[2023-03-16 04:31:43,751] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:31:43,751] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:31:43,751] [INFO] DQC Reference Directory: /var/lib/cwl/stge88f50b3-af5b-4102-81d5-1b8deeea7e96/dqc_reference
[2023-03-16 04:31:45,524] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:31:45,524] [INFO] Task started: Prodigal
[2023-03-16 04:31:45,524] [INFO] Running command: cat /var/lib/cwl/stg21bc346f-994b-4adf-9e97-eacc3e45d571/OceanDNA-b29683.fa | prodigal -d OceanDNA-b29683/cds.fna -a OceanDNA-b29683/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:31:59,404] [INFO] Task succeeded: Prodigal
[2023-03-16 04:31:59,404] [INFO] Task started: HMMsearch
[2023-03-16 04:31:59,404] [INFO] Running command: hmmsearch --tblout OceanDNA-b29683/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge88f50b3-af5b-4102-81d5-1b8deeea7e96/dqc_reference/reference_markers.hmm OceanDNA-b29683/protein.faa > /dev/null
[2023-03-16 04:31:59,593] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:31:59,593] [INFO] Found 6/6 markers.
[2023-03-16 04:31:59,611] [INFO] Query marker FASTA was written to OceanDNA-b29683/markers.fasta
[2023-03-16 04:31:59,611] [INFO] Task started: Blastn
[2023-03-16 04:31:59,611] [INFO] Running command: blastn -query OceanDNA-b29683/markers.fasta -db /var/lib/cwl/stge88f50b3-af5b-4102-81d5-1b8deeea7e96/dqc_reference/reference_markers.fasta -out OceanDNA-b29683/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:32:00,165] [INFO] Task succeeded: Blastn
[2023-03-16 04:32:00,166] [INFO] Selected 25 target genomes.
[2023-03-16 04:32:00,166] [INFO] Target genome list was writen to OceanDNA-b29683/target_genomes.txt
[2023-03-16 04:32:00,183] [INFO] Task started: fastANI
[2023-03-16 04:32:00,183] [INFO] Running command: fastANI --query /var/lib/cwl/stg21bc346f-994b-4adf-9e97-eacc3e45d571/OceanDNA-b29683.fa --refList OceanDNA-b29683/target_genomes.txt --output OceanDNA-b29683/fastani_result.tsv --threads 1
[2023-03-16 04:32:14,883] [INFO] Task succeeded: fastANI
[2023-03-16 04:32:14,883] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge88f50b3-af5b-4102-81d5-1b8deeea7e96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:32:14,884] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge88f50b3-af5b-4102-81d5-1b8deeea7e96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:32:14,890] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:32:14,890] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:32:14,890] [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
Planktomarina temperata	strain=RCA23	GCA_000738435.1	1284658	1284658	type	True	78.2546	290	703	95	below_threshold
Shimia marina	strain=CECT 7688	GCA_001458175.1	321267	321267	type	True	76.4424	53	703	95	below_threshold
Shimia marina	strain=DSM 26895	GCA_900112745.1	321267	321267	type	True	76.4424	53	703	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	76.0151	57	703	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	75.9358	55	703	95	below_threshold
Tritonibacter multivorans	strain=CECT 7557	GCA_001458415.1	928856	928856	type	True	75.8774	62	703	95	below_threshold
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	75.6972	55	703	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:32:14,890] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29683/tc_result.tsv
[2023-03-16 04:32:14,890] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:32:14,890] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:32:14,891] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge88f50b3-af5b-4102-81d5-1b8deeea7e96/dqc_reference/checkm_data
[2023-03-16 04:32:14,891] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:32:15,044] [INFO] Task started: CheckM
[2023-03-16 04:32:15,044] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29683/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29683/checkm_input OceanDNA-b29683/checkm_result
[2023-03-16 04:32:53,516] [INFO] Task succeeded: CheckM
[2023-03-16 04:32:53,516] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:32:53,534] [INFO] ===== Completeness check finished =====
[2023-03-16 04:32:53,534] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:32:53,534] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29683/markers.fasta)
[2023-03-16 04:32:53,536] [INFO] Task started: Blastn
[2023-03-16 04:32:53,536] [INFO] Running command: blastn -query OceanDNA-b29683/markers.fasta -db /var/lib/cwl/stge88f50b3-af5b-4102-81d5-1b8deeea7e96/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29683/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:32:54,337] [INFO] Task succeeded: Blastn
[2023-03-16 04:32:54,337] [INFO] Selected 12 target genomes.
[2023-03-16 04:32:54,338] [INFO] Target genome list was writen to OceanDNA-b29683/target_genomes_gtdb.txt
[2023-03-16 04:32:54,381] [INFO] Task started: fastANI
[2023-03-16 04:32:54,381] [INFO] Running command: fastANI --query /var/lib/cwl/stg21bc346f-994b-4adf-9e97-eacc3e45d571/OceanDNA-b29683.fa --refList OceanDNA-b29683/target_genomes_gtdb.txt --output OceanDNA-b29683/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:33:00,192] [INFO] Task succeeded: fastANI
[2023-03-16 04:33:00,197] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 04:33:00,197] [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_905182455.1	s__Planktomarina sp905182455	98.4304	541	703	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905182535.1	s__Planktomarina sp905182535	83.206	396	703	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	98.42	98.42	0.82	0.82	2	-
GCA_905182195.1	s__Planktomarina sp905182195	81.0227	336	703	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000981705.1	s__Planktomarina sp000981705	80.3087	372	703	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	98.80	98.80	0.86	0.86	2	-
GCF_000738435.1	s__Planktomarina temperata	78.2671	289	703	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	98.99	97.76	0.97	0.80	20	-
GCA_905181815.1	s__Planktomarina sp905181815	78.0	256	703	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016780825.1	s__Planktomarina sp016780825	77.7096	256	703	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:33:00,198] [INFO] GTDB search result was written to OceanDNA-b29683/result_gtdb.tsv
[2023-03-16 04:33:00,198] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:33:00,199] [INFO] DFAST_QC result json was written to OceanDNA-b29683/dqc_result.json
[2023-03-16 04:33:00,199] [INFO] DFAST_QC completed!
[2023-03-16 04:33:00,199] [INFO] Total running time: 0h1m16s