[2023-03-18 08:17:20,602] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:17:20,602] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:17:20,602] [INFO] DQC Reference Directory: /var/lib/cwl/stg4201668d-6f6b-45b9-b39c-9c6f897c84cf/dqc_reference
[2023-03-18 08:17:21,822] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:17:21,822] [INFO] Task started: Prodigal
[2023-03-18 08:17:21,822] [INFO] Running command: cat /var/lib/cwl/stg1e819a89-b5a1-495c-89c7-9588bb8c2404/OceanDNA-b23561.fa | prodigal -d OceanDNA-b23561/cds.fna -a OceanDNA-b23561/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:17:42,137] [INFO] Task succeeded: Prodigal
[2023-03-18 08:17:42,138] [INFO] Task started: HMMsearch
[2023-03-18 08:17:42,138] [INFO] Running command: hmmsearch --tblout OceanDNA-b23561/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4201668d-6f6b-45b9-b39c-9c6f897c84cf/dqc_reference/reference_markers.hmm OceanDNA-b23561/protein.faa > /dev/null
[2023-03-18 08:17:42,448] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:17:42,448] [INFO] Found 6/6 markers.
[2023-03-18 08:17:42,470] [INFO] Query marker FASTA was written to OceanDNA-b23561/markers.fasta
[2023-03-18 08:17:42,470] [INFO] Task started: Blastn
[2023-03-18 08:17:42,470] [INFO] Running command: blastn -query OceanDNA-b23561/markers.fasta -db /var/lib/cwl/stg4201668d-6f6b-45b9-b39c-9c6f897c84cf/dqc_reference/reference_markers.fasta -out OceanDNA-b23561/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:17:43,253] [INFO] Task succeeded: Blastn
[2023-03-18 08:17:43,254] [INFO] Selected 16 target genomes.
[2023-03-18 08:17:43,254] [INFO] Target genome list was writen to OceanDNA-b23561/target_genomes.txt
[2023-03-18 08:17:43,262] [INFO] Task started: fastANI
[2023-03-18 08:17:43,262] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e819a89-b5a1-495c-89c7-9588bb8c2404/OceanDNA-b23561.fa --refList OceanDNA-b23561/target_genomes.txt --output OceanDNA-b23561/fastani_result.tsv --threads 1
[2023-03-18 08:17:56,308] [INFO] Task succeeded: fastANI
[2023-03-18 08:17:56,308] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4201668d-6f6b-45b9-b39c-9c6f897c84cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:17:56,308] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4201668d-6f6b-45b9-b39c-9c6f897c84cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:17:56,317] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:17:56,318] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 08:17:56,318] [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	82.2145	717	1061	95	below_threshold
Hyphomonas oceanitis	strain=SCH89	GCA_000685295.1	81033	81033	type	True	82.1388	716	1061	95	below_threshold
Hyphomonas johnsonii	strain=MHS-2	GCA_000685275.1	81031	81031	type	True	81.5829	661	1061	95	below_threshold
Hyphomonas jannaschiana	strain=VP2	GCA_000685215.1	86	86	type	True	78.4841	403	1061	95	below_threshold
Hyphomonas adhaerens	strain=MHS-3	GCA_000685235.1	81029	81029	type	True	78.4304	400	1061	95	below_threshold
Hyphomonas sediminis	strain=WL0036	GCA_019679475.1	2866160	2866160	type	True	78.1554	316	1061	95	below_threshold
Hyphomonas beringensis	strain=25B14_1	GCA_000682755.1	1280946	1280946	type	True	78.0657	350	1061	95	below_threshold
Hyphomonas pacifica	strain=T16B2	GCA_000682675.1	1280941	1280941	type	True	77.9328	350	1061	95	below_threshold
Hyphomonas polymorpha	strain=PS728	GCA_000685315.1	74319	74319	type	True	77.8489	353	1061	95	below_threshold
Hyphomonas atlantica	strain=22II1-22F38	GCA_000682715.1	1280948	1280948	type	True	77.8018	319	1061	95	below_threshold
Henriciella mobilis	strain=M65	GCA_003576315.1	2305467	2305467	type	True	77.267	268	1061	95	below_threshold
Henriciella aquimarina	strain=LMG 24711	GCA_002088975.1	545261	545261	type	True	77.2489	259	1061	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	76.411	96	1061	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	76.3031	72	1061	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	76.0763	75	1061	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	75.8588	60	1061	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 08:17:56,318] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23561/tc_result.tsv
[2023-03-18 08:17:56,318] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:17:56,318] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:17:56,318] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4201668d-6f6b-45b9-b39c-9c6f897c84cf/dqc_reference/checkm_data
[2023-03-18 08:17:56,319] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:17:56,323] [INFO] Task started: CheckM
[2023-03-18 08:17:56,323] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23561/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23561/checkm_input OceanDNA-b23561/checkm_result
[2023-03-18 08:18:48,030] [INFO] Task succeeded: CheckM
[2023-03-18 08:18:48,030] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 08:18:48,033] [INFO] ===== Completeness check finished =====
[2023-03-18 08:18:48,033] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:18:48,033] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23561/markers.fasta)
[2023-03-18 08:18:48,033] [INFO] Task started: Blastn
[2023-03-18 08:18:48,033] [INFO] Running command: blastn -query OceanDNA-b23561/markers.fasta -db /var/lib/cwl/stg4201668d-6f6b-45b9-b39c-9c6f897c84cf/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23561/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:18:49,419] [INFO] Task succeeded: Blastn
[2023-03-18 08:18:49,419] [INFO] Selected 7 target genomes.
[2023-03-18 08:18:49,419] [INFO] Target genome list was writen to OceanDNA-b23561/target_genomes_gtdb.txt
[2023-03-18 08:18:49,482] [INFO] Task started: fastANI
[2023-03-18 08:18:49,482] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e819a89-b5a1-495c-89c7-9588bb8c2404/OceanDNA-b23561.fa --refList OceanDNA-b23561/target_genomes_gtdb.txt --output OceanDNA-b23561/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:18:55,019] [INFO] Task succeeded: fastANI
[2023-03-18 08:18:55,024] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:18:55,024] [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_000961795.1	s__Hyphomonas sp000961795	90.0114	855	1061	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	83.0069	746	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000682695.1	s__Hyphomonas chukchiensis	82.2222	717	1061	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	82.1275	717	1061	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	81.8749	681	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.92	99.88	0.98	0.97	4	-
GCF_000685275.1	s__Hyphomonas johnsonii	81.5834	660	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:18:55,024] [INFO] GTDB search result was written to OceanDNA-b23561/result_gtdb.tsv
[2023-03-18 08:18:55,024] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:18:55,026] [INFO] DFAST_QC result json was written to OceanDNA-b23561/dqc_result.json
[2023-03-18 08:18:55,026] [INFO] DFAST_QC completed!
[2023-03-18 08:18:55,026] [INFO] Total running time: 0h1m34s