[2023-03-16 05:52:41,067] [INFO] DFAST_QC pipeline started.
[2023-03-16 05:52:41,067] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 05:52:41,068] [INFO] DQC Reference Directory: /var/lib/cwl/stga64239b7-96b4-4663-b65d-ff1c4d39918c/dqc_reference
[2023-03-16 05:52:42,234] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 05:52:42,234] [INFO] Task started: Prodigal
[2023-03-16 05:52:42,234] [INFO] Running command: cat /var/lib/cwl/stgbd5bfebd-587d-492b-9776-a4c97eb224c9/OceanDNA-b23559.fa | prodigal -d OceanDNA-b23559/cds.fna -a OceanDNA-b23559/protein.faa -g 11 -q > /dev/null
[2023-03-16 05:52:49,046] [INFO] Task succeeded: Prodigal
[2023-03-16 05:52:49,046] [INFO] Task started: HMMsearch
[2023-03-16 05:52:49,046] [INFO] Running command: hmmsearch --tblout OceanDNA-b23559/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga64239b7-96b4-4663-b65d-ff1c4d39918c/dqc_reference/reference_markers.hmm OceanDNA-b23559/protein.faa > /dev/null
[2023-03-16 05:52:49,189] [INFO] Task succeeded: HMMsearch
[2023-03-16 05:52:49,190] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgbd5bfebd-587d-492b-9776-a4c97eb224c9/OceanDNA-b23559.fa]
[2023-03-16 05:52:49,207] [INFO] Query marker FASTA was written to OceanDNA-b23559/markers.fasta
[2023-03-16 05:52:49,207] [INFO] Task started: Blastn
[2023-03-16 05:52:49,207] [INFO] Running command: blastn -query OceanDNA-b23559/markers.fasta -db /var/lib/cwl/stga64239b7-96b4-4663-b65d-ff1c4d39918c/dqc_reference/reference_markers.fasta -out OceanDNA-b23559/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:52:49,699] [INFO] Task succeeded: Blastn
[2023-03-16 05:52:49,701] [INFO] Selected 10 target genomes.
[2023-03-16 05:52:49,701] [INFO] Target genome list was writen to OceanDNA-b23559/target_genomes.txt
[2023-03-16 05:52:49,711] [INFO] Task started: fastANI
[2023-03-16 05:52:49,711] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd5bfebd-587d-492b-9776-a4c97eb224c9/OceanDNA-b23559.fa --refList OceanDNA-b23559/target_genomes.txt --output OceanDNA-b23559/fastani_result.tsv --threads 1
[2023-03-16 05:52:56,809] [INFO] Task succeeded: fastANI
[2023-03-16 05:52:56,810] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga64239b7-96b4-4663-b65d-ff1c4d39918c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 05:52:56,810] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga64239b7-96b4-4663-b65d-ff1c4d39918c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 05:52:56,815] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 05:52:56,815] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 05:52:56,815] [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 oceanitis	strain=SCH89	GCA_000685295.1	81033	81033	type	True	91.7056	147	161	95	below_threshold
Hyphomonas chukchiensis	strain=BH-BN04-4	GCA_000682695.1	1280947	1280947	type	True	90.3344	147	161	95	below_threshold
Hyphomonas johnsonii	strain=MHS-2	GCA_000685275.1	81031	81031	type	True	80.4663	84	161	95	below_threshold
Hyphomonas adhaerens	strain=MHS-3	GCA_000685235.1	81029	81029	type	True	78.1064	51	161	95	below_threshold
Hyphomonas jannaschiana	strain=VP2	GCA_000685215.1	86	86	type	True	78.0664	58	161	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 05:52:56,816] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23559/tc_result.tsv
[2023-03-16 05:52:56,816] [INFO] ===== Taxonomy check completed =====
[2023-03-16 05:52:56,816] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 05:52:56,816] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga64239b7-96b4-4663-b65d-ff1c4d39918c/dqc_reference/checkm_data
[2023-03-16 05:52:56,817] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 05:52:56,821] [INFO] Task started: CheckM
[2023-03-16 05:52:56,821] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23559/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23559/checkm_input OceanDNA-b23559/checkm_result
[2023-03-16 05:53:19,790] [INFO] Task succeeded: CheckM
[2023-03-16 05:53:19,790] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.31%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 05:53:19,797] [INFO] ===== Completeness check finished =====
[2023-03-16 05:53:19,798] [INFO] ===== Start GTDB Search =====
[2023-03-16 05:53:19,798] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23559/markers.fasta)
[2023-03-16 05:53:19,799] [INFO] Task started: Blastn
[2023-03-16 05:53:19,799] [INFO] Running command: blastn -query OceanDNA-b23559/markers.fasta -db /var/lib/cwl/stga64239b7-96b4-4663-b65d-ff1c4d39918c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23559/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:53:20,348] [INFO] Task succeeded: Blastn
[2023-03-16 05:53:20,349] [INFO] Selected 7 target genomes.
[2023-03-16 05:53:20,350] [INFO] Target genome list was writen to OceanDNA-b23559/target_genomes_gtdb.txt
[2023-03-16 05:53:20,359] [INFO] Task started: fastANI
[2023-03-16 05:53:20,359] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd5bfebd-587d-492b-9776-a4c97eb224c9/OceanDNA-b23559.fa --refList OceanDNA-b23559/target_genomes_gtdb.txt --output OceanDNA-b23559/fastani_result_gtdb.tsv --threads 1
[2023-03-16 05:53:24,330] [INFO] Task succeeded: fastANI
[2023-03-16 05:53:24,334] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 05:53:24,335] [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_000685295.1	s__Hyphomonas oceanitis	91.7056	147	161	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	90.3344	147	161	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	85.6694	133	161	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	82.0876	99	161	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	80.8088	102	161	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	80.4663	84	161	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 05:53:24,335] [INFO] GTDB search result was written to OceanDNA-b23559/result_gtdb.tsv
[2023-03-16 05:53:24,336] [INFO] ===== GTDB Search completed =====
[2023-03-16 05:53:24,338] [INFO] DFAST_QC result json was written to OceanDNA-b23559/dqc_result.json
[2023-03-16 05:53:24,338] [INFO] DFAST_QC completed!
[2023-03-16 05:53:24,338] [INFO] Total running time: 0h0m43s