[2023-03-18 03:09:33,856] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:09:33,856] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:09:33,856] [INFO] DQC Reference Directory: /var/lib/cwl/stgf52388ce-e896-40da-bb3c-4c8248d5148a/dqc_reference
[2023-03-18 03:09:34,959] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:09:34,959] [INFO] Task started: Prodigal
[2023-03-18 03:09:34,959] [INFO] Running command: cat /var/lib/cwl/stg35132b81-49c8-4d06-b75d-db6f6f6bf57e/OceanDNA-b5219.fa | prodigal -d OceanDNA-b5219/cds.fna -a OceanDNA-b5219/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:09:42,408] [INFO] Task succeeded: Prodigal
[2023-03-18 03:09:42,409] [INFO] Task started: HMMsearch
[2023-03-18 03:09:42,409] [INFO] Running command: hmmsearch --tblout OceanDNA-b5219/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf52388ce-e896-40da-bb3c-4c8248d5148a/dqc_reference/reference_markers.hmm OceanDNA-b5219/protein.faa > /dev/null
[2023-03-18 03:09:42,558] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:09:42,559] [INFO] Found 6/6 markers.
[2023-03-18 03:09:42,570] [INFO] Query marker FASTA was written to OceanDNA-b5219/markers.fasta
[2023-03-18 03:09:42,570] [INFO] Task started: Blastn
[2023-03-18 03:09:42,570] [INFO] Running command: blastn -query OceanDNA-b5219/markers.fasta -db /var/lib/cwl/stgf52388ce-e896-40da-bb3c-4c8248d5148a/dqc_reference/reference_markers.fasta -out OceanDNA-b5219/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:09:43,112] [INFO] Task succeeded: Blastn
[2023-03-18 03:09:43,113] [INFO] Selected 30 target genomes.
[2023-03-18 03:09:43,114] [INFO] Target genome list was writen to OceanDNA-b5219/target_genomes.txt
[2023-03-18 03:09:43,127] [INFO] Task started: fastANI
[2023-03-18 03:09:43,127] [INFO] Running command: fastANI --query /var/lib/cwl/stg35132b81-49c8-4d06-b75d-db6f6f6bf57e/OceanDNA-b5219.fa --refList OceanDNA-b5219/target_genomes.txt --output OceanDNA-b5219/fastani_result.tsv --threads 1
[2023-03-18 03:09:58,975] [INFO] Task succeeded: fastANI
[2023-03-18 03:09:58,975] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf52388ce-e896-40da-bb3c-4c8248d5148a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:09:58,975] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf52388ce-e896-40da-bb3c-4c8248d5148a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:09:58,975] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:09:58,975] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 03:09:58,975] [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
--------------------------------------------------------------------------------
[2023-03-18 03:09:58,976] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5219/tc_result.tsv
[2023-03-18 03:09:58,976] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:09:58,976] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:09:58,976] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf52388ce-e896-40da-bb3c-4c8248d5148a/dqc_reference/checkm_data
[2023-03-18 03:09:58,978] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:09:58,981] [INFO] Task started: CheckM
[2023-03-18 03:09:58,981] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5219/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5219/checkm_input OceanDNA-b5219/checkm_result
[2023-03-18 03:10:22,981] [INFO] Task succeeded: CheckM
[2023-03-18 03:10:22,981] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 03:10:22,983] [INFO] ===== Completeness check finished =====
[2023-03-18 03:10:22,983] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:10:22,983] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5219/markers.fasta)
[2023-03-18 03:10:22,984] [INFO] Task started: Blastn
[2023-03-18 03:10:22,984] [INFO] Running command: blastn -query OceanDNA-b5219/markers.fasta -db /var/lib/cwl/stgf52388ce-e896-40da-bb3c-4c8248d5148a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5219/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:10:23,836] [INFO] Task succeeded: Blastn
[2023-03-18 03:10:23,836] [INFO] Selected 21 target genomes.
[2023-03-18 03:10:23,837] [INFO] Target genome list was writen to OceanDNA-b5219/target_genomes_gtdb.txt
[2023-03-18 03:10:23,933] [INFO] Task started: fastANI
[2023-03-18 03:10:23,933] [INFO] Running command: fastANI --query /var/lib/cwl/stg35132b81-49c8-4d06-b75d-db6f6f6bf57e/OceanDNA-b5219.fa --refList OceanDNA-b5219/target_genomes_gtdb.txt --output OceanDNA-b5219/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:10:33,754] [INFO] Task succeeded: fastANI
[2023-03-18 03:10:33,758] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 03:10:33,758] [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_003454845.1	s__UBA8444 sp003454845	97.8697	167	326	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA7312;g__UBA8444	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016779995.1	s__UBA8444 sp016779995	93.7134	306	326	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA7312;g__UBA8444	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002714805.1	s__UBA8444 sp002714805	86.7628	244	326	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA7312;g__UBA8444	95.0	95.59	95.59	0.86	0.86	2	-
GCA_016779935.1	s__GCA-2862585 sp016779935	78.125	134	326	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA7312;g__GCA-2862585	95.0	99.89	99.89	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-03-18 03:10:33,758] [INFO] GTDB search result was written to OceanDNA-b5219/result_gtdb.tsv
[2023-03-18 03:10:33,758] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:10:33,759] [INFO] DFAST_QC result json was written to OceanDNA-b5219/dqc_result.json
[2023-03-18 03:10:33,759] [INFO] DFAST_QC completed!
[2023-03-18 03:10:33,759] [INFO] Total running time: 0h0m60s