[2023-03-17 05:10:04,791] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:10:04,792] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:10:04,792] [INFO] DQC Reference Directory: /var/lib/cwl/stg055815aa-b127-42c6-a3a8-19835bf728c6/dqc_reference
[2023-03-17 05:10:06,006] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:10:06,006] [INFO] Task started: Prodigal
[2023-03-17 05:10:06,006] [INFO] Running command: cat /var/lib/cwl/stg933a2395-72c3-44ab-89a5-9124f4b574d1/OceanDNA-b6579.fa | prodigal -d OceanDNA-b6579/cds.fna -a OceanDNA-b6579/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:10:19,912] [INFO] Task succeeded: Prodigal
[2023-03-17 05:10:19,912] [INFO] Task started: HMMsearch
[2023-03-17 05:10:19,912] [INFO] Running command: hmmsearch --tblout OceanDNA-b6579/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg055815aa-b127-42c6-a3a8-19835bf728c6/dqc_reference/reference_markers.hmm OceanDNA-b6579/protein.faa > /dev/null
[2023-03-17 05:10:20,090] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:10:20,091] [INFO] Found 6/6 markers.
[2023-03-17 05:10:20,141] [INFO] Query marker FASTA was written to OceanDNA-b6579/markers.fasta
[2023-03-17 05:10:20,141] [INFO] Task started: Blastn
[2023-03-17 05:10:20,142] [INFO] Running command: blastn -query OceanDNA-b6579/markers.fasta -db /var/lib/cwl/stg055815aa-b127-42c6-a3a8-19835bf728c6/dqc_reference/reference_markers.fasta -out OceanDNA-b6579/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:10:20,735] [INFO] Task succeeded: Blastn
[2023-03-17 05:10:20,736] [INFO] Selected 25 target genomes.
[2023-03-17 05:10:20,736] [INFO] Target genome list was writen to OceanDNA-b6579/target_genomes.txt
[2023-03-17 05:10:20,751] [INFO] Task started: fastANI
[2023-03-17 05:10:20,751] [INFO] Running command: fastANI --query /var/lib/cwl/stg933a2395-72c3-44ab-89a5-9124f4b574d1/OceanDNA-b6579.fa --refList OceanDNA-b6579/target_genomes.txt --output OceanDNA-b6579/fastani_result.tsv --threads 1
[2023-03-17 05:10:34,238] [INFO] Task succeeded: fastANI
[2023-03-17 05:10:34,238] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg055815aa-b127-42c6-a3a8-19835bf728c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:10:34,238] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg055815aa-b127-42c6-a3a8-19835bf728c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:10:34,245] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2023-03-17 05:10:34,245] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 05:10:34,245] [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
Halomarinibacterium sedimenti	strain=CAU 1614	GCA_019312585.1	2857106	2857106	type	True	95.1027	517	576	95	conclusive
Ulvibacter litoralis	strain=KCTC 12104	GCA_014651275.1	227084	227084	type	True	76.438	129	576	95	below_threshold
Pukyongia salina	strain=RR4-38	GCA_002966125.1	2094025	2094025	type	True	76.3992	53	576	95	below_threshold
Ulvibacter litoralis	strain=DSM 16195	GCA_900102055.1	227084	227084	type	True	76.3945	128	576	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.3836	54	576	95	below_threshold
Aequorivita sinensis	strain=S1-10	GCA_006346335.1	1382458	1382458	type	True	76.3337	76	576	95	below_threshold
Patiriisocius marinus	strain=NBRC 109484	GCA_008974325.1	1397112	1397112	type	True	76.2979	65	576	95	below_threshold
Ulvibacter antarcticus	strain=DSM 23424	GCA_003688405.1	442714	442714	type	True	76.2642	84	576	95	below_threshold
Mesonia phycicola	strain=DSM 21425	GCA_900141885.1	579105	579105	type	True	75.4393	52	576	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 05:10:34,245] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6579/tc_result.tsv
[2023-03-17 05:10:34,246] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:10:34,246] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:10:34,246] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg055815aa-b127-42c6-a3a8-19835bf728c6/dqc_reference/checkm_data
[2023-03-17 05:10:34,247] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:10:34,271] [INFO] Task started: CheckM
[2023-03-17 05:10:34,271] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6579/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6579/checkm_input OceanDNA-b6579/checkm_result
[2023-03-17 05:11:12,097] [INFO] Task succeeded: CheckM
[2023-03-17 05:11:12,097] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.07%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:11:12,099] [INFO] ===== Completeness check finished =====
[2023-03-17 05:11:12,099] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:11:12,100] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6579/markers.fasta)
[2023-03-17 05:11:12,100] [INFO] Task started: Blastn
[2023-03-17 05:11:12,101] [INFO] Running command: blastn -query OceanDNA-b6579/markers.fasta -db /var/lib/cwl/stg055815aa-b127-42c6-a3a8-19835bf728c6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6579/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:11:13,021] [INFO] Task succeeded: Blastn
[2023-03-17 05:11:13,022] [INFO] Selected 24 target genomes.
