[2023-03-15 04:22:10,940] [INFO] DFAST_QC pipeline started.
[2023-03-15 04:22:10,940] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 04:22:10,940] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b532da3-48f5-4ea4-b84f-d31ffe0996f8/dqc_reference
[2023-03-15 04:22:12,025] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 04:22:12,026] [INFO] Task started: Prodigal
[2023-03-15 04:22:12,026] [INFO] Running command: cat /var/lib/cwl/stg8f8598ed-2cf6-468e-941e-681dd7507289/OceanDNA-b3410.fa | prodigal -d OceanDNA-b3410/cds.fna -a OceanDNA-b3410/protein.faa -g 11 -q > /dev/null
[2023-03-15 04:22:21,864] [INFO] Task succeeded: Prodigal
[2023-03-15 04:22:21,865] [INFO] Task started: HMMsearch
[2023-03-15 04:22:21,865] [INFO] Running command: hmmsearch --tblout OceanDNA-b3410/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b532da3-48f5-4ea4-b84f-d31ffe0996f8/dqc_reference/reference_markers.hmm OceanDNA-b3410/protein.faa > /dev/null
[2023-03-15 04:22:22,029] [INFO] Task succeeded: HMMsearch
[2023-03-15 04:22:22,030] [INFO] Found 6/6 markers.
[2023-03-15 04:22:22,049] [INFO] Query marker FASTA was written to OceanDNA-b3410/markers.fasta
[2023-03-15 04:22:22,050] [INFO] Task started: Blastn
[2023-03-15 04:22:22,050] [INFO] Running command: blastn -query OceanDNA-b3410/markers.fasta -db /var/lib/cwl/stg8b532da3-48f5-4ea4-b84f-d31ffe0996f8/dqc_reference/reference_markers.fasta -out OceanDNA-b3410/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:22:22,616] [INFO] Task succeeded: Blastn
[2023-03-15 04:22:22,616] [INFO] Selected 12 target genomes.
[2023-03-15 04:22:22,617] [INFO] Target genome list was writen to OceanDNA-b3410/target_genomes.txt
[2023-03-15 04:22:22,622] [INFO] Task started: fastANI
[2023-03-15 04:22:22,622] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f8598ed-2cf6-468e-941e-681dd7507289/OceanDNA-b3410.fa --refList OceanDNA-b3410/target_genomes.txt --output OceanDNA-b3410/fastani_result.tsv --threads 1
[2023-03-15 04:22:30,814] [INFO] Task succeeded: fastANI
[2023-03-15 04:22:30,815] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b532da3-48f5-4ea4-b84f-d31ffe0996f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 04:22:30,815] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b532da3-48f5-4ea4-b84f-d31ffe0996f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 04:22:30,821] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 04:22:30,821] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 04:22:30,821] [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
Rubrobacter tropicus	strain=SCSIO 52909	GCA_011492945.1	2653851	2653851	type	True	78.2177	189	468	95	below_threshold
Rubrobacter marinus	strain=SCSIO 52915	GCA_011492965.1	2653852	2653852	type	True	78.1248	199	468	95	below_threshold
Rubrobacter radiotolerans	strain=DSM 5868	GCA_900175965.1	42256	42256	type	True	77.5262	164	468	95	below_threshold
Rubrobacter aplysinae	strain=RV113	GCA_001029505.1	909625	909625	type	True	77.0906	143	468	95	below_threshold
Rubrobacter indicoceani	strain=SCSIO 08198	GCA_003568865.1	2051957	2051957	type	True	76.6419	109	468	95	below_threshold
Pseudonocardia parietis	strain=DSM 45256	GCA_017876315.1	570936	570936	type	True	75.0884	50	468	95	below_threshold
Pseudonocardia antarctica	strain=DSM 44749	GCA_013408715.1	237656	237656	type	True	75.0187	63	468	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 04:22:30,824] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3410/tc_result.tsv
[2023-03-15 04:22:30,827] [INFO] ===== Taxonomy check completed =====
[2023-03-15 04:22:30,827] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 04:22:30,827] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b532da3-48f5-4ea4-b84f-d31ffe0996f8/dqc_reference/checkm_data
[2023-03-15 04:22:30,828] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 04:22:30,836] [INFO] Task started: CheckM
[2023-03-15 04:22:30,836] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3410/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3410/checkm_input OceanDNA-b3410/checkm_result
[2023-03-15 04:22:59,571] [INFO] Task succeeded: CheckM
[2023-03-15 04:22:59,571] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.48%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 04:22:59,617] [INFO] ===== Completeness check finished =====
[2023-03-15 04:22:59,618] [INFO] ===== Start GTDB Search =====
[2023-03-15 04:22:59,618] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3410/markers.fasta)
[2023-03-15 04:22:59,619] [INFO] Task started: Blastn
[2023-03-15 04:22:59,619] [INFO] Running command: blastn -query OceanDNA-b3410/markers.fasta -db /var/lib/cwl/stg8b532da3-48f5-4ea4-b84f-d31ffe0996f8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3410/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:23:00,459] [INFO] Task succeeded: Blastn
[2023-03-15 04:23:00,463] [INFO] Selected 12 target genomes.
[2023-03-15 04:23:00,463] [INFO] Target genome list was writen to OceanDNA-b3410/target_genomes_gtdb.txt
[2023-03-15 04:23:00,475] [INFO] Task started: fastANI
[2023-03-15 04:23:00,476] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f8598ed-2cf6-468e-941e-681dd7507289/OceanDNA-b3410.fa --refList OceanDNA-b3410/target_genomes_gtdb.txt --output OceanDNA-b3410/fastani_result_gtdb.tsv --threads 1
[2023-03-15 04:23:07,435] [INFO] Task succeeded: fastANI
[2023-03-15 04:23:07,443] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 04:23:07,443] [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_007164525.1	s__Rubrobacter_B xylanophilus_A	89.1607	392	468	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__Rubrobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014185.1	s__Rubrobacter_B xylanophilus	88.579	401	468	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__Rubrobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004337705.1	s__Rubrobacter_C taiwanensis	80.6459	204	468	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__Rubrobacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004563715.1	s__SIRX01 sp004563715	79.0333	197	468	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SIRX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016781725.1	s__SCSIO-52909 sp016781725	78.3317	153	468	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52909	95.0	98.84	98.84	0.72	0.72	2	-
GCA_902805985.1	s__SCSIO-52909 sp902805985	78.3283	133	468	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52909	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902810695.1	s__CADDYV01 sp902810695	78.1662	173	468	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__CADDYV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013695915.1	s__Rubrobacter_A sp013695915	78.0761	140	468	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__Rubrobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016781705.1	s__SCSIO-52915 sp016781705	77.8994	119	468	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902812425.1	s__SCSIO-52909 sp902812425	77.5658	150	468	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52909	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900175965.1	s__Rubrobacter radiotolerans	77.5262	164	468	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__Rubrobacter	95.0	99.98	99.98	1.00	1.00	2	-
GCF_003568865.1	s__Rubrobacter indicoceani	76.6414	109	468	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__Rubrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 04:23:07,443] [INFO] GTDB search result was written to OceanDNA-b3410/result_gtdb.tsv
[2023-03-15 04:23:07,444] [INFO] ===== GTDB Search completed =====
[2023-03-15 04:23:07,445] [INFO] DFAST_QC result json was written to OceanDNA-b3410/dqc_result.json
[2023-03-15 04:23:07,445] [INFO] DFAST_QC completed!
[2023-03-15 04:23:07,445] [INFO] Total running time: 0h0m57s