[2023-03-14 11:13:58,985] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:13:58,985] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:13:58,985] [INFO] DQC Reference Directory: /var/lib/cwl/stgef7d4f33-bebc-43da-a9e8-facab5bfcc6a/dqc_reference
[2023-03-14 11:14:00,598] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:14:00,598] [INFO] Task started: Prodigal
[2023-03-14 11:14:00,598] [INFO] Running command: cat /var/lib/cwl/stgb23ac205-a952-4e41-bf77-0510908869db/OceanDNA-b30151.fa | prodigal -d OceanDNA-b30151/cds.fna -a OceanDNA-b30151/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:14:23,331] [INFO] Task succeeded: Prodigal
[2023-03-14 11:14:23,331] [INFO] Task started: HMMsearch
[2023-03-14 11:14:23,331] [INFO] Running command: hmmsearch --tblout OceanDNA-b30151/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgef7d4f33-bebc-43da-a9e8-facab5bfcc6a/dqc_reference/reference_markers.hmm OceanDNA-b30151/protein.faa > /dev/null
[2023-03-14 11:14:23,515] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:14:23,515] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgb23ac205-a952-4e41-bf77-0510908869db/OceanDNA-b30151.fa]
[2023-03-14 11:14:23,539] [INFO] Query marker FASTA was written to OceanDNA-b30151/markers.fasta
[2023-03-14 11:14:23,541] [INFO] Task started: Blastn
[2023-03-14 11:14:23,541] [INFO] Running command: blastn -query OceanDNA-b30151/markers.fasta -db /var/lib/cwl/stgef7d4f33-bebc-43da-a9e8-facab5bfcc6a/dqc_reference/reference_markers.fasta -out OceanDNA-b30151/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:14:24,362] [INFO] Task succeeded: Blastn
[2023-03-14 11:14:24,363] [INFO] Selected 14 target genomes.
[2023-03-14 11:14:24,363] [INFO] Target genome list was writen to OceanDNA-b30151/target_genomes.txt
[2023-03-14 11:14:24,375] [INFO] Task started: fastANI
[2023-03-14 11:14:24,375] [INFO] Running command: fastANI --query /var/lib/cwl/stgb23ac205-a952-4e41-bf77-0510908869db/OceanDNA-b30151.fa --refList OceanDNA-b30151/target_genomes.txt --output OceanDNA-b30151/fastani_result.tsv --threads 1
[2023-03-14 11:14:37,568] [INFO] Task succeeded: fastANI
[2023-03-14 11:14:37,569] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgef7d4f33-bebc-43da-a9e8-facab5bfcc6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:14:37,569] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgef7d4f33-bebc-43da-a9e8-facab5bfcc6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:14:37,578] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2023-03-14 11:14:37,578] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-14 11:14:37,578] [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
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	99.875	1134	1227	95	conclusive
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	99.8723	1211	1227	95	conclusive
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	84.3329	907	1227	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	83.9946	936	1227	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	81.6661	772	1227	95	below_threshold
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	81.5956	782	1227	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	81.1401	734	1227	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	79.6465	658	1227	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	79.1273	574	1227	95	below_threshold
Maritimibacter harenae	strain=DP07	GCA_009882975.1	2606218	2606218	type	True	78.8818	414	1227	95	below_threshold
Pseudooceanicola onchidii	strain=XY-99	GCA_004959925.1	2562279	2562279	type	True	78.1981	421	1227	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	77.9594	426	1227	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.7749	381	1227	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	77.4763	306	1227	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 11:14:37,578] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30151/tc_result.tsv
[2023-03-14 11:14:37,578] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:14:37,579] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:14:37,579] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgef7d4f33-bebc-43da-a9e8-facab5bfcc6a/dqc_reference/checkm_data
[2023-03-14 11:14:37,579] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:14:37,584] [INFO] Task started: CheckM
[2023-03-14 11:14:37,584] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30151/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30151/checkm_input OceanDNA-b30151/checkm_result
[2023-03-14 11:15:36,712] [INFO] Task succeeded: CheckM
[2023-03-14 11:15:36,712] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 49.48%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:15:36,715] [INFO] ===== Completeness check finished =====
[2023-03-14 11:15:36,715] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:15:36,715] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30151/markers.fasta)
[2023-03-14 11:15:36,717] [INFO] Task started: Blastn
[2023-03-14 11:15:36,717] [INFO] Running command: blastn -query OceanDNA-b30151/markers.fasta -db /var/lib/cwl/stgef7d4f33-bebc-43da-a9e8-facab5bfcc6a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30151/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:15:38,205] [INFO] Task succeeded: Blastn
[2023-03-14 11:15:38,205] [INFO] Selected 8 target genomes.
[2023-03-14 11:15:38,205] [INFO] Target genome list was writen to OceanDNA-b30151/target_genomes_gtdb.txt
[2023-03-14 11:15:38,215] [INFO] Task started: fastANI
[2023-03-14 11:15:38,215] [INFO] Running command: fastANI --query /var/lib/cwl/stgb23ac205-a952-4e41-bf77-0510908869db/OceanDNA-b30151.fa --refList OceanDNA-b30151/target_genomes_gtdb.txt --output OceanDNA-b30151/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:15:47,312] [INFO] Task succeeded: fastANI
[2023-03-14 11:15:47,318] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 11:15:47,318] [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_001969385.1	s__Salipiger profundus	99.8723	1211	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.85	99.64	0.97	0.94	5	conclusive
GCF_900102075.1	s__Salipiger thiooxidans	84.3056	910	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.34	95.88	0.90	0.85	6	-
GCF_000153725.1	s__Salipiger bermudensis	84.0043	935	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.06	97.75	0.87	0.75	4	-
GCF_001975705.1	s__Salipiger abyssi	82.9719	805	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000442255.1	s__Salipiger mucosus	82.6709	777	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017311415.1	s__Salipiger abyssi_A	82.6534	777	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015223355.1	s__Salipiger pacificus_B	81.5944	755	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255395.1	s__AWRV01 sp017255395	79.7894	629	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__AWRV01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:15:47,318] [INFO] GTDB search result was written to OceanDNA-b30151/result_gtdb.tsv
[2023-03-14 11:15:47,319] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:15:47,320] [INFO] DFAST_QC result json was written to OceanDNA-b30151/dqc_result.json
[2023-03-14 11:15:47,320] [INFO] DFAST_QC completed!
[2023-03-14 11:15:47,320] [INFO] Total running time: 0h1m48s