[2023-03-14 12:38:42,327] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:38:42,327] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:38:42,327] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0e86ccf-b2e7-415f-874a-bc7496be9833/dqc_reference
[2023-03-14 12:38:43,419] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:38:43,452] [INFO] Task started: Prodigal
[2023-03-14 12:38:43,452] [INFO] Running command: cat /var/lib/cwl/stga4abec96-42c5-422b-b16c-44c961b44bb9/OceanDNA-b8542.fa | prodigal -d OceanDNA-b8542/cds.fna -a OceanDNA-b8542/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:38:48,662] [INFO] Task succeeded: Prodigal
[2023-03-14 12:38:48,663] [INFO] Task started: HMMsearch
[2023-03-14 12:38:48,663] [INFO] Running command: hmmsearch --tblout OceanDNA-b8542/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0e86ccf-b2e7-415f-874a-bc7496be9833/dqc_reference/reference_markers.hmm OceanDNA-b8542/protein.faa > /dev/null
[2023-03-14 12:38:48,821] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:38:48,822] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga4abec96-42c5-422b-b16c-44c961b44bb9/OceanDNA-b8542.fa]
[2023-03-14 12:38:48,840] [INFO] Query marker FASTA was written to OceanDNA-b8542/markers.fasta
[2023-03-14 12:38:48,841] [INFO] Task started: Blastn
[2023-03-14 12:38:48,842] [INFO] Running command: blastn -query OceanDNA-b8542/markers.fasta -db /var/lib/cwl/stgf0e86ccf-b2e7-415f-874a-bc7496be9833/dqc_reference/reference_markers.fasta -out OceanDNA-b8542/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:38:49,421] [INFO] Task succeeded: Blastn
[2023-03-14 12:38:49,426] [INFO] Selected 22 target genomes.
[2023-03-14 12:38:49,426] [INFO] Target genome list was writen to OceanDNA-b8542/target_genomes.txt
[2023-03-14 12:38:49,438] [INFO] Task started: fastANI
[2023-03-14 12:38:49,438] [INFO] Running command: fastANI --query /var/lib/cwl/stga4abec96-42c5-422b-b16c-44c961b44bb9/OceanDNA-b8542.fa --refList OceanDNA-b8542/target_genomes.txt --output OceanDNA-b8542/fastani_result.tsv --threads 1
[2023-03-14 12:39:01,219] [INFO] Task succeeded: fastANI
[2023-03-14 12:39:01,219] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0e86ccf-b2e7-415f-874a-bc7496be9833/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:39:01,219] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0e86ccf-b2e7-415f-874a-bc7496be9833/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:39:01,219] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:39:01,219] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 12:39:01,219] [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 12:39:01,221] [INFO] DFAST Taxonomy check result was written to OceanDNA-b8542/tc_result.tsv
[2023-03-14 12:39:01,225] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:39:01,225] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:39:01,225] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0e86ccf-b2e7-415f-874a-bc7496be9833/dqc_reference/checkm_data
[2023-03-14 12:39:01,235] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:39:01,239] [INFO] Task started: CheckM
[2023-03-14 12:39:01,240] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b8542/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b8542/checkm_input OceanDNA-b8542/checkm_result
[2023-03-14 12:39:20,843] [INFO] Task succeeded: CheckM
[2023-03-14 12:39:20,844] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.65%
Contamintation: 6.31%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2023-03-14 12:39:20,863] [INFO] ===== Completeness check finished =====
[2023-03-14 12:39:20,864] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:39:20,864] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b8542/markers.fasta)
[2023-03-14 12:39:20,865] [INFO] Task started: Blastn
[2023-03-14 12:39:20,865] [INFO] Running command: blastn -query OceanDNA-b8542/markers.fasta -db /var/lib/cwl/stgf0e86ccf-b2e7-415f-874a-bc7496be9833/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b8542/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:39:21,802] [INFO] Task succeeded: Blastn
[2023-03-14 12:39:21,806] [INFO] Selected 9 target genomes.
[2023-03-14 12:39:21,806] [INFO] Target genome list was writen to OceanDNA-b8542/target_genomes_gtdb.txt
[2023-03-14 12:39:21,812] [INFO] Task started: fastANI
[2023-03-14 12:39:21,812] [INFO] Running command: fastANI --query /var/lib/cwl/stga4abec96-42c5-422b-b16c-44c961b44bb9/OceanDNA-b8542.fa --refList OceanDNA-b8542/target_genomes_gtdb.txt --output OceanDNA-b8542/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:39:23,702] [INFO] Task succeeded: fastANI
[2023-03-14 12:39:23,709] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 12:39:23,709] [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_902593165.1	s__MED-G11 sp902593165	91.8383	228	282	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	96.69	96.69	0.86	0.86	2	-
GCA_902594485.1	s__MED-G11 sp902594485	90.3354	172	282	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	97.32	97.18	0.70	0.65	3	-
GCA_902516925.1	s__MED-G11 sp902516925	89.383	173	282	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902519955.1	s__MED-G11 sp902519955	89.1535	201	282	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	99.88	99.84	0.80	0.74	3	-
GCA_902517365.1	s__MED-G11 sp902517365	88.0773	131	282	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902620455.1	s__MED-G11 sp902620455	83.3006	223	282	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	99.20	98.53	0.88	0.86	7	-
GCA_902622595.1	s__MED-G11 sp902622595	83.1586	238	282	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	96.81	96.16	0.93	0.91	12	-
GCA_902523665.1	s__MED-G11 sp902523665	82.7997	201	282	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902514615.1	s__MED-G11 sp902514615	79.2752	134	282	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 12:39:23,710] [INFO] GTDB search result was written to OceanDNA-b8542/result_gtdb.tsv
[2023-03-14 12:39:23,711] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:39:23,714] [INFO] DFAST_QC result json was written to OceanDNA-b8542/dqc_result.json
[2023-03-14 12:39:23,714] [INFO] DFAST_QC completed!
[2023-03-14 12:39:23,714] [INFO] Total running time: 0h0m41s