[2023-03-17 23:20:45,997] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:20:45,997] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:20:45,997] [INFO] DQC Reference Directory: /var/lib/cwl/stg941e988c-5d1a-4868-a1e6-7fa1736837a0/dqc_reference
[2023-03-17 23:20:47,116] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:20:47,117] [INFO] Task started: Prodigal
[2023-03-17 23:20:47,117] [INFO] Running command: cat /var/lib/cwl/stgb34dff1d-66c2-4cad-9080-456d0c72bd69/OceanDNA-b26699.fa | prodigal -d OceanDNA-b26699/cds.fna -a OceanDNA-b26699/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:21:09,749] [INFO] Task succeeded: Prodigal
[2023-03-17 23:21:09,749] [INFO] Task started: HMMsearch
[2023-03-17 23:21:09,749] [INFO] Running command: hmmsearch --tblout OceanDNA-b26699/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg941e988c-5d1a-4868-a1e6-7fa1736837a0/dqc_reference/reference_markers.hmm OceanDNA-b26699/protein.faa > /dev/null
[2023-03-17 23:21:09,960] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:21:09,960] [INFO] Found 6/6 markers.
[2023-03-17 23:21:09,986] [INFO] Query marker FASTA was written to OceanDNA-b26699/markers.fasta
[2023-03-17 23:21:09,987] [INFO] Task started: Blastn
[2023-03-17 23:21:09,987] [INFO] Running command: blastn -query OceanDNA-b26699/markers.fasta -db /var/lib/cwl/stg941e988c-5d1a-4868-a1e6-7fa1736837a0/dqc_reference/reference_markers.fasta -out OceanDNA-b26699/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:21:10,722] [INFO] Task succeeded: Blastn
[2023-03-17 23:21:10,724] [INFO] Selected 9 target genomes.
[2023-03-17 23:21:10,725] [INFO] Target genome list was writen to OceanDNA-b26699/target_genomes.txt
[2023-03-17 23:21:10,786] [INFO] Task started: fastANI
[2023-03-17 23:21:10,786] [INFO] Running command: fastANI --query /var/lib/cwl/stgb34dff1d-66c2-4cad-9080-456d0c72bd69/OceanDNA-b26699.fa --refList OceanDNA-b26699/target_genomes.txt --output OceanDNA-b26699/fastani_result.tsv --threads 1
[2023-03-17 23:21:18,288] [INFO] Task succeeded: fastANI
[2023-03-17 23:21:18,288] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg941e988c-5d1a-4868-a1e6-7fa1736837a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:21:18,289] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg941e988c-5d1a-4868-a1e6-7fa1736837a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:21:18,295] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2023-03-17 23:21:18,295] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 23:21:18,295] [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
Devosia indica	strain=IO390501	GCA_003056405.1	2079253	2079253	type	True	98.0397	1039	1171	95	conclusive
Devosia marina	strain=L53-10-65	GCA_009758415.1	2683198	2683198	type	True	91.3186	933	1171	95	below_threshold
Devosia subaequoris	strain=DSM 23447	GCA_014197055.1	395930	395930	type	True	87.8026	890	1171	95	below_threshold
Devosia subaequoris	strain=HST3-14	GCA_024158985.1	395930	395930	type	True	87.7738	883	1171	95	below_threshold
Devosia salina	strain=SCS-3	GCA_019504385.1	2860336	2860336	type	True	83.5119	858	1171	95	below_threshold
Devosia elaeis	strain=S37	GCA_001650025.1	1770058	1770058	type	True	81.9448	702	1171	95	below_threshold
Devosia beringensis	strain=S02	GCA_014926585.1	2657486	2657486	type	True	80.0978	612	1171	95	below_threshold
Devosia rhizoryzae	strain=LEGU1	GCA_016698665.1	2774137	2774137	type	True	79.8878	579	1171	95	below_threshold
Devosia oryziradicis	strain=G19	GCA_016698645.1	2801335	2801335	type	True	79.5605	566	1171	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 23:21:18,297] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26699/tc_result.tsv
[2023-03-17 23:21:18,298] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:21:18,298] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:21:18,298] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg941e988c-5d1a-4868-a1e6-7fa1736837a0/dqc_reference/checkm_data
[2023-03-17 23:21:18,299] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:21:18,305] [INFO] Task started: CheckM
[2023-03-17 23:21:18,306] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26699/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26699/checkm_input OceanDNA-b26699/checkm_result
[2023-03-17 23:22:14,532] [INFO] Task succeeded: CheckM
[2023-03-17 23:22:14,532] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.44%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 23:22:14,536] [INFO] ===== Completeness check finished =====
[2023-03-17 23:22:14,536] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:22:14,536] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26699/markers.fasta)
[2023-03-17 23:22:14,537] [INFO] Task started: Blastn
[2023-03-17 23:22:14,537] [INFO] Running command: blastn -query OceanDNA-b26699/markers.fasta -db /var/lib/cwl/stg941e988c-5d1a-4868-a1e6-7fa1736837a0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26699/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:22:15,782] [INFO] Task succeeded: Blastn
[2023-03-17 23:22:15,782] [INFO] Selected 9 target genomes.
[2023-03-17 23:22:15,782] [INFO] Target genome list was writen to OceanDNA-b26699/target_genomes_gtdb.txt
[2023-03-17 23:22:15,903] [INFO] Task started: fastANI
[2023-03-17 23:22:15,904] [INFO] Running command: fastANI --query /var/lib/cwl/stgb34dff1d-66c2-4cad-9080-456d0c72bd69/OceanDNA-b26699.fa --refList OceanDNA-b26699/target_genomes_gtdb.txt --output OceanDNA-b26699/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:22:23,832] [INFO] Task succeeded: fastANI
[2023-03-17 23:22:23,838] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 23:22:23,838] [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_003056405.1	s__Devosia indica	98.0397	1039	1171	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_009758415.1	s__Devosia marina	91.3186	933	1171	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	97.05	97.05	0.85	0.85	2	-
GCF_014197055.1	s__Devosia subaequoris	87.7945	890	1171	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016411825.1	s__Devosia sp016411825	82.2519	769	1171	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650025.1	s__Devosia elaeis	81.9433	703	1171	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177655.1	s__Devosia lucknowensis	81.0601	690	1171	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015158295.1	s__Devosia sp015158295	81.0109	616	1171	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000969445.1	s__Devosia chinhatensis	80.8135	615	1171	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018828145.1	s__Devosia sp018828145	80.1008	670	1171	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	99.99	99.98	0.99	0.98	4	-
--------------------------------------------------------------------------------
[2023-03-17 23:22:23,838] [INFO] GTDB search result was written to OceanDNA-b26699/result_gtdb.tsv
[2023-03-17 23:22:23,838] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:22:23,840] [INFO] DFAST_QC result json was written to OceanDNA-b26699/dqc_result.json
[2023-03-17 23:22:23,840] [INFO] DFAST_QC completed!
[2023-03-17 23:22:23,840] [INFO] Total running time: 0h1m38s