[2023-03-18 10:02:11,077] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:02:11,077] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:02:11,077] [INFO] DQC Reference Directory: /var/lib/cwl/stg61e5c5df-be62-4c96-a215-eeedbf943445/dqc_reference
[2023-03-18 10:02:12,160] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:02:12,161] [INFO] Task started: Prodigal
[2023-03-18 10:02:12,161] [INFO] Running command: cat /var/lib/cwl/stg802be469-746c-4d40-8513-b6d9ddb017fc/OceanDNA-b3330.fa | prodigal -d OceanDNA-b3330/cds.fna -a OceanDNA-b3330/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:02:21,120] [INFO] Task succeeded: Prodigal
[2023-03-18 10:02:21,121] [INFO] Task started: HMMsearch
[2023-03-18 10:02:21,121] [INFO] Running command: hmmsearch --tblout OceanDNA-b3330/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg61e5c5df-be62-4c96-a215-eeedbf943445/dqc_reference/reference_markers.hmm OceanDNA-b3330/protein.faa > /dev/null
[2023-03-18 10:02:21,264] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:02:21,264] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg802be469-746c-4d40-8513-b6d9ddb017fc/OceanDNA-b3330.fa]
[2023-03-18 10:02:21,283] [INFO] Query marker FASTA was written to OceanDNA-b3330/markers.fasta
[2023-03-18 10:02:21,283] [INFO] Task started: Blastn
[2023-03-18 10:02:21,283] [INFO] Running command: blastn -query OceanDNA-b3330/markers.fasta -db /var/lib/cwl/stg61e5c5df-be62-4c96-a215-eeedbf943445/dqc_reference/reference_markers.fasta -out OceanDNA-b3330/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:02:21,715] [INFO] Task succeeded: Blastn
[2023-03-18 10:02:21,715] [INFO] Selected 5 target genomes.
[2023-03-18 10:02:21,716] [INFO] Target genome list was writen to OceanDNA-b3330/target_genomes.txt
[2023-03-18 10:02:21,718] [INFO] Task started: fastANI
[2023-03-18 10:02:21,718] [INFO] Running command: fastANI --query /var/lib/cwl/stg802be469-746c-4d40-8513-b6d9ddb017fc/OceanDNA-b3330.fa --refList OceanDNA-b3330/target_genomes.txt --output OceanDNA-b3330/fastani_result.tsv --threads 1
[2023-03-18 10:02:25,024] [INFO] Task succeeded: fastANI
[2023-03-18 10:02:25,024] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg61e5c5df-be62-4c96-a215-eeedbf943445/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:02:25,024] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg61e5c5df-be62-4c96-a215-eeedbf943445/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:02:25,029] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:02:25,029] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 10:02:25,029] [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
Nocardioides marinus	strain=DSM 18248	GCA_013408145.1	374514	374514	type	True	87.6372	282	349	95	below_threshold
Nocardioides kribbensis	strain=DSM 16314	GCA_015070375.1	305517	305517	type	True	80.3166	218	349	95	below_threshold
Nocardioides ginsengisegetis	strain=DSM 21349	GCA_014138045.1	661491	661491	type	True	80.0264	201	349	95	below_threshold
Nocardioides ungokensis	strain=LMG 28591	GCA_013466985.1	1643322	1643322	type	True	79.3268	190	349	95	below_threshold
Nocardioides euryhalodurans	strain=MMS17-SY117	GCA_004564375.1	2518370	2518370	type	True	79.1438	172	349	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 10:02:25,030] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3330/tc_result.tsv
[2023-03-18 10:02:25,030] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:02:25,030] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:02:25,030] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg61e5c5df-be62-4c96-a215-eeedbf943445/dqc_reference/checkm_data
[2023-03-18 10:02:25,030] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:02:25,035] [INFO] Task started: CheckM
[2023-03-18 10:02:25,035] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3330/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3330/checkm_input OceanDNA-b3330/checkm_result
[2023-03-18 10:02:51,751] [INFO] Task succeeded: CheckM
[2023-03-18 10:02:51,751] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 33.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 10:02:51,753] [INFO] ===== Completeness check finished =====
[2023-03-18 10:02:51,753] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:02:51,754] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3330/markers.fasta)
[2023-03-18 10:02:51,754] [INFO] Task started: Blastn
[2023-03-18 10:02:51,754] [INFO] Running command: blastn -query OceanDNA-b3330/markers.fasta -db /var/lib/cwl/stg61e5c5df-be62-4c96-a215-eeedbf943445/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3330/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:02:52,132] [INFO] Task succeeded: Blastn
[2023-03-18 10:02:52,133] [INFO] Selected 5 target genomes.
[2023-03-18 10:02:52,133] [INFO] Target genome list was writen to OceanDNA-b3330/target_genomes_gtdb.txt
[2023-03-18 10:02:52,147] [INFO] Task started: fastANI
[2023-03-18 10:02:52,147] [INFO] Running command: fastANI --query /var/lib/cwl/stg802be469-746c-4d40-8513-b6d9ddb017fc/OceanDNA-b3330.fa --refList OceanDNA-b3330/target_genomes_gtdb.txt --output OceanDNA-b3330/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:02:55,542] [INFO] Task succeeded: fastANI
[2023-03-18 10:02:55,546] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 10:02:55,546] [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_013408145.1	s__Nocardioides marinus	87.6372	282	349	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	96.85	95.82	0.82	0.73	3	-
GCA_001627335.1	s__Nocardioides sp001627335	87.0323	251	349	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.38	96.50	0.91	0.88	12	-
GCF_013177455.1	s__Nocardioides sp013177455	80.7445	213	349	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.28	98.92	0.97	0.95	4	-
GCF_015070375.1	s__Nocardioides kribbensis	80.2912	219	349	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.79	97.79	0.94	0.92	3	-
GCA_002729525.1	s__Nocardioides sp002729525	79.6827	209	349	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 10:02:55,546] [INFO] GTDB search result was written to OceanDNA-b3330/result_gtdb.tsv
[2023-03-18 10:02:55,546] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:02:55,547] [INFO] DFAST_QC result json was written to OceanDNA-b3330/dqc_result.json
[2023-03-18 10:02:55,547] [INFO] DFAST_QC completed!
[2023-03-18 10:02:55,547] [INFO] Total running time: 0h0m44s