[2023-03-15 08:19:26,438] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:19:26,440] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:19:26,440] [INFO] DQC Reference Directory: /var/lib/cwl/stg0650da5b-be76-4833-a60c-2fea3382d3cf/dqc_reference
[2023-03-15 08:19:27,552] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:19:27,553] [INFO] Task started: Prodigal
[2023-03-15 08:19:27,553] [INFO] Running command: cat /var/lib/cwl/stg0d41fa2f-7a3c-48ca-8ff4-2d974b07b83d/OceanDNA-b23812.fa | prodigal -d OceanDNA-b23812/cds.fna -a OceanDNA-b23812/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:19:37,137] [INFO] Task succeeded: Prodigal
[2023-03-15 08:19:37,138] [INFO] Task started: HMMsearch
[2023-03-15 08:19:37,138] [INFO] Running command: hmmsearch --tblout OceanDNA-b23812/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0650da5b-be76-4833-a60c-2fea3382d3cf/dqc_reference/reference_markers.hmm OceanDNA-b23812/protein.faa > /dev/null
[2023-03-15 08:19:37,293] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:19:37,294] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg0d41fa2f-7a3c-48ca-8ff4-2d974b07b83d/OceanDNA-b23812.fa]
[2023-03-15 08:19:37,318] [INFO] Query marker FASTA was written to OceanDNA-b23812/markers.fasta
[2023-03-15 08:19:37,319] [INFO] Task started: Blastn
[2023-03-15 08:19:37,319] [INFO] Running command: blastn -query OceanDNA-b23812/markers.fasta -db /var/lib/cwl/stg0650da5b-be76-4833-a60c-2fea3382d3cf/dqc_reference/reference_markers.fasta -out OceanDNA-b23812/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:19:37,952] [INFO] Task succeeded: Blastn
[2023-03-15 08:19:37,959] [INFO] Selected 8 target genomes.
[2023-03-15 08:19:37,959] [INFO] Target genome list was writen to OceanDNA-b23812/target_genomes.txt
[2023-03-15 08:19:37,963] [INFO] Task started: fastANI
[2023-03-15 08:19:37,963] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d41fa2f-7a3c-48ca-8ff4-2d974b07b83d/OceanDNA-b23812.fa --refList OceanDNA-b23812/target_genomes.txt --output OceanDNA-b23812/fastani_result.tsv --threads 1
[2023-03-15 08:19:43,007] [INFO] Task succeeded: fastANI
[2023-03-15 08:19:43,007] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0650da5b-be76-4833-a60c-2fea3382d3cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:19:43,007] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0650da5b-be76-4833-a60c-2fea3382d3cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:19:43,020] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 08:19:43,020] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 08:19:43,020] [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 jannaschiana	strain=VP2	GCA_000685215.1	86	86	type	True	90.1693	414	442	95	below_threshold
Hyphomonas adhaerens	strain=MHS-3	GCA_000685235.1	81029	81029	type	True	86.1436	364	442	95	below_threshold
Hyphomonas beringensis	strain=25B14_1	GCA_000682755.1	1280946	1280946	type	True	78.5193	164	442	95	below_threshold
Hyphomonas atlantica	strain=22II1-22F38	GCA_000682715.1	1280948	1280948	type	True	77.9091	121	442	95	below_threshold
Hyphomonas chukchiensis	strain=BH-BN04-4	GCA_000682695.1	1280947	1280947	type	True	77.4952	176	442	95	below_threshold
Hyphomonas oceanitis	strain=SCH89	GCA_000685295.1	81033	81033	type	True	77.4682	155	442	95	below_threshold
Hyphomonas polymorpha	strain=PS728	GCA_000685315.1	74319	74319	type	True	77.1878	130	442	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 08:19:43,022] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23812/tc_result.tsv
[2023-03-15 08:19:43,025] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:19:43,025] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:19:43,025] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0650da5b-be76-4833-a60c-2fea3382d3cf/dqc_reference/checkm_data
[2023-03-15 08:19:43,026] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:19:43,120] [INFO] Task started: CheckM
[2023-03-15 08:19:43,121] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23812/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23812/checkm_input OceanDNA-b23812/checkm_result
[2023-03-15 08:20:12,768] [INFO] Task succeeded: CheckM
[2023-03-15 08:20:12,768] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.15%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 08:20:12,795] [INFO] ===== Completeness check finished =====
[2023-03-15 08:20:12,795] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:20:12,795] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23812/markers.fasta)
[2023-03-15 08:20:12,797] [INFO] Task started: Blastn
[2023-03-15 08:20:12,797] [INFO] Running command: blastn -query OceanDNA-b23812/markers.fasta -db /var/lib/cwl/stg0650da5b-be76-4833-a60c-2fea3382d3cf/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23812/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:20:13,958] [INFO] Task succeeded: Blastn
[2023-03-15 08:20:13,967] [INFO] Selected 5 target genomes.
[2023-03-15 08:20:13,967] [INFO] Target genome list was writen to OceanDNA-b23812/target_genomes_gtdb.txt
[2023-03-15 08:20:13,971] [INFO] Task started: fastANI
[2023-03-15 08:20:13,971] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d41fa2f-7a3c-48ca-8ff4-2d974b07b83d/OceanDNA-b23812.fa --refList OceanDNA-b23812/target_genomes_gtdb.txt --output OceanDNA-b23812/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:20:17,162] [INFO] Task succeeded: fastANI
[2023-03-15 08:20:17,166] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 08:20:17,166] [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_002700305.1	s__Hyphomonas sp002700305	99.7463	435	442	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.48	99.29	0.92	0.85	3	conclusive
GCF_000685215.1	s__Hyphomonas jannaschiana	90.1693	414	442	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685235.1	s__Hyphomonas adhaerens	86.1436	364	442	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	97.03	96.92	0.83	0.82	4	-
GCF_000682735.1	s__Hyphomonas sp000682735	85.6635	366	442	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.43	99.16	0.91	0.90	3	-
GCA_014763715.1	s__Hyphomonas sp014763715	84.0645	360	442	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 08:20:17,168] [INFO] GTDB search result was written to OceanDNA-b23812/result_gtdb.tsv
[2023-03-15 08:20:17,172] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:20:17,176] [INFO] DFAST_QC result json was written to OceanDNA-b23812/dqc_result.json
[2023-03-15 08:20:17,176] [INFO] DFAST_QC completed!
[2023-03-15 08:20:17,176] [INFO] Total running time: 0h0m51s