[2023-03-14 13:29:09,762] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:29:09,762] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:29:09,762] [INFO] DQC Reference Directory: /var/lib/cwl/stgc469875c-3fa9-4ebc-8c17-b5d3d59e823d/dqc_reference
[2023-03-14 13:29:10,854] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:29:10,855] [INFO] Task started: Prodigal
[2023-03-14 13:29:10,855] [INFO] Running command: cat /var/lib/cwl/stg2e015daa-b2f3-4527-9e4d-b07646b1296e/OceanDNA-b664.fa | prodigal -d OceanDNA-b664/cds.fna -a OceanDNA-b664/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:29:14,481] [INFO] Task succeeded: Prodigal
[2023-03-14 13:29:14,481] [INFO] Task started: HMMsearch
[2023-03-14 13:29:14,481] [INFO] Running command: hmmsearch --tblout OceanDNA-b664/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc469875c-3fa9-4ebc-8c17-b5d3d59e823d/dqc_reference/reference_markers.hmm OceanDNA-b664/protein.faa > /dev/null
[2023-03-14 13:29:14,625] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:29:14,626] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg2e015daa-b2f3-4527-9e4d-b07646b1296e/OceanDNA-b664.fa]
[2023-03-14 13:29:14,638] [INFO] Query marker FASTA was written to OceanDNA-b664/markers.fasta
[2023-03-14 13:29:14,639] [INFO] Task started: Blastn
[2023-03-14 13:29:14,639] [INFO] Running command: blastn -query OceanDNA-b664/markers.fasta -db /var/lib/cwl/stgc469875c-3fa9-4ebc-8c17-b5d3d59e823d/dqc_reference/reference_markers.fasta -out OceanDNA-b664/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:29:15,189] [INFO] Task succeeded: Blastn
[2023-03-14 13:29:15,190] [INFO] Selected 10 target genomes.
[2023-03-14 13:29:15,190] [INFO] Target genome list was writen to OceanDNA-b664/target_genomes.txt
[2023-03-14 13:29:15,197] [INFO] Task started: fastANI
[2023-03-14 13:29:15,197] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e015daa-b2f3-4527-9e4d-b07646b1296e/OceanDNA-b664.fa --refList OceanDNA-b664/target_genomes.txt --output OceanDNA-b664/fastani_result.tsv --threads 1
[2023-03-14 13:29:20,118] [INFO] Task succeeded: fastANI
[2023-03-14 13:29:20,119] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc469875c-3fa9-4ebc-8c17-b5d3d59e823d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:29:20,119] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc469875c-3fa9-4ebc-8c17-b5d3d59e823d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:29:20,119] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 13:29:20,119] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 13:29:20,119] [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 13:29:20,120] [INFO] DFAST Taxonomy check result was written to OceanDNA-b664/tc_result.tsv
[2023-03-14 13:29:20,120] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:29:20,120] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:29:20,120] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc469875c-3fa9-4ebc-8c17-b5d3d59e823d/dqc_reference/checkm_data
[2023-03-14 13:29:20,123] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:29:20,316] [INFO] Task started: CheckM
[2023-03-14 13:29:20,316] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b664/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b664/checkm_input OceanDNA-b664/checkm_result
[2023-03-14 13:29:36,222] [INFO] Task succeeded: CheckM
[2023-03-14 13:29:36,222] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.03%
Contamintation: 0.98%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 13:29:36,224] [INFO] ===== Completeness check finished =====
[2023-03-14 13:29:36,224] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:29:36,224] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b664/markers.fasta)
[2023-03-14 13:29:36,225] [INFO] Task started: Blastn
[2023-03-14 13:29:36,225] [INFO] Running command: blastn -query OceanDNA-b664/markers.fasta -db /var/lib/cwl/stgc469875c-3fa9-4ebc-8c17-b5d3d59e823d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b664/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:29:36,935] [INFO] Task succeeded: Blastn
[2023-03-14 13:29:36,936] [INFO] Selected 7 target genomes.
[2023-03-14 13:29:36,936] [INFO] Target genome list was writen to OceanDNA-b664/target_genomes_gtdb.txt
[2023-03-14 13:29:36,940] [INFO] Task started: fastANI
[2023-03-14 13:29:36,940] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e015daa-b2f3-4527-9e4d-b07646b1296e/OceanDNA-b664.fa --refList OceanDNA-b664/target_genomes_gtdb.txt --output OceanDNA-b664/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:29:38,599] [INFO] Task succeeded: fastANI
[2023-03-14 13:29:38,604] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 13:29:38,604] [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_002299135.1	s__MedAcidi-G1 sp002299135	90.1089	73	87	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__MedAcidi-G1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002716285.1	s__MedAcidi-G1 sp002716285	89.845	63	87	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__MedAcidi-G1	95.0	99.29	99.25	0.75	0.74	4	-
GCA_002729765.1	s__MedAcidi-G1 sp002729765	88.122	79	87	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__MedAcidi-G1	95.0	98.94	98.94	0.89	0.89	2	-
GCA_002699555.1	s__MedAcidi-G1 sp002699555	84.6805	59	87	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__MedAcidi-G1	95.0	95.71	95.71	0.59	0.59	2	-
GCA_003214465.1	s__MedAcidi-G1 sp003214465	83.1326	75	87	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__MedAcidi-G1	95.0	99.48	98.96	0.92	0.84	3	-
GCA_000817085.1	s__MedAcidi-G1 sp000817085	82.5052	69	87	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__MedAcidi-G1	95.0	99.46	99.15	0.88	0.85	6	-
GCA_002713545.1	s__MedAcidi-G1 sp002713545	82.2008	57	87	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__MedAcidi-G1	95.0	98.75	98.69	0.79	0.72	3	-
--------------------------------------------------------------------------------
[2023-03-14 13:29:38,604] [INFO] GTDB search result was written to OceanDNA-b664/result_gtdb.tsv
[2023-03-14 13:29:38,604] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:29:38,605] [INFO] DFAST_QC result json was written to OceanDNA-b664/dqc_result.json
[2023-03-14 13:29:38,605] [INFO] DFAST_QC completed!
[2023-03-14 13:29:38,606] [INFO] Total running time: 0h0m29s