[2023-03-17 05:54:59,361] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:54:59,362] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:54:59,362] [INFO] DQC Reference Directory: /var/lib/cwl/stg5492ab4f-8843-450b-92b1-b16a8762c02e/dqc_reference
[2023-03-17 05:55:01,046] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:55:01,046] [INFO] Task started: Prodigal
[2023-03-17 05:55:01,047] [INFO] Running command: cat /var/lib/cwl/stg4347bd56-6e03-48e6-b4a5-8da38ea51f56/OceanDNA-b1712.fa | prodigal -d OceanDNA-b1712/cds.fna -a OceanDNA-b1712/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:55:26,298] [INFO] Task succeeded: Prodigal
[2023-03-17 05:55:26,298] [INFO] Task started: HMMsearch
[2023-03-17 05:55:26,298] [INFO] Running command: hmmsearch --tblout OceanDNA-b1712/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5492ab4f-8843-450b-92b1-b16a8762c02e/dqc_reference/reference_markers.hmm OceanDNA-b1712/protein.faa > /dev/null
[2023-03-17 05:55:26,506] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:55:26,507] [INFO] Found 6/6 markers.
[2023-03-17 05:55:26,543] [INFO] Query marker FASTA was written to OceanDNA-b1712/markers.fasta
[2023-03-17 05:55:26,544] [INFO] Task started: Blastn
[2023-03-17 05:55:26,545] [INFO] Running command: blastn -query OceanDNA-b1712/markers.fasta -db /var/lib/cwl/stg5492ab4f-8843-450b-92b1-b16a8762c02e/dqc_reference/reference_markers.fasta -out OceanDNA-b1712/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:55:27,109] [INFO] Task succeeded: Blastn
[2023-03-17 05:55:27,115] [INFO] Selected 31 target genomes.
[2023-03-17 05:55:27,115] [INFO] Target genome list was writen to OceanDNA-b1712/target_genomes.txt
[2023-03-17 05:55:27,130] [INFO] Task started: fastANI
[2023-03-17 05:55:27,130] [INFO] Running command: fastANI --query /var/lib/cwl/stg4347bd56-6e03-48e6-b4a5-8da38ea51f56/OceanDNA-b1712.fa --refList OceanDNA-b1712/target_genomes.txt --output OceanDNA-b1712/fastani_result.tsv --threads 1
[2023-03-17 05:55:46,061] [INFO] Task succeeded: fastANI
[2023-03-17 05:55:46,062] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5492ab4f-8843-450b-92b1-b16a8762c02e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:55:46,062] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5492ab4f-8843-450b-92b1-b16a8762c02e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:55:46,065] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:55:46,066] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 05:55:46,066] [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
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	75.4746	57	1307	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	75.456	58	1307	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	75.3435	56	1307	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 05:55:46,069] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1712/tc_result.tsv
[2023-03-17 05:55:46,078] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:55:46,078] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:55:46,078] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5492ab4f-8843-450b-92b1-b16a8762c02e/dqc_reference/checkm_data
[2023-03-17 05:55:46,079] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:55:46,086] [INFO] Task started: CheckM
[2023-03-17 05:55:46,086] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1712/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1712/checkm_input OceanDNA-b1712/checkm_result
[2023-03-17 05:56:48,041] [INFO] Task succeeded: CheckM
[2023-03-17 05:56:48,041] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:56:48,170] [INFO] ===== Completeness check finished =====
[2023-03-17 05:56:48,170] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:56:48,170] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1712/markers.fasta)
[2023-03-17 05:56:48,171] [INFO] Task started: Blastn
[2023-03-17 05:56:48,171] [INFO] Running command: blastn -query OceanDNA-b1712/markers.fasta -db /var/lib/cwl/stg5492ab4f-8843-450b-92b1-b16a8762c02e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1712/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:56:48,963] [INFO] Task succeeded: Blastn
[2023-03-17 05:56:48,964] [INFO] Selected 26 target genomes.
[2023-03-17 05:56:48,964] [INFO] Target genome list was writen to OceanDNA-b1712/target_genomes_gtdb.txt
[2023-03-17 05:56:49,024] [INFO] Task started: fastANI
[2023-03-17 05:56:49,024] [INFO] Running command: fastANI --query /var/lib/cwl/stg4347bd56-6e03-48e6-b4a5-8da38ea51f56/OceanDNA-b1712.fa --refList OceanDNA-b1712/target_genomes_gtdb.txt --output OceanDNA-b1712/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:57:01,650] [INFO] Task succeeded: fastANI
[2023-03-17 05:57:01,654] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 05:57:01,655] [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_905182135.1	s__UBA10347 sp905182135	83.4628	628	1307	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA10347;g__UBA10347	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003485885.1	s__UBA10347 sp003485885	78.579	357	1307	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA10347;g__UBA10347	95.0	98.91	98.91	0.90	0.90	2	-
GCA_002694825.1	s__UBA11606 sp002694825	75.9351	60	1307	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	97.28	96.77	0.84	0.81	7	-
GCA_002729125.1	s__UBA11606 sp002729125	75.8315	51	1307	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	99.78	99.78	0.92	0.92	2	-
GCA_016649895.1	s__Actinomarinicola sp016649895	75.6687	51	1307	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__Actinomarinicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 05:57:01,655] [INFO] GTDB search result was written to OceanDNA-b1712/result_gtdb.tsv
[2023-03-17 05:57:01,655] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:57:01,656] [INFO] DFAST_QC result json was written to OceanDNA-b1712/dqc_result.json
[2023-03-17 05:57:01,656] [INFO] DFAST_QC completed!
[2023-03-17 05:57:01,656] [INFO] Total running time: 0h2m2s