[2023-03-16 20:26:50,901] [INFO] DFAST_QC pipeline started.
[2023-03-16 20:26:50,901] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 20:26:50,901] [INFO] DQC Reference Directory: /var/lib/cwl/stg9fe855cc-a93d-4d70-85b4-116825cad169/dqc_reference
[2023-03-16 20:26:51,985] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 20:26:51,989] [INFO] Task started: Prodigal
[2023-03-16 20:26:51,989] [INFO] Running command: cat /var/lib/cwl/stg298bc809-b635-45ca-9f1d-a63c2675e8cb/OceanDNA-b2904.fa | prodigal -d OceanDNA-b2904/cds.fna -a OceanDNA-b2904/protein.faa -g 11 -q > /dev/null
[2023-03-16 20:27:37,012] [INFO] Task succeeded: Prodigal
[2023-03-16 20:27:37,013] [INFO] Task started: HMMsearch
[2023-03-16 20:27:37,013] [INFO] Running command: hmmsearch --tblout OceanDNA-b2904/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9fe855cc-a93d-4d70-85b4-116825cad169/dqc_reference/reference_markers.hmm OceanDNA-b2904/protein.faa > /dev/null
[2023-03-16 20:27:37,225] [INFO] Task succeeded: HMMsearch
[2023-03-16 20:27:37,226] [INFO] Found 6/6 markers.
[2023-03-16 20:27:37,256] [INFO] Query marker FASTA was written to OceanDNA-b2904/markers.fasta
[2023-03-16 20:27:37,257] [INFO] Task started: Blastn
[2023-03-16 20:27:37,257] [INFO] Running command: blastn -query OceanDNA-b2904/markers.fasta -db /var/lib/cwl/stg9fe855cc-a93d-4d70-85b4-116825cad169/dqc_reference/reference_markers.fasta -out OceanDNA-b2904/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 20:27:38,300] [INFO] Task succeeded: Blastn
[2023-03-16 20:27:38,301] [INFO] Selected 13 target genomes.
[2023-03-16 20:27:38,301] [INFO] Target genome list was writen to OceanDNA-b2904/target_genomes.txt
[2023-03-16 20:27:38,306] [INFO] Task started: fastANI
[2023-03-16 20:27:38,307] [INFO] Running command: fastANI --query /var/lib/cwl/stg298bc809-b635-45ca-9f1d-a63c2675e8cb/OceanDNA-b2904.fa --refList OceanDNA-b2904/target_genomes.txt --output OceanDNA-b2904/fastani_result.tsv --threads 1
[2023-03-16 20:27:53,527] [INFO] Task succeeded: fastANI
[2023-03-16 20:27:53,527] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9fe855cc-a93d-4d70-85b4-116825cad169/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 20:27:53,528] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9fe855cc-a93d-4d70-85b4-116825cad169/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 20:27:53,536] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 20:27:53,536] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 20:27:53,537] [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
Rhodococcus yunnanensis	strain=NBRC 103083	GCA_001895005.1	278209	278209	type	True	80.289	802	1641	95	below_threshold
Rhodococcus kyotonensis	strain=JCM 23211	GCA_900188125.1	398843	398843	type	True	80.2	791	1641	95	below_threshold
Rhodococcus fascians	strain=LMG 3623	GCA_000761055.1	1828	1828	type	True	80.0349	685	1641	95	below_threshold
Rhodococcus fascians	strain=NBRC 12155	GCA_001894785.1	1828	1828	type	True	79.9804	681	1641	95	below_threshold
Rhodococcus pseudokoreensis	strain=R79	GCA_017068395.1	2811421	2811421	type	True	78.3498	518	1641	95	below_threshold
Prescottella defluvii	strain=Ca11	GCA_000738775.1	1323361	1323361	type	True	78.2937	424	1641	95	below_threshold
Rhodococcus wratislaviensis	strain=NBRC 100605	GCA_000583735.1	44752	44752	suspected-type	True	78.215	503	1641	95	below_threshold
Rhodococcus spelaei	strain=C9-5	GCA_006704125.1	2546320	2546320	type	True	78.1585	445	1641	95	below_threshold
Rhodococcus opacus	strain=DSM 43205	GCA_001646735.1	37919	37919	type	True	78.1255	503	1641	95	below_threshold
Prescottella equi	strain=DSM 20307	GCA_002094305.1	43767	43767	type	True	78.112	428	1641	95	below_threshold
Prescottella equi	strain=NCTC1621	GCA_900455845.1	43767	43767	type	True	78.1031	438	1641	95	below_threshold
Rhodococcus opacus	strain=ATCC 51881	GCA_012396235.1	37919	37919	type	True	78.1016	498	1641	95	below_threshold
Prescottella equi	strain=NBRC 101255	GCA_001552575.1	43767	43767	type	True	78.093	432	1641	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 20:27:53,537] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2904/tc_result.tsv
[2023-03-16 20:27:53,537] [INFO] ===== Taxonomy check completed =====
[2023-03-16 20:27:53,537] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 20:27:53,538] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9fe855cc-a93d-4d70-85b4-116825cad169/dqc_reference/checkm_data
