[2023-03-15 05:37:29,654] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:37:29,654] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:37:29,654] [INFO] DQC Reference Directory: /var/lib/cwl/stg9b0cf8d0-7365-4c44-a84b-164b28ca07cc/dqc_reference
[2023-03-15 05:37:30,736] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:37:30,736] [INFO] Task started: Prodigal
[2023-03-15 05:37:30,736] [INFO] Running command: cat /var/lib/cwl/stg91e5d8a1-c5be-4d23-a8bb-d5d6ecdad66a/OceanDNA-b9196.fa | prodigal -d OceanDNA-b9196/cds.fna -a OceanDNA-b9196/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:37:38,010] [INFO] Task succeeded: Prodigal
[2023-03-15 05:37:38,010] [INFO] Task started: HMMsearch
[2023-03-15 05:37:38,010] [INFO] Running command: hmmsearch --tblout OceanDNA-b9196/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9b0cf8d0-7365-4c44-a84b-164b28ca07cc/dqc_reference/reference_markers.hmm OceanDNA-b9196/protein.faa > /dev/null
[2023-03-15 05:37:38,151] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:37:38,152] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg91e5d8a1-c5be-4d23-a8bb-d5d6ecdad66a/OceanDNA-b9196.fa]
[2023-03-15 05:37:38,162] [INFO] Query marker FASTA was written to OceanDNA-b9196/markers.fasta
[2023-03-15 05:37:38,162] [INFO] Task started: Blastn
[2023-03-15 05:37:38,162] [INFO] Running command: blastn -query OceanDNA-b9196/markers.fasta -db /var/lib/cwl/stg9b0cf8d0-7365-4c44-a84b-164b28ca07cc/dqc_reference/reference_markers.fasta -out OceanDNA-b9196/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:37:38,710] [INFO] Task succeeded: Blastn
[2023-03-15 05:37:38,711] [INFO] Selected 24 target genomes.
[2023-03-15 05:37:38,711] [INFO] Target genome list was writen to OceanDNA-b9196/target_genomes.txt
[2023-03-15 05:37:38,721] [INFO] Task started: fastANI
[2023-03-15 05:37:38,722] [INFO] Running command: fastANI --query /var/lib/cwl/stg91e5d8a1-c5be-4d23-a8bb-d5d6ecdad66a/OceanDNA-b9196.fa --refList OceanDNA-b9196/target_genomes.txt --output OceanDNA-b9196/fastani_result.tsv --threads 1
[2023-03-15 05:37:52,606] [INFO] Task succeeded: fastANI
[2023-03-15 05:37:52,606] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9b0cf8d0-7365-4c44-a84b-164b28ca07cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:37:52,606] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9b0cf8d0-7365-4c44-a84b-164b28ca07cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:37:52,607] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:37:52,607] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 05:37:52,607] [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 05:37:52,607] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9196/tc_result.tsv
[2023-03-15 05:37:52,607] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:37:52,607] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:37:52,607] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9b0cf8d0-7365-4c44-a84b-164b28ca07cc/dqc_reference/checkm_data
[2023-03-15 05:37:52,610] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:37:52,641] [INFO] Task started: CheckM
[2023-03-15 05:37:52,641] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9196/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9196/checkm_input OceanDNA-b9196/checkm_result
[2023-03-15 05:38:16,659] [INFO] Task succeeded: CheckM
[2023-03-15 05:38:16,660] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.29%
Contamintation: 3.97%
Strain heterogeneity: 25.00%
--------------------------------------------------------------------------------
[2023-03-15 05:38:16,662] [INFO] ===== Completeness check finished =====
[2023-03-15 05:38:16,662] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:38:16,662] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9196/markers.fasta)
[2023-03-15 05:38:16,662] [INFO] Task started: Blastn
[2023-03-15 05:38:16,662] [INFO] Running command: blastn -query OceanDNA-b9196/markers.fasta -db /var/lib/cwl/stg9b0cf8d0-7365-4c44-a84b-164b28ca07cc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9196/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:38:17,479] [INFO] Task succeeded: Blastn
[2023-03-15 05:38:17,480] [INFO] Selected 16 target genomes.
[2023-03-15 05:38:17,480] [INFO] Target genome list was writen to OceanDNA-b9196/target_genomes_gtdb.txt
[2023-03-15 05:38:17,498] [INFO] Task started: fastANI
[2023-03-15 05:38:17,498] [INFO] Running command: fastANI --query /var/lib/cwl/stg91e5d8a1-c5be-4d23-a8bb-d5d6ecdad66a/OceanDNA-b9196.fa --refList OceanDNA-b9196/target_genomes_gtdb.txt --output OceanDNA-b9196/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:38:24,113] [INFO] Task succeeded: fastANI
[2023-03-15 05:38:24,119] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 05:38:24,119] [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_902546725.1	s__MS024-2A sp902546725	98.0536	238	319	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002167945.1	s__MS024-2A sp002167945	90.8956	275	319	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_011525195.1	s__MS024-2A sp011525195	77.7053	101	319	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_017858055.1	s__MS024-2A sp002384715	77.5464	122	319	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.54	99.54	0.94	0.94	2	-
GCA_017851655.1	s__MS024-2A sp017851655	77.362	120	319	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_002705385.1	s__MS024-2A sp002705385	77.3334	92	319	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	77.1419	69	319	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_009886625.1	s__MS024-2A sp009886625	77.1043	71	319	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	76.9982	63	319	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.61	99.48	0.88	0.84	16	-
--------------------------------------------------------------------------------
[2023-03-15 05:38:24,120] [INFO] GTDB search result was written to OceanDNA-b9196/result_gtdb.tsv
[2023-03-15 05:38:24,120] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:38:24,121] [INFO] DFAST_QC result json was written to OceanDNA-b9196/dqc_result.json
[2023-03-15 05:38:24,121] [INFO] DFAST_QC completed!
[2023-03-15 05:38:24,121] [INFO] Total running time: 0h0m54s