[2023-03-19 00:01:03,333] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:01:03,334] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:01:03,334] [INFO] DQC Reference Directory: /var/lib/cwl/stgb33633dc-bd3a-40a5-81b2-777756d90cc7/dqc_reference
[2023-03-19 00:01:04,696] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:01:04,696] [INFO] Task started: Prodigal
[2023-03-19 00:01:04,697] [INFO] Running command: cat /var/lib/cwl/stgd1c62b27-3031-407c-a1bf-07bef4a0bac7/OceanDNA-b23725.fa | prodigal -d OceanDNA-b23725/cds.fna -a OceanDNA-b23725/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:01:27,403] [INFO] Task succeeded: Prodigal
[2023-03-19 00:01:27,404] [INFO] Task started: HMMsearch
[2023-03-19 00:01:27,404] [INFO] Running command: hmmsearch --tblout OceanDNA-b23725/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb33633dc-bd3a-40a5-81b2-777756d90cc7/dqc_reference/reference_markers.hmm OceanDNA-b23725/protein.faa > /dev/null
[2023-03-19 00:01:27,706] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:01:27,707] [INFO] Found 6/6 markers.
[2023-03-19 00:01:27,729] [INFO] Query marker FASTA was written to OceanDNA-b23725/markers.fasta
[2023-03-19 00:01:27,729] [INFO] Task started: Blastn
[2023-03-19 00:01:27,729] [INFO] Running command: blastn -query OceanDNA-b23725/markers.fasta -db /var/lib/cwl/stgb33633dc-bd3a-40a5-81b2-777756d90cc7/dqc_reference/reference_markers.fasta -out OceanDNA-b23725/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:01:28,479] [INFO] Task succeeded: Blastn
[2023-03-19 00:01:28,480] [INFO] Selected 14 target genomes.
[2023-03-19 00:01:28,480] [INFO] Target genome list was writen to OceanDNA-b23725/target_genomes.txt
[2023-03-19 00:01:28,488] [INFO] Task started: fastANI
[2023-03-19 00:01:28,488] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1c62b27-3031-407c-a1bf-07bef4a0bac7/OceanDNA-b23725.fa --refList OceanDNA-b23725/target_genomes.txt --output OceanDNA-b23725/fastani_result.tsv --threads 1
[2023-03-19 00:01:39,127] [INFO] Task succeeded: fastANI
[2023-03-19 00:01:39,128] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb33633dc-bd3a-40a5-81b2-777756d90cc7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:01:39,128] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb33633dc-bd3a-40a5-81b2-777756d90cc7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:01:39,137] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:01:39,137] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 00:01:39,137] [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 atlantica	strain=22II1-22F38	GCA_000682715.1	1280948	1280948	type	True	81.7167	703	1182	95	below_threshold
Hyphomonas pacifica	strain=T16B2	GCA_000682675.1	1280941	1280941	type	True	80.1982	546	1182	95	below_threshold
Hyphomonas beringensis	strain=25B14_1	GCA_000682755.1	1280946	1280946	type	True	79.7738	565	1182	95	below_threshold
Hyphomonas chukchiensis	strain=BH-BN04-4	GCA_000682695.1	1280947	1280947	type	True	79.7675	423	1182	95	below_threshold
Hyphomonas oceanitis	strain=SCH89	GCA_000685295.1	81033	81033	type	True	78.8767	388	1182	95	below_threshold
Hyphomonas jannaschiana	strain=VP2	GCA_000685215.1	86	86	type	True	78.682	411	1182	95	below_threshold
Henriciella aquimarina	strain=LMG 24711	GCA_002088975.1	545261	545261	type	True	78.5878	225	1182	95	below_threshold
Hyphomonas adhaerens	strain=MHS-3	GCA_000685235.1	81029	81029	type	True	78.4229	410	1182	95	below_threshold
Hyphomonas johnsonii	strain=MHS-2	GCA_000685275.1	81031	81031	type	True	78.0036	368	1182	95	below_threshold
Hyphomonas sediminis	strain=WL0036	GCA_019679475.1	2866160	2866160	type	True	77.4927	259	1182	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	75.6604	73	1182	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:01:39,137] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23725/tc_result.tsv
[2023-03-19 00:01:39,137] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:01:39,137] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:01:39,138] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb33633dc-bd3a-40a5-81b2-777756d90cc7/dqc_reference/checkm_data
[2023-03-19 00:01:39,138] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:01:39,144] [INFO] Task started: CheckM
[2023-03-19 00:01:39,144] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23725/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23725/checkm_input OceanDNA-b23725/checkm_result
[2023-03-19 00:02:35,376] [INFO] Task succeeded: CheckM
[2023-03-19 00:02:35,376] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:02:35,379] [INFO] ===== Completeness check finished =====
[2023-03-19 00:02:35,379] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:02:35,379] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23725/markers.fasta)
[2023-03-19 00:02:35,379] [INFO] Task started: Blastn
[2023-03-19 00:02:35,379] [INFO] Running command: blastn -query OceanDNA-b23725/markers.fasta -db /var/lib/cwl/stgb33633dc-bd3a-40a5-81b2-777756d90cc7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23725/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:02:36,766] [INFO] Task succeeded: Blastn
[2023-03-19 00:02:36,767] [INFO] Selected 12 target genomes.
[2023-03-19 00:02:36,767] [INFO] Target genome list was writen to OceanDNA-b23725/target_genomes_gtdb.txt
[2023-03-19 00:02:36,831] [INFO] Task started: fastANI
[2023-03-19 00:02:36,832] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1c62b27-3031-407c-a1bf-07bef4a0bac7/OceanDNA-b23725.fa --refList OceanDNA-b23725/target_genomes_gtdb.txt --output OceanDNA-b23725/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:02:45,472] [INFO] Task succeeded: fastANI
[2023-03-19 00:02:45,479] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 00:02:45,479] [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_000682775.1	s__Hyphomonas sp000682775	95.6421	993	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	95.72	95.47	0.88	0.83	38	conclusive
GCA_002414505.1	s__Hyphomonas sp002414505	84.9444	732	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.04	98.84	0.81	0.74	4	-
GCA_017792385.1	s__Hyphomonas sp017792385	81.7584	759	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000682715.1	s__Hyphomonas atlantica	81.7167	703	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	98.47	98.11	0.91	0.87	6	-
GCA_018222605.1	s__Hyphomonas sp002695785	80.5877	596	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.58	99.58	0.85	0.85	2	-
GCF_000682755.1	s__Hyphomonas beringensis	79.7833	564	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000682735.1	s__Hyphomonas sp000682735	79.2923	423	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.43	99.16	0.91	0.90	3	-
GCA_000961695.1	s__Hyphomonas sp000961695	79.113	401	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685215.1	s__Hyphomonas jannaschiana	78.6924	410	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002088975.1	s__Henriciella aquimarina	78.6235	223	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:02:45,479] [INFO] GTDB search result was written to OceanDNA-b23725/result_gtdb.tsv
[2023-03-19 00:02:45,479] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:02:45,481] [INFO] DFAST_QC result json was written to OceanDNA-b23725/dqc_result.json
[2023-03-19 00:02:45,481] [INFO] DFAST_QC completed!
[2023-03-19 00:02:45,481] [INFO] Total running time: 0h1m42s