[2023-03-17 11:08:00,483] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:08:00,484] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:08:00,484] [INFO] DQC Reference Directory: /var/lib/cwl/stg163c5890-e885-4ffa-a6e3-c7b040122c12/dqc_reference
[2023-03-17 11:08:01,655] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:08:01,656] [INFO] Task started: Prodigal
[2023-03-17 11:08:01,656] [INFO] Running command: cat /var/lib/cwl/stg00707503-30f3-4ee8-bfca-32a3b1e5482f/OceanDNA-b21040.fa | prodigal -d OceanDNA-b21040/cds.fna -a OceanDNA-b21040/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:08:20,759] [INFO] Task succeeded: Prodigal
[2023-03-17 11:08:20,759] [INFO] Task started: HMMsearch
[2023-03-17 11:08:20,759] [INFO] Running command: hmmsearch --tblout OceanDNA-b21040/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg163c5890-e885-4ffa-a6e3-c7b040122c12/dqc_reference/reference_markers.hmm OceanDNA-b21040/protein.faa > /dev/null
[2023-03-17 11:08:20,979] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:08:20,979] [INFO] Found 6/6 markers.
[2023-03-17 11:08:21,011] [INFO] Query marker FASTA was written to OceanDNA-b21040/markers.fasta
[2023-03-17 11:08:21,013] [INFO] Task started: Blastn
[2023-03-17 11:08:21,013] [INFO] Running command: blastn -query OceanDNA-b21040/markers.fasta -db /var/lib/cwl/stg163c5890-e885-4ffa-a6e3-c7b040122c12/dqc_reference/reference_markers.fasta -out OceanDNA-b21040/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:08:21,725] [INFO] Task succeeded: Blastn
[2023-03-17 11:08:21,726] [INFO] Selected 31 target genomes.
[2023-03-17 11:08:21,726] [INFO] Target genome list was writen to OceanDNA-b21040/target_genomes.txt
[2023-03-17 11:08:21,743] [INFO] Task started: fastANI
[2023-03-17 11:08:21,743] [INFO] Running command: fastANI --query /var/lib/cwl/stg00707503-30f3-4ee8-bfca-32a3b1e5482f/OceanDNA-b21040.fa --refList OceanDNA-b21040/target_genomes.txt --output OceanDNA-b21040/fastani_result.tsv --threads 1
[2023-03-17 11:08:44,162] [INFO] Task succeeded: fastANI
[2023-03-17 11:08:44,162] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg163c5890-e885-4ffa-a6e3-c7b040122c12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:08:44,162] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg163c5890-e885-4ffa-a6e3-c7b040122c12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:08:44,169] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:08:44,169] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 11:08:44,170] [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
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	75.1527	81	946	95	below_threshold
Pyxidicoccus caerfyrddinensis	strain=CA032A	GCA_010894405.1	2709663	2709663	type	True	75.0861	83	946	95	below_threshold
Vulgatibacter incomptus	strain=DSM 27710	GCA_001263175.1	1391653	1391653	type	True	75.0328	54	946	95	below_threshold
Pyxidicoccus fallax	strain=DSM 14698	GCA_012933655.1	394095	394095	type	True	74.9913	88	946	95	below_threshold
Corallococcus llansteffanensis	strain=CA051B	GCA_003612055.1	2316731	2316731	type	True	74.891	57	946	95	below_threshold
Corallococcus sicarius	strain=CA040B	GCA_003611735.1	2316726	2316726	type	True	74.8856	64	946	95	below_threshold
Solirubrobacter pauli	strain=DSM 14954	GCA_003633755.1	166793	166793	type	True	74.7986	81	946	95	below_threshold
Conexibacter arvalis	strain=DSM 23288	GCA_014199525.1	912552	912552	type	True	74.7605	103	946	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	74.7315	54	946	95	below_threshold
Microbacterium ulmi	strain=CECT 5976	GCA_011759705.1	179095	179095	type	True	74.649	50	946	95	below_threshold
Solimonas variicoloris	strain=DSM 15731	GCA_000382285.1	254408	254408	type	True	74.5901	52	946	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 11:08:44,170] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21040/tc_result.tsv
[2023-03-17 11:08:44,170] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:08:44,170] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:08:44,170] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg163c5890-e885-4ffa-a6e3-c7b040122c12/dqc_reference/checkm_data
[2023-03-17 11:08:44,171] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:08:44,177] [INFO] Task started: CheckM
[2023-03-17 11:08:44,177] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21040/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21040/checkm_input OceanDNA-b21040/checkm_result
[2023-03-17 11:09:33,066] [INFO] Task succeeded: CheckM
[2023-03-17 11:09:33,066] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.51%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:09:33,070] [INFO] ===== Completeness check finished =====
[2023-03-17 11:09:33,070] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:09:33,071] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21040/markers.fasta)
[2023-03-17 11:09:33,072] [INFO] Task started: Blastn
[2023-03-17 11:09:33,072] [INFO] Running command: blastn -query OceanDNA-b21040/markers.fasta -db /var/lib/cwl/stg163c5890-e885-4ffa-a6e3-c7b040122c12/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21040/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:09:34,337] [INFO] Task succeeded: Blastn
[2023-03-17 11:09:34,338] [INFO] Selected 19 target genomes.
