[2023-03-18 05:17:48,207] [INFO] DFAST_QC pipeline started.
[2023-03-18 05:17:48,207] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 05:17:48,207] [INFO] DQC Reference Directory: /var/lib/cwl/stga3f7990d-5664-4463-86c8-a359af53e824/dqc_reference
[2023-03-18 05:17:49,289] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 05:17:49,289] [INFO] Task started: Prodigal
[2023-03-18 05:17:49,289] [INFO] Running command: cat /var/lib/cwl/stg5e3ba197-b9a8-49bc-96c9-3a77139a0618/OceanDNA-b9009.fa | prodigal -d OceanDNA-b9009/cds.fna -a OceanDNA-b9009/protein.faa -g 11 -q > /dev/null
[2023-03-18 05:17:55,167] [INFO] Task succeeded: Prodigal
[2023-03-18 05:17:55,167] [INFO] Task started: HMMsearch
[2023-03-18 05:17:55,167] [INFO] Running command: hmmsearch --tblout OceanDNA-b9009/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga3f7990d-5664-4463-86c8-a359af53e824/dqc_reference/reference_markers.hmm OceanDNA-b9009/protein.faa > /dev/null
[2023-03-18 05:17:55,327] [INFO] Task succeeded: HMMsearch
[2023-03-18 05:17:55,328] [INFO] Found 6/6 markers.
[2023-03-18 05:17:55,336] [INFO] Query marker FASTA was written to OceanDNA-b9009/markers.fasta
[2023-03-18 05:17:55,337] [INFO] Task started: Blastn
[2023-03-18 05:17:55,337] [INFO] Running command: blastn -query OceanDNA-b9009/markers.fasta -db /var/lib/cwl/stga3f7990d-5664-4463-86c8-a359af53e824/dqc_reference/reference_markers.fasta -out OceanDNA-b9009/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:17:55,859] [INFO] Task succeeded: Blastn
[2023-03-18 05:17:55,860] [INFO] Selected 25 target genomes.
[2023-03-18 05:17:55,860] [INFO] Target genome list was writen to OceanDNA-b9009/target_genomes.txt
[2023-03-18 05:17:55,875] [INFO] Task started: fastANI
[2023-03-18 05:17:55,875] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e3ba197-b9a8-49bc-96c9-3a77139a0618/OceanDNA-b9009.fa --refList OceanDNA-b9009/target_genomes.txt --output OceanDNA-b9009/fastani_result.tsv --threads 1
[2023-03-18 05:18:09,933] [INFO] Task succeeded: fastANI
[2023-03-18 05:18:09,934] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga3f7990d-5664-4463-86c8-a359af53e824/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 05:18:09,934] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga3f7990d-5664-4463-86c8-a359af53e824/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 05:18:09,934] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 05:18:09,934] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 05:18:09,934] [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 05:18:09,935] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9009/tc_result.tsv
[2023-03-18 05:18:09,935] [INFO] ===== Taxonomy check completed =====
[2023-03-18 05:18:09,935] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 05:18:09,935] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga3f7990d-5664-4463-86c8-a359af53e824/dqc_reference/checkm_data
[2023-03-18 05:18:09,937] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 05:18:09,955] [INFO] Task started: CheckM
[2023-03-18 05:18:09,955] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9009/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9009/checkm_input OceanDNA-b9009/checkm_result
[2023-03-18 05:18:30,265] [INFO] Task succeeded: CheckM
[2023-03-18 05:18:30,266] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 6.25%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 05:18:30,268] [INFO] ===== Completeness check finished =====
[2023-03-18 05:18:30,268] [INFO] ===== Start GTDB Search =====
[2023-03-18 05:18:30,268] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9009/markers.fasta)
[2023-03-18 05:18:30,269] [INFO] Task started: Blastn
[2023-03-18 05:18:30,269] [INFO] Running command: blastn -query OceanDNA-b9009/markers.fasta -db /var/lib/cwl/stga3f7990d-5664-4463-86c8-a359af53e824/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9009/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:18:31,008] [INFO] Task succeeded: Blastn
[2023-03-18 05:18:31,009] [INFO] Selected 13 target genomes.
[2023-03-18 05:18:31,009] [INFO] Target genome list was writen to OceanDNA-b9009/target_genomes_gtdb.txt
[2023-03-18 05:18:31,023] [INFO] Task started: fastANI
[2023-03-18 05:18:31,023] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e3ba197-b9a8-49bc-96c9-3a77139a0618/OceanDNA-b9009.fa --refList OceanDNA-b9009/target_genomes_gtdb.txt --output OceanDNA-b9009/fastani_result_gtdb.tsv --threads 1
[2023-03-18 05:18:34,820] [INFO] Task succeeded: fastANI
[2023-03-18 05:18:34,825] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 05:18:34,825] [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_902613595.1	s__MS024-2A sp902613595	93.5582	290	318	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_003130815.1	s__MS024-2A sp003130815	84.8248	256	318	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_902561795.1	s__MS024-2A sp902561795	84.7659	242	318	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_002167525.1	s__MS024-2A sp002167525	84.6408	202	318	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	98.89	98.89	0.72	0.72	2	-
GCA_902618245.1	s__MS024-2A sp902618245	84.6085	253	318	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	98.05	96.19	0.87	0.86	3	-
GCA_002714815.1	s__MS024-2A sp002714815	76.9508	87	318	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 05:18:34,825] [INFO] GTDB search result was written to OceanDNA-b9009/result_gtdb.tsv
[2023-03-18 05:18:34,826] [INFO] ===== GTDB Search completed =====
[2023-03-18 05:18:34,826] [INFO] DFAST_QC result json was written to OceanDNA-b9009/dqc_result.json
[2023-03-18 05:18:34,826] [INFO] DFAST_QC completed!
[2023-03-18 05:18:34,826] [INFO] Total running time: 0h0m47s