[2023-03-19 03:28:07,297] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:28:07,297] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:28:07,297] [INFO] DQC Reference Directory: /var/lib/cwl/stg33eb6ed5-61ea-4043-b28f-3e7878bf9169/dqc_reference
[2023-03-19 03:28:08,416] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:28:08,416] [INFO] Task started: Prodigal
[2023-03-19 03:28:08,416] [INFO] Running command: cat /var/lib/cwl/stgd3348898-6c16-4632-bce9-82ec01e6d549/OceanDNA-b7211.fa | prodigal -d OceanDNA-b7211/cds.fna -a OceanDNA-b7211/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:28:27,567] [INFO] Task succeeded: Prodigal
[2023-03-19 03:28:27,567] [INFO] Task started: HMMsearch
[2023-03-19 03:28:27,567] [INFO] Running command: hmmsearch --tblout OceanDNA-b7211/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg33eb6ed5-61ea-4043-b28f-3e7878bf9169/dqc_reference/reference_markers.hmm OceanDNA-b7211/protein.faa > /dev/null
[2023-03-19 03:28:27,749] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:28:27,750] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd3348898-6c16-4632-bce9-82ec01e6d549/OceanDNA-b7211.fa]
[2023-03-19 03:28:27,770] [INFO] Query marker FASTA was written to OceanDNA-b7211/markers.fasta
[2023-03-19 03:28:27,770] [INFO] Task started: Blastn
[2023-03-19 03:28:27,770] [INFO] Running command: blastn -query OceanDNA-b7211/markers.fasta -db /var/lib/cwl/stg33eb6ed5-61ea-4043-b28f-3e7878bf9169/dqc_reference/reference_markers.fasta -out OceanDNA-b7211/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:28:28,315] [INFO] Task succeeded: Blastn
[2023-03-19 03:28:28,315] [INFO] Selected 14 target genomes.
[2023-03-19 03:28:28,316] [INFO] Target genome list was writen to OceanDNA-b7211/target_genomes.txt
[2023-03-19 03:28:28,323] [INFO] Task started: fastANI
[2023-03-19 03:28:28,323] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3348898-6c16-4632-bce9-82ec01e6d549/OceanDNA-b7211.fa --refList OceanDNA-b7211/target_genomes.txt --output OceanDNA-b7211/fastani_result.tsv --threads 1
[2023-03-19 03:28:36,607] [INFO] Task succeeded: fastANI
[2023-03-19 03:28:36,607] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg33eb6ed5-61ea-4043-b28f-3e7878bf9169/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:28:36,607] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg33eb6ed5-61ea-4043-b28f-3e7878bf9169/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:28:36,615] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2023-03-19 03:28:36,615] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-19 03:28:36,615] [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
Gramella flava	strain=JLT2011	GCA_002120265.1	1486245	1486245	type	True	98.0955	763	822	95	conclusive
Gramella flava	strain=JLT2011	GCA_001951155.1	1486245	1486245	type	True	98.0799	773	822	95	conclusive
Gramella fulva	strain=SH35	GCA_003024155.1	2126553	2126553	type	True	77.8242	238	822	95	below_threshold
Gramella gaetbulicola	strain=DSM 23082	GCA_003054225.1	703340	703340	type	True	77.7664	220	822	95	below_threshold
Gramella crocea	strain=YB25	GCA_022410465.1	2904124	2904124	type	True	77.6182	200	822	95	below_threshold
Gramella portivictoriae	strain=DSM 23547	GCA_000423045.1	326069	326069	type	True	77.5972	173	822	95	below_threshold
Gramella lutea	strain=YJ019	GCA_022489035.1	1607951	1607951	type	True	77.5543	196	822	95	below_threshold
Gramella aestuarii	strain=BS12	GCA_009735585.1	1028746	1028746	type	True	77.3386	220	822	95	below_threshold
Gramella forsetii	strain=CGMCC 1.15422	GCA_014642775.1	411153	411153	type	True	77.2551	189	822	95	below_threshold
Gramella forsetii	strain=KT0803	GCA_000060345.1	411153	411153	type	True	77.2256	188	822	95	below_threshold
Salegentibacter echinorum	strain=DSM 24579	GCA_900129445.1	1073325	1073325	type	True	76.5927	84	822	95	below_threshold
Salegentibacter salegens	strain=DSM 5424	GCA_003001895.1	143223	143223	type	True	76.4143	109	822	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 03:28:36,615] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7211/tc_result.tsv
[2023-03-19 03:28:36,615] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:28:36,616] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:28:36,616] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg33eb6ed5-61ea-4043-b28f-3e7878bf9169/dqc_reference/checkm_data
[2023-03-19 03:28:36,616] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:28:36,621] [INFO] Task started: CheckM
[2023-03-19 03:28:36,621] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7211/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7211/checkm_input OceanDNA-b7211/checkm_result
[2023-03-19 03:29:27,459] [INFO] Task succeeded: CheckM
[2023-03-19 03:29:27,459] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 03:29:27,461] [INFO] ===== Completeness check finished =====
[2023-03-19 03:29:27,462] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:29:27,462] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7211/markers.fasta)
[2023-03-19 03:29:27,462] [INFO] Task started: Blastn
[2023-03-19 03:29:27,462] [INFO] Running command: blastn -query OceanDNA-b7211/markers.fasta -db /var/lib/cwl/stg33eb6ed5-61ea-4043-b28f-3e7878bf9169/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7211/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:29:28,238] [INFO] Task succeeded: Blastn
[2023-03-19 03:29:28,239] [INFO] Selected 12 target genomes.
[2023-03-19 03:29:28,239] [INFO] Target genome list was writen to OceanDNA-b7211/target_genomes_gtdb.txt
[2023-03-19 03:29:28,247] [INFO] Task started: fastANI
[2023-03-19 03:29:28,247] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3348898-6c16-4632-bce9-82ec01e6d549/OceanDNA-b7211.fa --refList OceanDNA-b7211/target_genomes_gtdb.txt --output OceanDNA-b7211/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:29:35,541] [INFO] Task succeeded: fastANI
[2023-03-19 03:29:35,548] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 03:29:35,548] [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_001951155.1	s__Gramella flava	98.0799	773	822	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	99.04	98.07	0.94	0.88	3	conclusive
GCF_003024155.1	s__Gramella fulva	77.8242	238	822	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054225.1	s__Gramella gaetbulicola	77.7818	219	822	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009735695.1	s__Gramella sp009735695	77.6336	234	822	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423045.1	s__Gramella portivictoriae	77.5972	173	822	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004332155.1	s__Gramella sp004332155	77.4635	196	822	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009735585.1	s__Gramella aestuarii	77.3386	220	822	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000060345.1	s__Gramella forsetii	77.2256	188	822	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000423065.1	s__Gramella echinicola	77.1653	202	822	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	97.44	97.44	0.87	0.87	2	-
GCF_004362395.1	s__Salegentibacter sp004362395	76.8196	99	822	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142975.1	s__Salegentibacter salegens	76.4387	110	822	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-19 03:29:35,549] [INFO] GTDB search result was written to OceanDNA-b7211/result_gtdb.tsv
[2023-03-19 03:29:35,549] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:29:35,550] [INFO] DFAST_QC result json was written to OceanDNA-b7211/dqc_result.json
[2023-03-19 03:29:35,550] [INFO] DFAST_QC completed!
[2023-03-19 03:29:35,550] [INFO] Total running time: 0h1m28s