[2023-03-15 03:14:16,305] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:14:16,305] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:14:16,306] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2ce29b0-e13a-4cd4-9d36-f7d8ff6c7bb7/dqc_reference
[2023-03-15 03:14:17,486] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:14:17,486] [INFO] Task started: Prodigal
[2023-03-15 03:14:17,487] [INFO] Running command: cat /var/lib/cwl/stg2f80a5fe-1d95-4bcb-8f7b-ee89c4c56510/OceanDNA-b6012.fa | prodigal -d OceanDNA-b6012/cds.fna -a OceanDNA-b6012/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:14:26,004] [INFO] Task succeeded: Prodigal
[2023-03-15 03:14:26,004] [INFO] Task started: HMMsearch
[2023-03-15 03:14:26,004] [INFO] Running command: hmmsearch --tblout OceanDNA-b6012/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2ce29b0-e13a-4cd4-9d36-f7d8ff6c7bb7/dqc_reference/reference_markers.hmm OceanDNA-b6012/protein.faa > /dev/null
[2023-03-15 03:14:26,177] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:14:26,177] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2f80a5fe-1d95-4bcb-8f7b-ee89c4c56510/OceanDNA-b6012.fa]
[2023-03-15 03:14:26,195] [INFO] Query marker FASTA was written to OceanDNA-b6012/markers.fasta
[2023-03-15 03:14:26,195] [INFO] Task started: Blastn
[2023-03-15 03:14:26,195] [INFO] Running command: blastn -query OceanDNA-b6012/markers.fasta -db /var/lib/cwl/stgb2ce29b0-e13a-4cd4-9d36-f7d8ff6c7bb7/dqc_reference/reference_markers.fasta -out OceanDNA-b6012/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:14:26,708] [INFO] Task succeeded: Blastn
[2023-03-15 03:14:26,709] [INFO] Selected 16 target genomes.
[2023-03-15 03:14:26,709] [INFO] Target genome list was writen to OceanDNA-b6012/target_genomes.txt
[2023-03-15 03:14:26,718] [INFO] Task started: fastANI
[2023-03-15 03:14:26,718] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f80a5fe-1d95-4bcb-8f7b-ee89c4c56510/OceanDNA-b6012.fa --refList OceanDNA-b6012/target_genomes.txt --output OceanDNA-b6012/fastani_result.tsv --threads 1
[2023-03-15 03:14:35,464] [INFO] Task succeeded: fastANI
[2023-03-15 03:14:35,464] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2ce29b0-e13a-4cd4-9d36-f7d8ff6c7bb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 03:14:35,465] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2ce29b0-e13a-4cd4-9d36-f7d8ff6c7bb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 03:14:35,465] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 03:14:35,465] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 03:14:35,465] [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 03:14:35,465] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6012/tc_result.tsv
[2023-03-15 03:14:35,465] [INFO] ===== Taxonomy check completed =====
[2023-03-15 03:14:35,465] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:14:35,465] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2ce29b0-e13a-4cd4-9d36-f7d8ff6c7bb7/dqc_reference/checkm_data
[2023-03-15 03:14:35,468] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:14:35,481] [INFO] Task started: CheckM
[2023-03-15 03:14:35,481] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6012/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6012/checkm_input OceanDNA-b6012/checkm_result
[2023-03-15 03:15:02,329] [INFO] Task succeeded: CheckM
[2023-03-15 03:15:02,330] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 51.85%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 03:15:02,331] [INFO] ===== Completeness check finished =====
[2023-03-15 03:15:02,332] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:15:02,332] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6012/markers.fasta)
[2023-03-15 03:15:02,332] [INFO] Task started: Blastn
[2023-03-15 03:15:02,332] [INFO] Running command: blastn -query OceanDNA-b6012/markers.fasta -db /var/lib/cwl/stgb2ce29b0-e13a-4cd4-9d36-f7d8ff6c7bb7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6012/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:15:03,075] [INFO] Task succeeded: Blastn
[2023-03-15 03:15:03,076] [INFO] Selected 13 target genomes.
[2023-03-15 03:15:03,076] [INFO] Target genome list was writen to OceanDNA-b6012/target_genomes_gtdb.txt
[2023-03-15 03:15:03,087] [INFO] Task started: fastANI
[2023-03-15 03:15:03,088] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f80a5fe-1d95-4bcb-8f7b-ee89c4c56510/OceanDNA-b6012.fa --refList OceanDNA-b6012/target_genomes_gtdb.txt --output OceanDNA-b6012/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:15:07,700] [INFO] Task succeeded: fastANI
[2023-03-15 03:15:07,704] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 03:15:07,705] [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_003023665.1	s__UBA10364 sp003023665	95.0032	270	321	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	98.70	98.70	0.79	0.79	2	conclusive
GCA_902614915.1	s__UBA10364 sp902614915	86.5823	229	321	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707525.1	s__UBA10364 sp002707525	82.7822	257	321	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018623275.1	s__UBA10364 sp018623275	77.6704	57	321	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002430755.1	s__UBA10364 sp002430755	77.3825	61	321	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003545085.1	s__UBA10364 sp003545085	77.0883	57	321	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 03:15:07,705] [INFO] GTDB search result was written to OceanDNA-b6012/result_gtdb.tsv
[2023-03-15 03:15:07,705] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:15:07,706] [INFO] DFAST_QC result json was written to OceanDNA-b6012/dqc_result.json
[2023-03-15 03:15:07,706] [INFO] DFAST_QC completed!
[2023-03-15 03:15:07,706] [INFO] Total running time: 0h0m51s