[2023-03-19 04:11:06,923] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:11:06,923] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:11:06,923] [INFO] DQC Reference Directory: /var/lib/cwl/stg8414baeb-484c-4287-a0de-bce41db3608e/dqc_reference
[2023-03-19 04:11:08,543] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:11:08,544] [INFO] Task started: Prodigal
[2023-03-19 04:11:08,544] [INFO] Running command: cat /var/lib/cwl/stgc55453e2-931f-40d6-834e-ac2116f011cd/OceanDNA-b35233.fa | prodigal -d OceanDNA-b35233/cds.fna -a OceanDNA-b35233/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:11:18,732] [INFO] Task succeeded: Prodigal
[2023-03-19 04:11:18,732] [INFO] Task started: HMMsearch
[2023-03-19 04:11:18,732] [INFO] Running command: hmmsearch --tblout OceanDNA-b35233/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8414baeb-484c-4287-a0de-bce41db3608e/dqc_reference/reference_markers.hmm OceanDNA-b35233/protein.faa > /dev/null
[2023-03-19 04:11:18,901] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:11:18,901] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgc55453e2-931f-40d6-834e-ac2116f011cd/OceanDNA-b35233.fa]
[2023-03-19 04:11:18,920] [INFO] Query marker FASTA was written to OceanDNA-b35233/markers.fasta
[2023-03-19 04:11:18,920] [INFO] Task started: Blastn
[2023-03-19 04:11:18,920] [INFO] Running command: blastn -query OceanDNA-b35233/markers.fasta -db /var/lib/cwl/stg8414baeb-484c-4287-a0de-bce41db3608e/dqc_reference/reference_markers.fasta -out OceanDNA-b35233/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:11:19,377] [INFO] Task succeeded: Blastn
[2023-03-19 04:11:19,377] [INFO] Selected 9 target genomes.
[2023-03-19 04:11:19,377] [INFO] Target genome list was writen to OceanDNA-b35233/target_genomes.txt
[2023-03-19 04:11:19,382] [INFO] Task started: fastANI
[2023-03-19 04:11:19,382] [INFO] Running command: fastANI --query /var/lib/cwl/stgc55453e2-931f-40d6-834e-ac2116f011cd/OceanDNA-b35233.fa --refList OceanDNA-b35233/target_genomes.txt --output OceanDNA-b35233/fastani_result.tsv --threads 1
[2023-03-19 04:11:27,095] [INFO] Task succeeded: fastANI
[2023-03-19 04:11:27,095] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8414baeb-484c-4287-a0de-bce41db3608e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:11:27,095] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8414baeb-484c-4287-a0de-bce41db3608e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:11:27,102] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2023-03-19 04:11:27,102] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-19 04:11:27,102] [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
Shewanella marinintestina	strain=LMG 21403	GCA_023283845.1	190305	190305	type	True	98.0048	588	603	95	conclusive
Shewanella sairae	strain=JCM 11563	GCA_019655015.1	190310	190310	type	True	88.2045	516	603	95	below_threshold
Shewanella sairae	strain=LMG 21408	GCA_023283535.1	190310	190310	type	True	88.2008	521	603	95	below_threshold
Shewanella fidelis	strain=ATCC BAA-318	GCA_000518605.1	173509	173509	type	True	82.5227	461	603	95	below_threshold
Shewanella halifaxensis	strain=HAW-EB4	GCA_000019185.1	271098	271098	type	True	81.8857	409	603	95	below_threshold
Shewanella schlegeliana	strain=JCM 11561	GCA_016765635.1	190308	190308	type	True	81.7299	394	603	95	below_threshold
Shewanella schlegeliana	strain=LMG 21406	GCA_023283605.1	190308	190308	type	True	81.7031	405	603	95	below_threshold
Shewanella abyssi	strain=DSM 17171	GCA_023284025.1	311789	311789	type	True	79.6357	259	603	95	below_threshold
Shewanella gelidimarina	strain=ATCC 700752	GCA_023283945.1	56813	56813	type	True	79.4099	271	603	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:11:27,102] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35233/tc_result.tsv
[2023-03-19 04:11:27,102] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:11:27,102] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:11:27,102] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8414baeb-484c-4287-a0de-bce41db3608e/dqc_reference/checkm_data
[2023-03-19 04:11:27,103] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:11:27,107] [INFO] Task started: CheckM
[2023-03-19 04:11:27,107] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35233/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35233/checkm_input OceanDNA-b35233/checkm_result
[2023-03-19 04:11:57,627] [INFO] Task succeeded: CheckM
[2023-03-19 04:11:57,627] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 37.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:11:57,630] [INFO] ===== Completeness check finished =====
[2023-03-19 04:11:57,630] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:11:57,630] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35233/markers.fasta)
[2023-03-19 04:11:57,630] [INFO] Task started: Blastn
[2023-03-19 04:11:57,630] [INFO] Running command: blastn -query OceanDNA-b35233/markers.fasta -db /var/lib/cwl/stg8414baeb-484c-4287-a0de-bce41db3608e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35233/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:11:58,090] [INFO] Task succeeded: Blastn
[2023-03-19 04:11:58,091] [INFO] Selected 8 target genomes.
[2023-03-19 04:11:58,091] [INFO] Target genome list was writen to OceanDNA-b35233/target_genomes_gtdb.txt
[2023-03-19 04:11:58,097] [INFO] Task started: fastANI
[2023-03-19 04:11:58,097] [INFO] Running command: fastANI --query /var/lib/cwl/stgc55453e2-931f-40d6-834e-ac2116f011cd/OceanDNA-b35233.fa --refList OceanDNA-b35233/target_genomes_gtdb.txt --output OceanDNA-b35233/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:12:04,824] [INFO] Task succeeded: fastANI
[2023-03-19 04:12:04,829] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:12:04,829] [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_000518605.1	s__Shewanella fidelis	82.5227	461	603	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.11	97.11	0.90	0.90	2	-
GCF_000018285.1	s__Shewanella pealeana	82.3904	421	603	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000019185.1	s__Shewanella halifaxensis	81.8857	409	603	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016765635.1	s__Shewanella schlegeliana	81.7299	394	603	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014885.1	s__Shewanella piezotolerans	80.0071	275	603	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016757755.1	s__Shewanella sp016757755	79.8744	270	603	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836205.1	s__Shewanella sp002836205	79.3856	281	603	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.46	99.13	0.96	0.92	4	-
GCF_009663145.1	s__Shewanella sp009663145	77.8721	123	603	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:12:04,829] [INFO] GTDB search result was written to OceanDNA-b35233/result_gtdb.tsv
[2023-03-19 04:12:04,830] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:12:04,831] [INFO] DFAST_QC result json was written to OceanDNA-b35233/dqc_result.json
[2023-03-19 04:12:04,831] [INFO] DFAST_QC completed!
[2023-03-19 04:12:04,831] [INFO] Total running time: 0h0m58s