[2023-03-14 11:06:15,084] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:06:15,084] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:06:15,084] [INFO] DQC Reference Directory: /var/lib/cwl/stg9afc9cc5-8457-4803-ad22-609883c14550/dqc_reference
[2023-03-14 11:06:16,185] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:06:16,187] [INFO] Task started: Prodigal
[2023-03-14 11:06:16,187] [INFO] Running command: cat /var/lib/cwl/stg619e12a8-0899-4352-b089-4a1454b53617/OceanDNA-b12248.fa | prodigal -d OceanDNA-b12248/cds.fna -a OceanDNA-b12248/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:06:27,447] [INFO] Task succeeded: Prodigal
[2023-03-14 11:06:27,447] [INFO] Task started: HMMsearch
[2023-03-14 11:06:27,447] [INFO] Running command: hmmsearch --tblout OceanDNA-b12248/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9afc9cc5-8457-4803-ad22-609883c14550/dqc_reference/reference_markers.hmm OceanDNA-b12248/protein.faa > /dev/null
[2023-03-14 11:06:27,608] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:06:27,609] [INFO] Found 6/6 markers.
[2023-03-14 11:06:27,622] [INFO] Query marker FASTA was written to OceanDNA-b12248/markers.fasta
[2023-03-14 11:06:27,623] [INFO] Task started: Blastn
[2023-03-14 11:06:27,623] [INFO] Running command: blastn -query OceanDNA-b12248/markers.fasta -db /var/lib/cwl/stg9afc9cc5-8457-4803-ad22-609883c14550/dqc_reference/reference_markers.fasta -out OceanDNA-b12248/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:06:28,168] [INFO] Task succeeded: Blastn
[2023-03-14 11:06:28,169] [INFO] Selected 29 target genomes.
[2023-03-14 11:06:28,169] [INFO] Target genome list was writen to OceanDNA-b12248/target_genomes.txt
[2023-03-14 11:06:28,190] [INFO] Task started: fastANI
[2023-03-14 11:06:28,190] [INFO] Running command: fastANI --query /var/lib/cwl/stg619e12a8-0899-4352-b089-4a1454b53617/OceanDNA-b12248.fa --refList OceanDNA-b12248/target_genomes.txt --output OceanDNA-b12248/fastani_result.tsv --threads 1
[2023-03-14 11:06:42,140] [INFO] Task succeeded: fastANI
[2023-03-14 11:06:42,140] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9afc9cc5-8457-4803-ad22-609883c14550/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:06:42,140] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9afc9cc5-8457-4803-ad22-609883c14550/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:06:42,144] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:06:42,144] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 11:06:42,144] [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
Aureivirga marina	strain=LMG 26721	GCA_015767265.1	1182451	1182451	type	True	75.1552	51	634	95	below_threshold
Lutibacter citreus	strain=1KV19	GCA_003260195.1	2138210	2138210	type	True	74.7612	52	634	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 11:06:42,144] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12248/tc_result.tsv
[2023-03-14 11:06:42,144] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:06:42,145] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:06:42,145] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9afc9cc5-8457-4803-ad22-609883c14550/dqc_reference/checkm_data
[2023-03-14 11:06:42,145] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:06:42,280] [INFO] Task started: CheckM
[2023-03-14 11:06:42,280] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12248/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12248/checkm_input OceanDNA-b12248/checkm_result
[2023-03-14 11:07:13,822] [INFO] Task succeeded: CheckM
[2023-03-14 11:07:13,823] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:07:13,827] [INFO] ===== Completeness check finished =====
[2023-03-14 11:07:13,827] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:07:13,828] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12248/markers.fasta)
[2023-03-14 11:07:13,829] [INFO] Task started: Blastn
[2023-03-14 11:07:13,829] [INFO] Running command: blastn -query OceanDNA-b12248/markers.fasta -db /var/lib/cwl/stg9afc9cc5-8457-4803-ad22-609883c14550/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12248/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:07:14,556] [INFO] Task succeeded: Blastn
[2023-03-14 11:07:14,557] [INFO] Selected 18 target genomes.
[2023-03-14 11:07:14,557] [INFO] Target genome list was writen to OceanDNA-b12248/target_genomes_gtdb.txt
[2023-03-14 11:07:14,580] [INFO] Task started: fastANI
[2023-03-14 11:07:14,580] [INFO] Running command: fastANI --query /var/lib/cwl/stg619e12a8-0899-4352-b089-4a1454b53617/OceanDNA-b12248.fa --refList OceanDNA-b12248/target_genomes_gtdb.txt --output OceanDNA-b12248/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:07:22,090] [INFO] Task succeeded: fastANI
[2023-03-14 11:07:22,097] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 11:07:22,097] [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_905182525.1	s__MED-G20 sp905182525	96.0457	561	634	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	96.07	96.07	0.86	0.86	2	conclusive
GCA_016780365.1	s__MED-G20 sp016780365	78.9145	283	634	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	98.18	97.06	0.79	0.71	6	-
GCA_002713405.1	s__MED-G20 sp002713405	78.4735	292	634	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181675.1	s__MED-G20 sp905181675	78.4089	274	634	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686655.1	s__MED-G20 sp002686655	77.7029	241	634	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	96.65	96.65	0.87	0.87	2	-
GCA_002691605.1	s__MED-G20 sp002691605	77.0655	223	634	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	96.19	95.12	0.79	0.76	3	-
GCA_002721285.1	s__SP287 sp002721285	76.8327	87	634	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__SP287	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002723085.1	s__GCA-2723085 sp002723085	76.4239	137	634	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__GCA-2723085	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015767265.1	s__Aureivirga marina	75.1552	51	634	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureivirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:07:22,097] [INFO] GTDB search result was written to OceanDNA-b12248/result_gtdb.tsv
[2023-03-14 11:07:22,098] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:07:22,099] [INFO] DFAST_QC result json was written to OceanDNA-b12248/dqc_result.json
[2023-03-14 11:07:22,099] [INFO] DFAST_QC completed!
[2023-03-14 11:07:22,099] [INFO] Total running time: 0h1m7s