[2023-03-15 16:32:13,204] [INFO] DFAST_QC pipeline started.
[2023-03-15 16:32:13,206] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 16:32:13,207] [INFO] DQC Reference Directory: /var/lib/cwl/stgbac27661-d44c-44ec-8cc3-a575d2707b6b/dqc_reference
[2023-03-15 16:32:15,406] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 16:32:15,407] [INFO] Task started: Prodigal
[2023-03-15 16:32:15,407] [INFO] Running command: cat /var/lib/cwl/stgfdc8fdff-68b4-4bca-915e-da758c21aa60/OceanDNA-b23556.fa | prodigal -d OceanDNA-b23556/cds.fna -a OceanDNA-b23556/protein.faa -g 11 -q > /dev/null
[2023-03-15 16:32:37,259] [INFO] Task succeeded: Prodigal
[2023-03-15 16:32:37,259] [INFO] Task started: HMMsearch
[2023-03-15 16:32:37,260] [INFO] Running command: hmmsearch --tblout OceanDNA-b23556/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbac27661-d44c-44ec-8cc3-a575d2707b6b/dqc_reference/reference_markers.hmm OceanDNA-b23556/protein.faa > /dev/null
[2023-03-15 16:32:37,495] [INFO] Task succeeded: HMMsearch
[2023-03-15 16:32:37,495] [INFO] Found 6/6 markers.
[2023-03-15 16:32:37,526] [INFO] Query marker FASTA was written to OceanDNA-b23556/markers.fasta
[2023-03-15 16:32:37,527] [INFO] Task started: Blastn
[2023-03-15 16:32:37,527] [INFO] Running command: blastn -query OceanDNA-b23556/markers.fasta -db /var/lib/cwl/stgbac27661-d44c-44ec-8cc3-a575d2707b6b/dqc_reference/reference_markers.fasta -out OceanDNA-b23556/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:32:38,334] [INFO] Task succeeded: Blastn
[2023-03-15 16:32:38,338] [INFO] Selected 15 target genomes.
[2023-03-15 16:32:38,338] [INFO] Target genome list was writen to OceanDNA-b23556/target_genomes.txt
[2023-03-15 16:32:38,346] [INFO] Task started: fastANI
[2023-03-15 16:32:38,347] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdc8fdff-68b4-4bca-915e-da758c21aa60/OceanDNA-b23556.fa --refList OceanDNA-b23556/target_genomes.txt --output OceanDNA-b23556/fastani_result.tsv --threads 1
[2023-03-15 16:32:50,146] [INFO] Task succeeded: fastANI
[2023-03-15 16:32:50,146] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbac27661-d44c-44ec-8cc3-a575d2707b6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 16:32:50,147] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbac27661-d44c-44ec-8cc3-a575d2707b6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 16:32:50,156] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 16:32:50,156] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 16:32:50,156] [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
Hyphomonas chukchiensis	strain=BH-BN04-4	GCA_000682695.1	1280947	1280947	type	True	90.5903	979	1146	95	below_threshold
Hyphomonas oceanitis	strain=SCH89	GCA_000685295.1	81033	81033	type	True	89.8801	959	1146	95	below_threshold
Hyphomonas johnsonii	strain=MHS-2	GCA_000685275.1	81031	81031	type	True	81.5838	703	1146	95	below_threshold
Hyphomonas jannaschiana	strain=VP2	GCA_000685215.1	86	86	type	True	78.9506	455	1146	95	below_threshold
Hyphomonas adhaerens	strain=MHS-3	GCA_000685235.1	81029	81029	type	True	78.8204	442	1146	95	below_threshold
Hyphomonas beringensis	strain=25B14_1	GCA_000682755.1	1280946	1280946	type	True	78.4073	410	1146	95	below_threshold
Hyphomonas pacifica	strain=T16B2	GCA_000682675.1	1280941	1280941	type	True	78.3289	389	1146	95	below_threshold
Hyphomonas polymorpha	strain=PS728	GCA_000685315.1	74319	74319	type	True	78.1929	393	1146	95	below_threshold
Hyphomonas atlantica	strain=22II1-22F38	GCA_000682715.1	1280948	1280948	type	True	78.145	356	1146	95	below_threshold
Hyphomonas sediminis	strain=WL0036	GCA_019679475.1	2866160	2866160	type	True	78.0998	374	1146	95	below_threshold