[2023-03-16 20:27:53,538] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 20:27:53,678] [INFO] Task started: CheckM
[2023-03-16 20:27:53,678] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2904/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2904/checkm_input OceanDNA-b2904/checkm_result
[2023-03-16 20:29:32,002] [INFO] Task succeeded: CheckM
[2023-03-16 20:29:32,002] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 20:29:32,006] [INFO] ===== Completeness check finished =====
[2023-03-16 20:29:32,006] [INFO] ===== Start GTDB Search =====
[2023-03-16 20:29:32,006] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2904/markers.fasta)
[2023-03-16 20:29:32,007] [INFO] Task started: Blastn
[2023-03-16 20:29:32,008] [INFO] Running command: blastn -query OceanDNA-b2904/markers.fasta -db /var/lib/cwl/stg9fe855cc-a93d-4d70-85b4-116825cad169/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2904/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 20:29:33,456] [INFO] Task succeeded: Blastn
[2023-03-16 20:29:33,457] [INFO] Selected 17 target genomes.
[2023-03-16 20:29:33,457] [INFO] Target genome list was writen to OceanDNA-b2904/target_genomes_gtdb.txt
[2023-03-16 20:29:33,478] [INFO] Task started: fastANI
[2023-03-16 20:29:33,478] [INFO] Running command: fastANI --query /var/lib/cwl/stg298bc809-b635-45ca-9f1d-a63c2675e8cb/OceanDNA-b2904.fa --refList OceanDNA-b2904/target_genomes_gtdb.txt --output OceanDNA-b2904/fastani_result_gtdb.tsv --threads 1
[2023-03-16 20:29:52,147] [INFO] Task succeeded: fastANI
[2023-03-16 20:29:52,157] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 20:29:52,158] [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
GCF_017168235.1	s__Rhodococcus_B sp001942265	98.3567	1488	1641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	98.66	98.66	0.86	0.86	2	conclusive
GCF_001647195.1	s__Rhodococcus_B sp001647195	80.9609	812	1641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002259415.1	s__Rhodococcus_B sp002259415	80.7213	797	1641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	98.80	98.78	0.88	0.88	4	-
GCF_000760735.1	s__Rhodococcus_B fascians_E	80.5558	811	1641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	98.84	98.47	0.88	0.82	19	-
GCF_003688915.1	s__Rhodococcus_B sp000813105	80.5117	747	1641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	98.08	98.08	0.88	0.88	2	-
GCF_001645385.1	s__Rhodococcus_B kyotonensis_B	80.3601	774	1641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	98.37	97.70	0.89	0.87	3	-
GCF_003386655.1	s__Rhodococcus_B sp003386655	80.3243	787	1641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003641205.1	s__Rhodococcus_B sp003641205	80.3037	806	1641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001895005.1	s__Rhodococcus_B yunnanensis	80.3035	800	1641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188125.1	s__Rhodococcus_B kyotonensis	80.2192	787	1641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002258785.1	s__Rhodococcus_B sp002258785	80.1075	695	1641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000954115.1	s__Rhodococcus_B sp000954115	80.004	694	1641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	98.26	98.19	0.90	0.89	13	-
GCF_002258315.1	s__Rhodococcus_B sp002258315	79.9629	732	1641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001894785.1	s__Rhodococcus_B fascians	79.9476	686	1641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	97.73	95.09	0.88	0.82	43	-
GCF_002259405.1	s__Rhodococcus_B sp002259405	79.8504	705	1641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	98.26	98.16	0.87	0.86	5	-
GCF_000760935.2	s__Rhodococcus_B sp002259335	79.685	699	1641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	96.52	96.34	0.85	0.83	9	-
GCF_004795915.1	s__Rhodococcus_B sp004795915	79.2849	657	1641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-16 20:29:52,158] [INFO] GTDB search result was written to OceanDNA-b2904/result_gtdb.tsv
[2023-03-16 20:29:52,159] [INFO] ===== GTDB Search completed =====
[2023-03-16 20:29:52,161] [INFO] DFAST_QC result json was written to OceanDNA-b2904/dqc_result.json
[2023-03-16 20:29:52,161] [INFO] DFAST_QC completed!
[2023-03-16 20:29:52,161] [INFO] Total running time: 0h3m1s