[2023-03-18 07:29:29,816] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:29:29,816] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:29:29,816] [INFO] DQC Reference Directory: /var/lib/cwl/stgef8760f5-6008-490a-826f-710a2143fb48/dqc_reference
[2023-03-18 07:29:30,933] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:29:30,933] [INFO] Task started: Prodigal
[2023-03-18 07:29:30,933] [INFO] Running command: cat /var/lib/cwl/stgd9b4ff01-e218-44ed-9b7b-f8b5f33d0961/OceanDNA-b9187.fa | prodigal -d OceanDNA-b9187/cds.fna -a OceanDNA-b9187/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:29:41,234] [INFO] Task succeeded: Prodigal
[2023-03-18 07:29:41,234] [INFO] Task started: HMMsearch
[2023-03-18 07:29:41,234] [INFO] Running command: hmmsearch --tblout OceanDNA-b9187/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgef8760f5-6008-490a-826f-710a2143fb48/dqc_reference/reference_markers.hmm OceanDNA-b9187/protein.faa > /dev/null
[2023-03-18 07:29:41,419] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:29:41,419] [INFO] Found 6/6 markers.
[2023-03-18 07:29:41,431] [INFO] Query marker FASTA was written to OceanDNA-b9187/markers.fasta
[2023-03-18 07:29:41,431] [INFO] Task started: Blastn
[2023-03-18 07:29:41,431] [INFO] Running command: blastn -query OceanDNA-b9187/markers.fasta -db /var/lib/cwl/stgef8760f5-6008-490a-826f-710a2143fb48/dqc_reference/reference_markers.fasta -out OceanDNA-b9187/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:29:41,962] [INFO] Task succeeded: Blastn
[2023-03-18 07:29:41,963] [INFO] Selected 37 target genomes.
[2023-03-18 07:29:41,963] [INFO] Target genome list was writen to OceanDNA-b9187/target_genomes.txt
[2023-03-18 07:29:41,981] [INFO] Task started: fastANI
[2023-03-18 07:29:41,982] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9b4ff01-e218-44ed-9b7b-f8b5f33d0961/OceanDNA-b9187.fa --refList OceanDNA-b9187/target_genomes.txt --output OceanDNA-b9187/fastani_result.tsv --threads 1
[2023-03-18 07:30:04,161] [INFO] Task succeeded: fastANI
[2023-03-18 07:30:04,161] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgef8760f5-6008-490a-826f-710a2143fb48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:30:04,162] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgef8760f5-6008-490a-826f-710a2143fb48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:30:04,162] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:30:04,162] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 07:30:04,162] [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 07:30:04,162] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9187/tc_result.tsv
[2023-03-18 07:30:04,162] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:30:04,162] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:30:04,162] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgef8760f5-6008-490a-826f-710a2143fb48/dqc_reference/checkm_data
[2023-03-18 07:30:04,165] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:30:04,167] [INFO] Task started: CheckM
[2023-03-18 07:30:04,168] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9187/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9187/checkm_input OceanDNA-b9187/checkm_result
[2023-03-18 07:30:34,247] [INFO] Task succeeded: CheckM
[2023-03-18 07:30:34,248] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:30:34,249] [INFO] ===== Completeness check finished =====
[2023-03-18 07:30:34,250] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:30:34,250] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9187/markers.fasta)
[2023-03-18 07:30:34,250] [INFO] Task started: Blastn
[2023-03-18 07:30:34,250] [INFO] Running command: blastn -query OceanDNA-b9187/markers.fasta -db /var/lib/cwl/stgef8760f5-6008-490a-826f-710a2143fb48/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9187/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:30:35,020] [INFO] Task succeeded: Blastn
[2023-03-18 07:30:35,021] [INFO] Selected 25 target genomes.
[2023-03-18 07:30:35,021] [INFO] Target genome list was writen to OceanDNA-b9187/target_genomes_gtdb.txt
[2023-03-18 07:30:35,478] [INFO] Task started: fastANI
[2023-03-18 07:30:35,478] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9b4ff01-e218-44ed-9b7b-f8b5f33d0961/OceanDNA-b9187.fa --refList OceanDNA-b9187/target_genomes_gtdb.txt --output OceanDNA-b9187/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:30:45,421] [INFO] Task succeeded: fastANI
[2023-03-18 07:30:45,429] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 07:30:45,429] [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_011525195.1	s__MS024-2A sp011525195	79.6917	316	534	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_902546725.1	s__MS024-2A sp902546725	77.8835	130	534	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_002167945.1	s__MS024-2A sp002167945	77.8689	145	534	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	77.0325	102	534	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	77.014	98	534	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_017851655.1	s__MS024-2A sp017851655	76.8465	134	534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.55	99.53	0.87	0.86	3	-
GCA_008081175.1	s__MS024-2A sp008081175	76.8293	54	534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.02	98.61	0.90	0.80	6	-
GCA_002714815.1	s__MS024-2A sp002714815	76.8073	75	534	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_905181895.1	s__MS024-2A sp905181895	76.7647	52	534	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	76.7387	92	534	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_002292265.1	s__MS024-2A sp002292265	76.6811	104	534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.71	99.21	0.94	0.92	6	-
GCA_010031465.1	s__MS024-2A sp010031465	76.6212	73	534	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_902512755.1	s__MS024-2A sp902512755	76.4698	54	534	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 07:30:45,430] [INFO] GTDB search result was written to OceanDNA-b9187/result_gtdb.tsv
[2023-03-18 07:30:45,430] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:30:45,431] [INFO] DFAST_QC result json was written to OceanDNA-b9187/dqc_result.json
[2023-03-18 07:30:45,431] [INFO] DFAST_QC completed!
[2023-03-18 07:30:45,431] [INFO] Total running time: 0h1m16s