST_QC result json was written to OceanDNA-b20820/dqc_result.json
[2023-03-14 11:15:24,972] [INFO] DFAST_QC completed!
[2023-03-14 11:15:24,972] [INFO] Total running time: 0h1m12s