Henriciella mobilis	strain=M65	GCA_003576315.1	2305467	2305467	type	True	77.5703	272	1146	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	75.8003	68	1146	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	75.7706	66	1146	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	75.7706	66	1146	95	below_threshold
Methylobacterium hispanicum	strain=DSM 16372	GCA_022179285.1	270350	270350	type	True	75.603	79	1146	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 16:32:50,159] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23556/tc_result.tsv
[2023-03-15 16:32:50,161] [INFO] ===== Taxonomy check completed =====
[2023-03-15 16:32:50,162] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 16:32:50,162] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbac27661-d44c-44ec-8cc3-a575d2707b6b/dqc_reference/checkm_data
[2023-03-15 16:32:50,162] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 16:32:50,178] [INFO] Task started: CheckM
[2023-03-15 16:32:50,178] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23556/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23556/checkm_input OceanDNA-b23556/checkm_result
[2023-03-15 16:33:45,198] [INFO] Task succeeded: CheckM
[2023-03-15 16:33:45,199] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 16:33:45,258] [INFO] ===== Completeness check finished =====
[2023-03-15 16:33:45,258] [INFO] ===== Start GTDB Search =====
[2023-03-15 16:33:45,258] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23556/markers.fasta)
[2023-03-15 16:33:45,259] [INFO] Task started: Blastn
[2023-03-15 16:33:45,259] [INFO] Running command: blastn -query OceanDNA-b23556/markers.fasta -db /var/lib/cwl/stgbac27661-d44c-44ec-8cc3-a575d2707b6b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23556/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:33:46,786] [INFO] Task succeeded: Blastn
[2023-03-15 16:33:46,790] [INFO] Selected 7 target genomes.
[2023-03-15 16:33:46,790] [INFO] Target genome list was writen to OceanDNA-b23556/target_genomes_gtdb.txt
[2023-03-15 16:33:46,798] [INFO] Task started: fastANI
[2023-03-15 16:33:46,798] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdc8fdff-68b4-4bca-915e-da758c21aa60/OceanDNA-b23556.fa --refList OceanDNA-b23556/target_genomes_gtdb.txt --output OceanDNA-b23556/fastani_result_gtdb.tsv --threads 1
[2023-03-15 16:33:53,021] [INFO] Task succeeded: fastANI
[2023-03-15 16:33:53,026] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 16:33:53,026] [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_000682695.1	s__Hyphomonas chukchiensis	90.5903	979	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685295.1	s__Hyphomonas oceanitis	89.8754	960	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018827375.1	s__Hyphomonas sp018827375	88.3849	971	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.92	99.88	0.98	0.97	4	-
GCA_000961795.1	s__Hyphomonas sp000961795	82.6997	694	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018830285.1	s__Hyphomonas sp018830285	82.4129	746	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685275.1	s__Hyphomonas johnsonii	81.5934	702	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018819265.1	s__Filomicrobium sp018819265	75.8265	53	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Filomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 16:33:53,028] [INFO] GTDB search result was written to OceanDNA-b23556/result_gtdb.tsv
[2023-03-15 16:33:53,031] [INFO] ===== GTDB Search completed =====
[2023-03-15 16:33:53,035] [INFO] DFAST_QC result json was written to OceanDNA-b23556/dqc_result.json
[2023-03-15 16:33:53,035] [INFO] DFAST_QC completed!
[2023-03-15 16:33:53,035] [INFO] Total running time: 0h1m40s