[2023-03-17 11:09:34,338] [INFO] Target genome list was writen to OceanDNA-b21040/target_genomes_gtdb.txt
[2023-03-17 11:09:34,887] [INFO] Task started: fastANI
[2023-03-17 11:09:34,887] [INFO] Running command: fastANI --query /var/lib/cwl/stg00707503-30f3-4ee8-bfca-32a3b1e5482f/OceanDNA-b21040.fa --refList OceanDNA-b21040/target_genomes_gtdb.txt --output OceanDNA-b21040/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:09:48,272] [INFO] Task succeeded: fastANI
[2023-03-17 11:09:48,281] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 11:09:48,281] [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_013215605.1	s__JABSQW01 sp013215605	98.8544	882	946	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__SMWR01;g__JABSQW01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013215615.1	s__JABSQX01 sp013215615	76.7943	163	946	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__SMWR01;g__JABSQX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004356735.1	s__SMWR01 sp004356735	76.7934	87	946	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__SMWR01;g__SMWR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576805.1	s__PR03 sp003576805	76.2726	183	946	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__PR03;g__PR03	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002729515.1	s__GCA-2729515 sp002729515	76.2353	108	946	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__SMWR01;g__GCA-2729515	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002687015.1	s__GCA-2687015 sp002687015	76.1456	144	946	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA6930;g__GCA-2687015	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011055735.1	s__DSOP01 sp011055735	76.1149	189	946	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA6930;g__DSOP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018262315.1	s__PR03 sp018262315	75.94	85	946	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__PR03;g__PR03	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713665.1	s__JADJOR01 sp016713665	75.9276	173	946	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__JADJOR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016875395.1	s__VGRF01 sp016875395	75.846	173	946	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA6930;g__VGRF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016875225.1	s__VGRW01 sp016875225	75.7528	100	946	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__SZUA-336;f__SZUA-336;g__VGRW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003520425.1	s__UBA9160 sp003520425	75.4478	64	946	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA9160;g__UBA9160	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213895.1	s__JACQZJ01 sp016213895	74.8635	57	946	d__Bacteria;p__Planctomycetota;c__B15-G4;o__B15-G4;f__JADJEK01;g__JACQZJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016790695.1	s__JAEUOS01 sp016790695	74.7776	71	946	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__JAEUOS01;g__JAEUOS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016209015.1	s__JACQWY01 sp016209015	74.6288	63	946	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ga0077536;f__Ga0077536;g__JACQWY01	95.0	99.49	99.49	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-03-17 11:09:48,281] [INFO] GTDB search result was written to OceanDNA-b21040/result_gtdb.tsv
[2023-03-17 11:09:48,281] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:09:48,283] [INFO] DFAST_QC result json was written to OceanDNA-b21040/dqc_result.json
[2023-03-17 11:09:48,283] [INFO] DFAST_QC completed!
[2023-03-17 11:09:48,283] [INFO] Total running time: 0h1m48s