[2023-03-18 03:09:33,541] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:09:33,542] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:09:33,542] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b33d029-f229-4354-bc87-794f1d74a99a/dqc_reference
[2023-03-18 03:09:34,688] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:09:34,689] [INFO] Task started: Prodigal
[2023-03-18 03:09:34,689] [INFO] Running command: cat /var/lib/cwl/stgf86fa650-ae74-4217-9d74-af3dda4d3c86/OceanDNA-b22494.fa | prodigal -d OceanDNA-b22494/cds.fna -a OceanDNA-b22494/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:10:02,632] [INFO] Task succeeded: Prodigal
[2023-03-18 03:10:02,633] [INFO] Task started: HMMsearch
[2023-03-18 03:10:02,633] [INFO] Running command: hmmsearch --tblout OceanDNA-b22494/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b33d029-f229-4354-bc87-794f1d74a99a/dqc_reference/reference_markers.hmm OceanDNA-b22494/protein.faa > /dev/null
[2023-03-18 03:10:02,924] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:10:02,925] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgf86fa650-ae74-4217-9d74-af3dda4d3c86/OceanDNA-b22494.fa]
[2023-03-18 03:10:02,960] [INFO] Query marker FASTA was written to OceanDNA-b22494/markers.fasta
[2023-03-18 03:10:02,960] [INFO] Task started: Blastn
[2023-03-18 03:10:02,960] [INFO] Running command: blastn -query OceanDNA-b22494/markers.fasta -db /var/lib/cwl/stg2b33d029-f229-4354-bc87-794f1d74a99a/dqc_reference/reference_markers.fasta -out OceanDNA-b22494/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:10:03,582] [INFO] Task succeeded: Blastn
[2023-03-18 03:10:03,583] [INFO] Selected 16 target genomes.
[2023-03-18 03:10:03,583] [INFO] Target genome list was writen to OceanDNA-b22494/target_genomes.txt
[2023-03-18 03:10:03,596] [INFO] Task started: fastANI
[2023-03-18 03:10:03,596] [INFO] Running command: fastANI --query /var/lib/cwl/stgf86fa650-ae74-4217-9d74-af3dda4d3c86/OceanDNA-b22494.fa --refList OceanDNA-b22494/target_genomes.txt --output OceanDNA-b22494/fastani_result.tsv --threads 1
[2023-03-18 03:10:20,319] [INFO] Task succeeded: fastANI
[2023-03-18 03:10:20,320] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2b33d029-f229-4354-bc87-794f1d74a99a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:10:20,320] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2b33d029-f229-4354-bc87-794f1d74a99a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:10:20,324] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:10:20,324] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 03:10:20,324] [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
Roseiconus nitratireducens	strain=JC645	GCA_008629675.1	2605748	2605748	type	True	75.9911	57	705	95	below_threshold
Crateriforma conspicua	strain=Mal65	GCA_007752935.1	2527996	2527996	type	True	75.5431	68	705	95	below_threshold
Roseimaritima sediminicola	strain=JC651	GCA_009618275.1	2662066	2662066	type	True	75.4668	67	705	95	below_threshold
Stieleria neptunia	strain=Enr13	GCA_007754155.1	2527979	2527979	type	True	75.3474	73	705	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 03:10:20,325] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22494/tc_result.tsv
[2023-03-18 03:10:20,325] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:10:20,325] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:10:20,325] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b33d029-f229-4354-bc87-794f1d74a99a/dqc_reference/checkm_data
[2023-03-18 03:10:20,326] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:10:20,332] [INFO] Task started: CheckM
[2023-03-18 03:10:20,332] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22494/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22494/checkm_input OceanDNA-b22494/checkm_result
[2023-03-18 03:11:27,960] [INFO] Task succeeded: CheckM
[2023-03-18 03:11:27,960] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.68%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 03:11:27,963] [INFO] ===== Completeness check finished =====
[2023-03-18 03:11:27,964] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:11:27,964] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22494/markers.fasta)
[2023-03-18 03:11:27,964] [INFO] Task started: Blastn
[2023-03-18 03:11:27,964] [INFO] Running command: blastn -query OceanDNA-b22494/markers.fasta -db /var/lib/cwl/stg2b33d029-f229-4354-bc87-794f1d74a99a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22494/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:11:28,814] [INFO] Task succeeded: Blastn
[2023-03-18 03:11:28,815] [INFO] Selected 16 target genomes.
[2023-03-18 03:11:28,815] [INFO] Target genome list was writen to OceanDNA-b22494/target_genomes_gtdb.txt
[2023-03-18 03:11:28,920] [INFO] Task started: fastANI
[2023-03-18 03:11:28,920] [INFO] Running command: fastANI --query /var/lib/cwl/stgf86fa650-ae74-4217-9d74-af3dda4d3c86/OceanDNA-b22494.fa --refList OceanDNA-b22494/target_genomes_gtdb.txt --output OceanDNA-b22494/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:11:45,614] [INFO] Task succeeded: fastANI
[2023-03-18 03:11:45,619] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 03:11:45,619] [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_012290005.1	s__Crateriforma spongiae	75.7106	61	705	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Crateriforma	95.0	98.43	98.43	0.93	0.93	2	-
GCF_014154935.1	s__Stieleria sp014154935	75.5554	87	705	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007752935.1	s__Crateriforma conspicua	75.5431	68	705	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Crateriforma	95.0	98.96	98.96	0.93	0.93	2	-
GCA_007753675.1	s__Stieleria sp007753675	75.4885	77	705	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009618275.1	s__Roseimaritima sp009618275	75.4668	67	705	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Roseimaritima	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010367455.1	s__Laterigemmans baculatus	75.4184	57	705	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Laterigemmans	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007754155.1	s__Stieleria neptunia	75.3612	72	705	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 03:11:45,619] [INFO] GTDB search result was written to OceanDNA-b22494/result_gtdb.tsv
[2023-03-18 03:11:45,619] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:11:45,620] [INFO] DFAST_QC result json was written to OceanDNA-b22494/dqc_result.json
[2023-03-18 03:11:45,620] [INFO] DFAST_QC completed!
[2023-03-18 03:11:45,620] [INFO] Total running time: 0h2m12s