[2023-03-18 00:58:44,627] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:58:44,627] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:58:44,627] [INFO] DQC Reference Directory: /var/lib/cwl/stgc563eb5f-16f3-496e-af75-826dab2ba061/dqc_reference
[2023-03-18 00:58:46,297] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:58:46,298] [INFO] Task started: Prodigal
[2023-03-18 00:58:46,298] [INFO] Running command: cat /var/lib/cwl/stg3e409b42-ed54-457c-b220-e4ffdc56b738/OceanDNA-b9153.fa | prodigal -d OceanDNA-b9153/cds.fna -a OceanDNA-b9153/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:58:52,402] [INFO] Task succeeded: Prodigal
[2023-03-18 00:58:52,402] [INFO] Task started: HMMsearch
[2023-03-18 00:58:52,402] [INFO] Running command: hmmsearch --tblout OceanDNA-b9153/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc563eb5f-16f3-496e-af75-826dab2ba061/dqc_reference/reference_markers.hmm OceanDNA-b9153/protein.faa > /dev/null
[2023-03-18 00:58:52,565] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:58:52,566] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3e409b42-ed54-457c-b220-e4ffdc56b738/OceanDNA-b9153.fa]
[2023-03-18 00:58:52,577] [INFO] Query marker FASTA was written to OceanDNA-b9153/markers.fasta
[2023-03-18 00:58:52,577] [INFO] Task started: Blastn
[2023-03-18 00:58:52,578] [INFO] Running command: blastn -query OceanDNA-b9153/markers.fasta -db /var/lib/cwl/stgc563eb5f-16f3-496e-af75-826dab2ba061/dqc_reference/reference_markers.fasta -out OceanDNA-b9153/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:58:53,326] [INFO] Task succeeded: Blastn
[2023-03-18 00:58:53,327] [INFO] Selected 24 target genomes.
[2023-03-18 00:58:53,328] [INFO] Target genome list was writen to OceanDNA-b9153/target_genomes.txt
[2023-03-18 00:58:53,344] [INFO] Task started: fastANI
[2023-03-18 00:58:53,344] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e409b42-ed54-457c-b220-e4ffdc56b738/OceanDNA-b9153.fa --refList OceanDNA-b9153/target_genomes.txt --output OceanDNA-b9153/fastani_result.tsv --threads 1
[2023-03-18 00:59:08,149] [INFO] Task succeeded: fastANI
[2023-03-18 00:59:08,150] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc563eb5f-16f3-496e-af75-826dab2ba061/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:59:08,150] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc563eb5f-16f3-496e-af75-826dab2ba061/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:59:08,150] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:59:08,150] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 00:59:08,150] [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 00:59:08,152] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9153/tc_result.tsv
[2023-03-18 00:59:08,152] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:59:08,152] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:59:08,152] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc563eb5f-16f3-496e-af75-826dab2ba061/dqc_reference/checkm_data
[2023-03-18 00:59:08,154] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:59:08,157] [INFO] Task started: CheckM
[2023-03-18 00:59:08,157] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9153/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9153/checkm_input OceanDNA-b9153/checkm_result
[2023-03-18 00:59:28,949] [INFO] Task succeeded: CheckM
[2023-03-18 00:59:28,950] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.20%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:59:28,956] [INFO] ===== Completeness check finished =====
[2023-03-18 00:59:28,956] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:59:28,956] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9153/markers.fasta)
[2023-03-18 00:59:28,957] [INFO] Task started: Blastn
[2023-03-18 00:59:28,957] [INFO] Running command: blastn -query OceanDNA-b9153/markers.fasta -db /var/lib/cwl/stgc563eb5f-16f3-496e-af75-826dab2ba061/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9153/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:59:29,750] [INFO] Task succeeded: Blastn
[2023-03-18 00:59:29,753] [INFO] Selected 23 target genomes.
[2023-03-18 00:59:29,753] [INFO] Target genome list was writen to OceanDNA-b9153/target_genomes_gtdb.txt
[2023-03-18 00:59:29,797] [INFO] Task started: fastANI
[2023-03-18 00:59:29,797] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e409b42-ed54-457c-b220-e4ffdc56b738/OceanDNA-b9153.fa --refList OceanDNA-b9153/target_genomes_gtdb.txt --output OceanDNA-b9153/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:59:37,265] [INFO] Task succeeded: fastANI
[2023-03-18 00:59:37,273] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 00:59:37,273] [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_002169865.1	s__MS024-2A sp002169865	99.2521	176	331	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_902606525.1	s__MS024-2A sp902606525	91.2492	185	331	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	78.8069	123	331	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	77.7161	142	331	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_002714815.1	s__MS024-2A sp002714815	77.6084	93	331	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	76.8817	50	331	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	76.8801	65	331	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_902618245.1	s__MS024-2A sp902618245	76.6267	80	331	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_002167525.1	s__MS024-2A sp002167525	76.5766	71	331	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_905182305.1	s__MS024-2A sp905182305	76.5659	61	331	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	76.5578	80	331	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	76.5165	57	331	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_905480425.1	s__MS024-2A sp905480425	76.4621	66	331	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_902561795.1	s__MS024-2A sp902561795	76.4184	73	331	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 00:59:37,274] [INFO] GTDB search result was written to OceanDNA-b9153/result_gtdb.tsv
[2023-03-18 00:59:37,274] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:59:37,276] [INFO] DFAST_QC result json was written to OceanDNA-b9153/dqc_result.json
[2023-03-18 00:59:37,276] [INFO] DFAST_QC completed!
[2023-03-18 00:59:37,276] [INFO] Total running time: 0h0m53s