[2023-03-19 04:58:34,615] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:58:34,615] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:58:34,615] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd60f9ac-091f-4771-b6a5-263784e5805d/dqc_reference
[2023-03-19 04:58:36,122] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:58:36,122] [INFO] Task started: Prodigal
[2023-03-19 04:58:36,123] [INFO] Running command: cat /var/lib/cwl/stgc782fdc2-3954-4ef7-8811-e34471eb38ee/OceanDNA-b3420.fa | prodigal -d OceanDNA-b3420/cds.fna -a OceanDNA-b3420/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:58:42,993] [INFO] Task succeeded: Prodigal
[2023-03-19 04:58:42,994] [INFO] Task started: HMMsearch
[2023-03-19 04:58:42,994] [INFO] Running command: hmmsearch --tblout OceanDNA-b3420/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd60f9ac-091f-4771-b6a5-263784e5805d/dqc_reference/reference_markers.hmm OceanDNA-b3420/protein.faa > /dev/null
[2023-03-19 04:58:43,146] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:58:43,146] [INFO] Found 6/6 markers.
[2023-03-19 04:58:43,164] [INFO] Query marker FASTA was written to OceanDNA-b3420/markers.fasta
[2023-03-19 04:58:43,165] [INFO] Task started: Blastn
[2023-03-19 04:58:43,165] [INFO] Running command: blastn -query OceanDNA-b3420/markers.fasta -db /var/lib/cwl/stgdd60f9ac-091f-4771-b6a5-263784e5805d/dqc_reference/reference_markers.fasta -out OceanDNA-b3420/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:58:43,718] [INFO] Task succeeded: Blastn
[2023-03-19 04:58:43,719] [INFO] Selected 16 target genomes.
[2023-03-19 04:58:43,719] [INFO] Target genome list was writen to OceanDNA-b3420/target_genomes.txt
[2023-03-19 04:58:43,727] [INFO] Task started: fastANI
[2023-03-19 04:58:43,727] [INFO] Running command: fastANI --query /var/lib/cwl/stgc782fdc2-3954-4ef7-8811-e34471eb38ee/OceanDNA-b3420.fa --refList OceanDNA-b3420/target_genomes.txt --output OceanDNA-b3420/fastani_result.tsv --threads 1
[2023-03-19 04:58:54,367] [INFO] Task succeeded: fastANI
[2023-03-19 04:58:54,367] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd60f9ac-091f-4771-b6a5-263784e5805d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:58:54,367] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd60f9ac-091f-4771-b6a5-263784e5805d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:58:54,375] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:58:54,375] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 04:58:54,375] [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
Conexibacter arvalis	strain=DSM 23288	GCA_014199525.1	912552	912552	type	True	77.3264	97	371	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	76.6981	91	371	95	below_threshold
Capillimicrobium parvum	strain=0166_1	GCA_021172045.1	2884022	2884022	type	True	76.6192	87	371	95	below_threshold
Conexibacter woesei	strain=DSM 14684	GCA_000025265.1	191495	191495	type	True	76.6133	100	371	95	below_threshold
Solirubrobacter pauli	strain=DSM 14954	GCA_003633755.1	166793	166793	type	True	76.612	71	371	95	below_threshold
Patulibacter medicamentivorans	strain=I11	GCA_000240225.2	1097667	1097667	type	True	76.6015	85	371	95	below_threshold
Baekduia soli	strain=BR7-21	GCA_007970665.1	496014	496014	type	True	76.5227	91	371	95	below_threshold
Patulibacter americanus	strain=DSM 16676	GCA_000420025.1	588672	588672	type	True	76.4898	50	371	95	below_threshold
Patulibacter minatonensis	strain=DSM 18081	GCA_000519325.1	298163	298163	type	True	76.3644	62	371	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:58:54,375] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3420/tc_result.tsv
[2023-03-19 04:58:54,375] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:58:54,375] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:58:54,375] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd60f9ac-091f-4771-b6a5-263784e5805d/dqc_reference/checkm_data
[2023-03-19 04:58:54,376] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:58:54,379] [INFO] Task started: CheckM
[2023-03-19 04:58:54,379] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3420/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3420/checkm_input OceanDNA-b3420/checkm_result
[2023-03-19 04:59:17,153] [INFO] Task succeeded: CheckM
[2023-03-19 04:59:17,153] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:59:17,155] [INFO] ===== Completeness check finished =====
[2023-03-19 04:59:17,155] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:59:17,156] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3420/markers.fasta)
[2023-03-19 04:59:17,156] [INFO] Task started: Blastn
[2023-03-19 04:59:17,156] [INFO] Running command: blastn -query OceanDNA-b3420/markers.fasta -db /var/lib/cwl/stgdd60f9ac-091f-4771-b6a5-263784e5805d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3420/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:59:18,005] [INFO] Task succeeded: Blastn
[2023-03-19 04:59:18,006] [INFO] Selected 9 target genomes.
[2023-03-19 04:59:18,006] [INFO] Target genome list was writen to OceanDNA-b3420/target_genomes_gtdb.txt
[2023-03-19 04:59:18,014] [INFO] Task started: fastANI
[2023-03-19 04:59:18,014] [INFO] Running command: fastANI --query /var/lib/cwl/stgc782fdc2-3954-4ef7-8811-e34471eb38ee/OceanDNA-b3420.fa --refList OceanDNA-b3420/target_genomes_gtdb.txt --output OceanDNA-b3420/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:59:21,315] [INFO] Task succeeded: fastANI
[2023-03-19 04:59:21,323] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:59:21,323] [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_903953065.1	s__F1-60-MAGs163 sp903953065	90.0153	191	371	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__F1-60-MAGs163	95.0	98.55	98.39	0.73	0.73	3	-
GCA_903959665.1	s__F1-60-MAGs163 sp903959665	85.4352	235	371	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__F1-60-MAGs163	95.0	99.27	99.00	0.86	0.79	34	-
GCA_016462245.1	s__F1-60-MAGs163 sp016462245	84.7236	259	371	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__F1-60-MAGs163	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005798685.1	s__F1-60-MAGs163 sp005798685	84.5005	291	371	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__F1-60-MAGs163	95.0	99.86	99.84	0.96	0.95	3	-
GCA_009699615.1	s__F1-60-MAGs163 sp009699615	82.5211	214	371	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__F1-60-MAGs163	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903821395.1	s__F1-60-MAGs163 sp903821395	82.379	249	371	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__F1-60-MAGs163	95.0	99.66	99.66	0.90	0.90	2	-
GCA_009699565.1	s__F1-60-MAGs163 sp009699565	79.9956	190	371	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__F1-60-MAGs163	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009699245.1	s__F1-60-MAGs163 sp009699245	77.345	100	371	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__F1-60-MAGs163	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806175.1	s__CADCVQ01 sp902806175	76.6094	78	371	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__CADCVQ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:59:21,324] [INFO] GTDB search result was written to OceanDNA-b3420/result_gtdb.tsv
[2023-03-19 04:59:21,324] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:59:21,326] [INFO] DFAST_QC result json was written to OceanDNA-b3420/dqc_result.json
[2023-03-19 04:59:21,326] [INFO] DFAST_QC completed!
[2023-03-19 04:59:21,326] [INFO] Total running time: 0h0m47s