[2023-03-17 00:26:56,227] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:26:56,227] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:26:56,227] [INFO] DQC Reference Directory: /var/lib/cwl/stgb52eb0b2-d824-4d43-a631-38dcdcbd4437/dqc_reference
[2023-03-17 00:26:57,320] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:26:57,320] [INFO] Task started: Prodigal
[2023-03-17 00:26:57,320] [INFO] Running command: cat /var/lib/cwl/stg24183a8b-20f7-43b5-9766-abf2f5df2a47/OceanDNA-b9243.fa | prodigal -d OceanDNA-b9243/cds.fna -a OceanDNA-b9243/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:27:08,553] [INFO] Task succeeded: Prodigal
[2023-03-17 00:27:08,554] [INFO] Task started: HMMsearch
[2023-03-17 00:27:08,554] [INFO] Running command: hmmsearch --tblout OceanDNA-b9243/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb52eb0b2-d824-4d43-a631-38dcdcbd4437/dqc_reference/reference_markers.hmm OceanDNA-b9243/protein.faa > /dev/null
[2023-03-17 00:27:08,714] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:27:08,715] [INFO] Found 6/6 markers.
[2023-03-17 00:27:08,728] [INFO] Query marker FASTA was written to OceanDNA-b9243/markers.fasta
[2023-03-17 00:27:08,729] [INFO] Task started: Blastn
[2023-03-17 00:27:08,729] [INFO] Running command: blastn -query OceanDNA-b9243/markers.fasta -db /var/lib/cwl/stgb52eb0b2-d824-4d43-a631-38dcdcbd4437/dqc_reference/reference_markers.fasta -out OceanDNA-b9243/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:27:09,292] [INFO] Task succeeded: Blastn
[2023-03-17 00:27:09,294] [INFO] Selected 35 target genomes.
[2023-03-17 00:27:09,294] [INFO] Target genome list was writen to OceanDNA-b9243/target_genomes.txt
[2023-03-17 00:27:09,304] [INFO] Task started: fastANI
[2023-03-17 00:27:09,304] [INFO] Running command: fastANI --query /var/lib/cwl/stg24183a8b-20f7-43b5-9766-abf2f5df2a47/OceanDNA-b9243.fa --refList OceanDNA-b9243/target_genomes.txt --output OceanDNA-b9243/fastani_result.tsv --threads 1
[2023-03-17 00:30:34,494] [INFO] Task succeeded: fastANI
[2023-03-17 00:30:34,494] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb52eb0b2-d824-4d43-a631-38dcdcbd4437/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:30:34,495] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb52eb0b2-d824-4d43-a631-38dcdcbd4437/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:30:34,495] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 00:30:34,495] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 00:30:34,495] [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
--------------------------------------------------------------------------------
[2023-03-17 00:30:34,495] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9243/tc_result.tsv
[2023-03-17 00:30:34,495] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:30:34,495] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:30:34,495] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb52eb0b2-d824-4d43-a631-38dcdcbd4437/dqc_reference/checkm_data
[2023-03-17 00:30:34,498] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:30:34,511] [INFO] Task started: CheckM
[2023-03-17 00:30:34,511] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9243/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9243/checkm_input OceanDNA-b9243/checkm_result
[2023-03-17 00:31:06,900] [INFO] Task succeeded: CheckM
[2023-03-17 00:31:06,900] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 00:31:06,902] [INFO] ===== Completeness check finished =====
[2023-03-17 00:31:06,902] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:31:06,902] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9243/markers.fasta)
[2023-03-17 00:31:06,904] [INFO] Task started: Blastn
[2023-03-17 00:31:06,904] [INFO] Running command: blastn -query OceanDNA-b9243/markers.fasta -db /var/lib/cwl/stgb52eb0b2-d824-4d43-a631-38dcdcbd4437/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9243/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:31:07,758] [INFO] Task succeeded: Blastn
[2023-03-17 00:31:07,759] [INFO] Selected 20 target genomes.
[2023-03-17 00:31:07,759] [INFO] Target genome list was writen to OceanDNA-b9243/target_genomes_gtdb.txt
[2023-03-17 00:31:07,871] [INFO] Task started: fastANI
[2023-03-17 00:31:07,872] [INFO] Running command: fastANI --query /var/lib/cwl/stg24183a8b-20f7-43b5-9766-abf2f5df2a47/OceanDNA-b9243.fa --refList OceanDNA-b9243/target_genomes_gtdb.txt --output OceanDNA-b9243/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:31:14,236] [INFO] Task succeeded: fastANI
[2023-03-17 00:31:14,245] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 00:31:14,245] [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_002167945.1	s__MS024-2A sp002167945	92.6295	451	559	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	90.5299	377	559	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	77.8593	156	559	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_002705385.1	s__MS024-2A sp002705385	77.5828	122	559	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_902616905.1	s__MS024-2A sp902616905	77.548	50	559	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_017851655.1	s__MS024-2A sp017851655	77.433	175	559	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_017858055.1	s__MS024-2A sp002384715	77.242	159	559	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_002292265.1	s__MS024-2A sp002292265	76.9983	112	559	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_018699935.1	s__MS024-2A sp018699935	76.8162	73	559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.36	99.36	0.92	0.92	2	-
GCA_000173095.1	s__MS024-2A sp000173095	76.7735	105	559	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_905182305.1	s__MS024-2A sp905182305	76.7341	86	559	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_008081175.1	s__MS024-2A sp008081175	76.4674	73	559	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_902561795.1	s__MS024-2A sp902561795	76.4303	52	559	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	76.3461	58	559	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	76.2532	63	559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 00:31:14,246] [INFO] GTDB search result was written to OceanDNA-b9243/result_gtdb.tsv
[2023-03-17 00:31:14,246] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:31:14,247] [INFO] DFAST_QC result json was written to OceanDNA-b9243/dqc_result.json
[2023-03-17 00:31:14,247] [INFO] DFAST_QC completed!
[2023-03-17 00:31:14,247] [INFO] Total running time: 0h4m18s