[2023-03-18 03:28:30,669] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:28:30,669] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:28:30,669] [INFO] DQC Reference Directory: /var/lib/cwl/stg7bf37be9-daff-46e3-9991-895285aa01fa/dqc_reference
[2023-03-18 03:28:31,752] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:28:31,753] [INFO] Task started: Prodigal
[2023-03-18 03:28:31,753] [INFO] Running command: cat /var/lib/cwl/stg7563d89c-1559-404b-9911-b0b71582b31b/OceanDNA-b30709.fa | prodigal -d OceanDNA-b30709/cds.fna -a OceanDNA-b30709/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:28:52,302] [INFO] Task succeeded: Prodigal
[2023-03-18 03:28:52,302] [INFO] Task started: HMMsearch
[2023-03-18 03:28:52,302] [INFO] Running command: hmmsearch --tblout OceanDNA-b30709/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7bf37be9-daff-46e3-9991-895285aa01fa/dqc_reference/reference_markers.hmm OceanDNA-b30709/protein.faa > /dev/null
[2023-03-18 03:28:52,497] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:28:52,497] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg7563d89c-1559-404b-9911-b0b71582b31b/OceanDNA-b30709.fa]
[2023-03-18 03:28:52,519] [INFO] Query marker FASTA was written to OceanDNA-b30709/markers.fasta
[2023-03-18 03:28:52,519] [INFO] Task started: Blastn
[2023-03-18 03:28:52,519] [INFO] Running command: blastn -query OceanDNA-b30709/markers.fasta -db /var/lib/cwl/stg7bf37be9-daff-46e3-9991-895285aa01fa/dqc_reference/reference_markers.fasta -out OceanDNA-b30709/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:28:53,218] [INFO] Task succeeded: Blastn
[2023-03-18 03:28:53,219] [INFO] Selected 11 target genomes.
[2023-03-18 03:28:53,219] [INFO] Target genome list was writen to OceanDNA-b30709/target_genomes.txt
[2023-03-18 03:28:53,226] [INFO] Task started: fastANI
[2023-03-18 03:28:53,226] [INFO] Running command: fastANI --query /var/lib/cwl/stg7563d89c-1559-404b-9911-b0b71582b31b/OceanDNA-b30709.fa --refList OceanDNA-b30709/target_genomes.txt --output OceanDNA-b30709/fastani_result.tsv --threads 1
[2023-03-18 03:29:01,736] [INFO] Task succeeded: fastANI
[2023-03-18 03:29:01,736] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7bf37be9-daff-46e3-9991-895285aa01fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:29:01,736] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7bf37be9-daff-46e3-9991-895285aa01fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:29:01,743] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:29:01,743] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 03:29:01,743] [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
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	85.8073	765	1039	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	85.5024	736	1039	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	84.2768	663	1039	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	79.4032	473	1039	95	below_threshold
Gemmobacter aquatilis	strain=DSM 3857	GCA_900110025.1	933059	933059	type	True	79.2843	429	1039	95	below_threshold
Gemmobacter caeruleus	strain=N8	GCA_008271655.1	2595004	2595004	type	True	78.9698	432	1039	95	below_threshold
Gemmobacter straminiformis	strain=CAM-8	GCA_014243445.1	2045119	2045119	type	True	78.6385	399	1039	95	below_threshold
Rhodobacter thermarum	strain=YIM 73036	GCA_003574395.1	2670345	2670345	type	True	78.3183	366	1039	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	78.246	339	1039	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	77.7978	278	1039	95	below_threshold
Pseudogemmobacter bohemicus	strain=Cd-10	GCA_003290025.1	2250708	2250708	type	True	77.4849	301	1039	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 03:29:01,744] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30709/tc_result.tsv
[2023-03-18 03:29:01,744] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:29:01,744] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:29:01,744] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7bf37be9-daff-46e3-9991-895285aa01fa/dqc_reference/checkm_data
[2023-03-18 03:29:01,745] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:29:01,750] [INFO] Task started: CheckM
[2023-03-18 03:29:01,750] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30709/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30709/checkm_input OceanDNA-b30709/checkm_result
[2023-03-18 03:29:56,678] [INFO] Task succeeded: CheckM
[2023-03-18 03:29:56,678] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 03:29:56,681] [INFO] ===== Completeness check finished =====
[2023-03-18 03:29:56,681] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:29:56,681] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30709/markers.fasta)
[2023-03-18 03:29:56,681] [INFO] Task started: Blastn
[2023-03-18 03:29:56,681] [INFO] Running command: blastn -query OceanDNA-b30709/markers.fasta -db /var/lib/cwl/stg7bf37be9-daff-46e3-9991-895285aa01fa/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30709/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:29:57,823] [INFO] Task succeeded: Blastn
[2023-03-18 03:29:57,824] [INFO] Selected 5 target genomes.
[2023-03-18 03:29:57,824] [INFO] Target genome list was writen to OceanDNA-b30709/target_genomes_gtdb.txt
[2023-03-18 03:29:57,846] [INFO] Task started: fastANI
[2023-03-18 03:29:57,846] [INFO] Running command: fastANI --query /var/lib/cwl/stg7563d89c-1559-404b-9911-b0b71582b31b/OceanDNA-b30709.fa --refList OceanDNA-b30709/target_genomes_gtdb.txt --output OceanDNA-b30709/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:30:02,162] [INFO] Task succeeded: fastANI
[2023-03-18 03:30:02,166] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 03:30:02,166] [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_010915705.1	s__ETT8 sp010915705	85.7927	766	1039	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002794355.1	s__ETT8 sp002794355	85.6811	766	1039	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003443995.1	s__ETT8 sp003443995	85.5205	734	1039	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745575.1	s__ETT8 sp004745575	84.2768	663	1039	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	97.69	97.69	0.90	0.90	2	-
GCF_002900965.1	s__ETT8 sp002900965	83.8682	655	1039	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 03:30:02,166] [INFO] GTDB search result was written to OceanDNA-b30709/result_gtdb.tsv
[2023-03-18 03:30:02,166] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:30:02,167] [INFO] DFAST_QC result json was written to OceanDNA-b30709/dqc_result.json
[2023-03-18 03:30:02,168] [INFO] DFAST_QC completed!
[2023-03-18 03:30:02,168] [INFO] Total running time: 0h1m31s