[2023-03-15 11:31:26,694] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:31:26,697] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:31:26,697] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c6ffdaf-d594-4a2f-b123-602c388bcdad/dqc_reference
[2023-03-15 11:31:27,786] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:31:27,787] [INFO] Task started: Prodigal
[2023-03-15 11:31:27,787] [INFO] Running command: cat /var/lib/cwl/stg9344dde3-7646-4511-a7d2-a84959518e8a/OceanDNA-b32974.fa | prodigal -d OceanDNA-b32974/cds.fna -a OceanDNA-b32974/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:31:40,436] [INFO] Task succeeded: Prodigal
[2023-03-15 11:31:40,436] [INFO] Task started: HMMsearch
[2023-03-15 11:31:40,436] [INFO] Running command: hmmsearch --tblout OceanDNA-b32974/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c6ffdaf-d594-4a2f-b123-602c388bcdad/dqc_reference/reference_markers.hmm OceanDNA-b32974/protein.faa > /dev/null
[2023-03-15 11:31:40,657] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:31:40,658] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg9344dde3-7646-4511-a7d2-a84959518e8a/OceanDNA-b32974.fa]
[2023-03-15 11:31:40,690] [INFO] Query marker FASTA was written to OceanDNA-b32974/markers.fasta
[2023-03-15 11:31:40,692] [INFO] Task started: Blastn
[2023-03-15 11:31:40,692] [INFO] Running command: blastn -query OceanDNA-b32974/markers.fasta -db /var/lib/cwl/stg4c6ffdaf-d594-4a2f-b123-602c388bcdad/dqc_reference/reference_markers.fasta -out OceanDNA-b32974/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:31:41,393] [INFO] Task succeeded: Blastn
[2023-03-15 11:31:41,397] [INFO] Selected 26 target genomes.
[2023-03-15 11:31:41,397] [INFO] Target genome list was writen to OceanDNA-b32974/target_genomes.txt
[2023-03-15 11:31:41,408] [INFO] Task started: fastANI
[2023-03-15 11:31:41,408] [INFO] Running command: fastANI --query /var/lib/cwl/stg9344dde3-7646-4511-a7d2-a84959518e8a/OceanDNA-b32974.fa --refList OceanDNA-b32974/target_genomes.txt --output OceanDNA-b32974/fastani_result.tsv --threads 1
[2023-03-15 11:31:59,509] [INFO] Task succeeded: fastANI
[2023-03-15 11:31:59,509] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c6ffdaf-d594-4a2f-b123-602c388bcdad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:31:59,510] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c6ffdaf-d594-4a2f-b123-602c388bcdad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:31:59,562] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:31:59,562] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 11:31:59,562] [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
Hwanghaeella grinnelliae	strain=Gri0909	GCA_004005845.1	2500179	2500179	type	True	87.0537	378	417	95	below_threshold
Pacificispira spongiicola	strain=KN72	GCA_012926505.1	2729598	2729598	type	True	76.9168	62	417	95	below_threshold
Marivibrio halodurans	strain=CGMCC 1.15697	GCA_017963645.1	2039722	2039722	type	True	76.0576	55	417	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	75.2807	51	417	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:31:59,565] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32974/tc_result.tsv
[2023-03-15 11:31:59,565] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:31:59,565] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:31:59,565] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c6ffdaf-d594-4a2f-b123-602c388bcdad/dqc_reference/checkm_data
[2023-03-15 11:31:59,566] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:31:59,574] [INFO] Task started: CheckM
[2023-03-15 11:31:59,574] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32974/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32974/checkm_input OceanDNA-b32974/checkm_result
[2023-03-15 11:32:38,411] [INFO] Task succeeded: CheckM
[2023-03-15 11:32:38,411] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.66%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:32:38,453] [INFO] ===== Completeness check finished =====
[2023-03-15 11:32:38,453] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:32:38,453] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32974/markers.fasta)
[2023-03-15 11:32:38,454] [INFO] Task started: Blastn
[2023-03-15 11:32:38,454] [INFO] Running command: blastn -query OceanDNA-b32974/markers.fasta -db /var/lib/cwl/stg4c6ffdaf-d594-4a2f-b123-602c388bcdad/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32974/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:32:39,541] [INFO] Task succeeded: Blastn
[2023-03-15 11:32:39,544] [INFO] Selected 26 target genomes.
[2023-03-15 11:32:39,545] [INFO] Target genome list was writen to OceanDNA-b32974/target_genomes_gtdb.txt
[2023-03-15 11:32:39,583] [INFO] Task started: fastANI
[2023-03-15 11:32:39,583] [INFO] Running command: fastANI --query /var/lib/cwl/stg9344dde3-7646-4511-a7d2-a84959518e8a/OceanDNA-b32974.fa --refList OceanDNA-b32974/target_genomes_gtdb.txt --output OceanDNA-b32974/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:32:56,163] [INFO] Task succeeded: fastANI
[2023-03-15 11:32:56,166] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:32:56,166] [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_004005845.1	s__Hwanghaeella grinnelliae	87.0537	378	417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__Hwanghaeella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017792345.1	s__GCA-2696645 sp017792345	77.4512	68	417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__GCA-2696645	95.0	95.39	95.37	0.96	0.95	3	-
GCA_012926505.1	s__GCA-2696645 sp012926505	76.9168	62	417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__GCA-2696645	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017963645.1	s__Marivibrio halodurans	76.0576	55	417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__Marivibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:32:56,170] [INFO] GTDB search result was written to OceanDNA-b32974/result_gtdb.tsv
[2023-03-15 11:32:56,170] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:32:56,174] [INFO] DFAST_QC result json was written to OceanDNA-b32974/dqc_result.json
[2023-03-15 11:32:56,174] [INFO] DFAST_QC completed!
[2023-03-15 11:32:56,174] [INFO] Total running time: 0h1m29s