[2023-03-17 05:11:13,022] [INFO] Target genome list was writen to OceanDNA-b6579/target_genomes_gtdb.txt
[2023-03-17 05:11:13,258] [INFO] Task started: fastANI
[2023-03-17 05:11:13,259] [INFO] Running command: fastANI --query /var/lib/cwl/stg933a2395-72c3-44ab-89a5-9124f4b574d1/OceanDNA-b6579.fa --refList OceanDNA-b6579/target_genomes_gtdb.txt --output OceanDNA-b6579/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:11:24,442] [INFO] Task succeeded: fastANI
[2023-03-17 05:11:24,452] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 05:11:24,452] [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_002694465.1	s__IN17 sp002694465	94.2355	519	576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__IN17	95.0	99.93	99.93	0.95	0.95	2	-
GCA_002707025.1	s__IN17 sp002707025	77.6361	167	576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__IN17	95.0	99.83	99.78	0.96	0.93	3	-
GCF_014641635.1	s__Aquaticitalea lipolytica	77.0632	64	576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquaticitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364245.1	s__Marixanthomonas sp002364245	77.0602	58	576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813135.1	s__Altibacter sp002813135	76.9663	111	576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Altibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001641085.1	s__Aequorivita soesokkakensis	76.912	87	576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	97.26	97.26	0.92	0.92	2	-
GCA_013002065.1	s__SMXJ01 sp013002065	76.7245	82	576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SMXJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002631855.1	s__Marixanthomonas sp002631855	76.7158	87	576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114265.1	s__Flaviramulus basaltis	76.4432	73	576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102055.1	s__Ulvibacter litoralis	76.3945	128	576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacter	95.0	99.98	99.98	1.00	1.00	2	-
GCA_011044175.1	s__Marinirhabdus sp011044175	76.3784	103	576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006346335.1	s__Aequorivita sinensis	76.359	75	576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	97.40	96.22	0.90	0.88	3	-
GCA_002715485.1	s__Aequorivita sp002715485	76.2905	86	576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.49	99.49	0.87	0.87	2	-
GCA_000170815.1	s__Patiriisocius sp000170815	76.1487	73	576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Patiriisocius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002426015.1	s__Aquaticitalea sp002426015	76.0886	58	576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquaticitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019090365.1	s__GCA-002733185 sp019090365	75.9051	73	576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141885.1	s__Mesonia phycicola	75.4393	52	576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 05:11:24,452] [INFO] GTDB search result was written to OceanDNA-b6579/result_gtdb.tsv
[2023-03-17 05:11:24,453] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:11:24,454] [INFO] DFAST_QC result json was written to OceanDNA-b6579/dqc_result.json
[2023-03-17 05:11:24,454] [INFO] DFAST_QC completed!
[2023-03-17 05:11:24,454] [INFO] Total running time: 0h1m20s