[2023-03-15 08:09:45,441] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:09:45,441] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:09:45,442] [INFO] DQC Reference Directory: /var/lib/cwl/stgd2061bdd-f797-4bd5-a7ff-1045775e9bce/dqc_reference
[2023-03-15 08:09:46,866] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:09:46,866] [INFO] Task started: Prodigal
[2023-03-15 08:09:46,866] [INFO] Running command: cat /var/lib/cwl/stgbe6c24b8-ba84-4d71-a013-d5ae02d1d4e6/OceanDNA-b869.fa | prodigal -d OceanDNA-b869/cds.fna -a OceanDNA-b869/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:09:55,303] [INFO] Task succeeded: Prodigal
[2023-03-15 08:09:55,303] [INFO] Task started: HMMsearch
[2023-03-15 08:09:55,304] [INFO] Running command: hmmsearch --tblout OceanDNA-b869/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd2061bdd-f797-4bd5-a7ff-1045775e9bce/dqc_reference/reference_markers.hmm OceanDNA-b869/protein.faa > /dev/null
[2023-03-15 08:09:55,496] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:09:55,496] [INFO] Found 6/6 markers.
[2023-03-15 08:09:55,515] [INFO] Query marker FASTA was written to OceanDNA-b869/markers.fasta
[2023-03-15 08:09:55,517] [INFO] Task started: Blastn
[2023-03-15 08:09:55,517] [INFO] Running command: blastn -query OceanDNA-b869/markers.fasta -db /var/lib/cwl/stgd2061bdd-f797-4bd5-a7ff-1045775e9bce/dqc_reference/reference_markers.fasta -out OceanDNA-b869/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:09:56,023] [INFO] Task succeeded: Blastn
[2023-03-15 08:09:56,023] [INFO] Selected 11 target genomes.
[2023-03-15 08:09:56,024] [INFO] Target genome list was writen to OceanDNA-b869/target_genomes.txt
[2023-03-15 08:09:56,031] [INFO] Task started: fastANI
[2023-03-15 08:09:56,031] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe6c24b8-ba84-4d71-a013-d5ae02d1d4e6/OceanDNA-b869.fa --refList OceanDNA-b869/target_genomes.txt --output OceanDNA-b869/fastani_result.tsv --threads 1
[2023-03-15 08:10:00,536] [INFO] Task succeeded: fastANI
[2023-03-15 08:10:00,537] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd2061bdd-f797-4bd5-a7ff-1045775e9bce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:10:00,537] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd2061bdd-f797-4bd5-a7ff-1045775e9bce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:10:00,537] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 08:10:00,537] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 08:10:00,537] [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 08:10:00,537] [INFO] DFAST Taxonomy check result was written to OceanDNA-b869/tc_result.tsv
[2023-03-15 08:10:00,538] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:10:00,538] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:10:00,538] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd2061bdd-f797-4bd5-a7ff-1045775e9bce/dqc_reference/checkm_data
[2023-03-15 08:10:00,541] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:10:00,592] [INFO] Task started: CheckM
[2023-03-15 08:10:00,592] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b869/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b869/checkm_input OceanDNA-b869/checkm_result
[2023-03-15 08:10:26,830] [INFO] Task succeeded: CheckM
[2023-03-15 08:10:26,830] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 08:10:26,837] [INFO] ===== Completeness check finished =====
[2023-03-15 08:10:26,837] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:10:26,837] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b869/markers.fasta)
[2023-03-15 08:10:26,837] [INFO] Task started: Blastn
[2023-03-15 08:10:26,838] [INFO] Running command: blastn -query OceanDNA-b869/markers.fasta -db /var/lib/cwl/stgd2061bdd-f797-4bd5-a7ff-1045775e9bce/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b869/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:10:27,579] [INFO] Task succeeded: Blastn
[2023-03-15 08:10:27,581] [INFO] Selected 10 target genomes.
[2023-03-15 08:10:27,582] [INFO] Target genome list was writen to OceanDNA-b869/target_genomes_gtdb.txt
[2023-03-15 08:10:27,595] [INFO] Task started: fastANI
[2023-03-15 08:10:27,595] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe6c24b8-ba84-4d71-a013-d5ae02d1d4e6/OceanDNA-b869.fa --refList OceanDNA-b869/target_genomes_gtdb.txt --output OceanDNA-b869/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:10:31,528] [INFO] Task succeeded: fastANI
[2023-03-15 08:10:31,534] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 08:10:31,534] [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_003214465.1	s__MedAcidi-G1 sp003214465	98.9242	438	491	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	conclusive
GCA_002713545.1	s__MedAcidi-G1 sp002713545	88.3525	341	491	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	-
GCA_000817085.1	s__MedAcidi-G1 sp000817085	85.0749	396	491	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_002299135.1	s__MedAcidi-G1 sp002299135	84.5771	323	491	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	84.1211	328	491	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	83.8444	370	491	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	82.4398	290	491	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_002721755.1	s__MedAcidi-G1 sp002721755	78.991	233	491	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	-
--------------------------------------------------------------------------------
[2023-03-15 08:10:31,535] [INFO] GTDB search result was written to OceanDNA-b869/result_gtdb.tsv
[2023-03-15 08:10:31,535] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:10:31,537] [INFO] DFAST_QC result json was written to OceanDNA-b869/dqc_result.json
[2023-03-15 08:10:31,537] [INFO] DFAST_QC completed!
[2023-03-15 08:10:31,537] [INFO] Total running time: 0h0m46s