[2023-03-16 23:05:03,844] [INFO] DFAST_QC pipeline started.
[2023-03-16 23:05:03,844] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 23:05:03,845] [INFO] DQC Reference Directory: /var/lib/cwl/stge26d62e4-248f-4810-a82c-3e4d6c532ae0/dqc_reference
[2023-03-16 23:05:05,100] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 23:05:05,100] [INFO] Task started: Prodigal
[2023-03-16 23:05:05,100] [INFO] Running command: cat /var/lib/cwl/stg6be3237f-e7a0-43d6-875d-347f81beb85a/OceanDNA-b9152.fa | prodigal -d OceanDNA-b9152/cds.fna -a OceanDNA-b9152/protein.faa -g 11 -q > /dev/null
[2023-03-16 23:05:09,919] [INFO] Task succeeded: Prodigal
[2023-03-16 23:05:09,919] [INFO] Task started: HMMsearch
[2023-03-16 23:05:09,919] [INFO] Running command: hmmsearch --tblout OceanDNA-b9152/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge26d62e4-248f-4810-a82c-3e4d6c532ae0/dqc_reference/reference_markers.hmm OceanDNA-b9152/protein.faa > /dev/null
[2023-03-16 23:05:10,093] [INFO] Task succeeded: HMMsearch
[2023-03-16 23:05:10,093] [INFO] Found 6/6 markers.
[2023-03-16 23:05:10,101] [INFO] Query marker FASTA was written to OceanDNA-b9152/markers.fasta
[2023-03-16 23:05:10,102] [INFO] Task started: Blastn
[2023-03-16 23:05:10,102] [INFO] Running command: blastn -query OceanDNA-b9152/markers.fasta -db /var/lib/cwl/stge26d62e4-248f-4810-a82c-3e4d6c532ae0/dqc_reference/reference_markers.fasta -out OceanDNA-b9152/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:05:10,639] [INFO] Task succeeded: Blastn
[2023-03-16 23:05:10,640] [INFO] Selected 28 target genomes.
[2023-03-16 23:05:10,640] [INFO] Target genome list was writen to OceanDNA-b9152/target_genomes.txt
[2023-03-16 23:05:10,655] [INFO] Task started: fastANI
[2023-03-16 23:05:10,655] [INFO] Running command: fastANI --query /var/lib/cwl/stg6be3237f-e7a0-43d6-875d-347f81beb85a/OceanDNA-b9152.fa --refList OceanDNA-b9152/target_genomes.txt --output OceanDNA-b9152/fastani_result.tsv --threads 1
[2023-03-16 23:05:27,857] [INFO] Task succeeded: fastANI
[2023-03-16 23:05:27,857] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge26d62e4-248f-4810-a82c-3e4d6c532ae0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 23:05:27,858] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge26d62e4-248f-4810-a82c-3e4d6c532ae0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 23:05:27,858] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 23:05:27,858] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 23:05:27,858] [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
--------------------------------------------------------------------------------
[2023-03-16 23:05:27,858] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9152/tc_result.tsv
[2023-03-16 23:05:27,858] [INFO] ===== Taxonomy check completed =====
[2023-03-16 23:05:27,858] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 23:05:27,858] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge26d62e4-248f-4810-a82c-3e4d6c532ae0/dqc_reference/checkm_data
[2023-03-16 23:05:27,861] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 23:05:27,864] [INFO] Task started: CheckM
[2023-03-16 23:05:27,864] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9152/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9152/checkm_input OceanDNA-b9152/checkm_result
[2023-03-16 23:05:46,632] [INFO] Task succeeded: CheckM
[2023-03-16 23:05:46,632] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 23:05:46,634] [INFO] ===== Completeness check finished =====
[2023-03-16 23:05:46,634] [INFO] ===== Start GTDB Search =====
[2023-03-16 23:05:46,634] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9152/markers.fasta)
[2023-03-16 23:05:46,635] [INFO] Task started: Blastn
[2023-03-16 23:05:46,635] [INFO] Running command: blastn -query OceanDNA-b9152/markers.fasta -db /var/lib/cwl/stge26d62e4-248f-4810-a82c-3e4d6c532ae0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9152/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:05:47,448] [INFO] Task succeeded: Blastn
[2023-03-16 23:05:47,449] [INFO] Selected 24 target genomes.
[2023-03-16 23:05:47,450] [INFO] Target genome list was writen to OceanDNA-b9152/target_genomes_gtdb.txt
[2023-03-16 23:05:48,011] [INFO] Task started: fastANI
[2023-03-16 23:05:48,011] [INFO] Running command: fastANI --query /var/lib/cwl/stg6be3237f-e7a0-43d6-875d-347f81beb85a/OceanDNA-b9152.fa --refList OceanDNA-b9152/target_genomes_gtdb.txt --output OceanDNA-b9152/fastani_result_gtdb.tsv --threads 1
[2023-03-16 23:05:57,131] [INFO] Task succeeded: fastANI
[2023-03-16 23:05:57,138] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 23:05:57,138] [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_902512755.1	s__MS024-2A sp902512755	82.791	117	250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902517245.1	s__MS024-2A sp902517245	79.0282	124	250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902606525.1	s__MS024-2A sp902606525	78.6098	88	250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002169865.1	s__MS024-2A sp002169865	78.3239	74	250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017852075.1	s__MS024-2A sp017852075	76.9858	56	250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.70	99.69	0.95	0.94	3	-
GCA_905480425.1	s__MS024-2A sp905480425	76.8875	73	250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	95.11	95.11	0.87	0.87	2	-
GCA_002714815.1	s__MS024-2A sp002714815	76.7563	78	250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182305.1	s__MS024-2A sp905182305	76.6772	62	250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009886625.1	s__MS024-2A sp009886625	76.323	76	250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000173095.1	s__MS024-2A sp000173095	76.2256	63	250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.61	99.48	0.88	0.84	16	-
GCA_003130815.1	s__MS024-2A sp003130815	75.979	50	250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 23:05:57,138] [INFO] GTDB search result was written to OceanDNA-b9152/result_gtdb.tsv
[2023-03-16 23:05:57,138] [INFO] ===== GTDB Search completed =====
[2023-03-16 23:05:57,139] [INFO] DFAST_QC result json was written to OceanDNA-b9152/dqc_result.json
[2023-03-16 23:05:57,139] [INFO] DFAST_QC completed!
[2023-03-16 23:05:57,140] [INFO] Total running time: 0h0m53s