[2023-03-16 06:12:34,974] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:12:34,977] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:12:34,977] [INFO] DQC Reference Directory: /var/lib/cwl/stg57197809-3b93-4879-899b-8fdb653a290b/dqc_reference
[2023-03-16 06:12:36,625] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:12:36,626] [INFO] Task started: Prodigal
[2023-03-16 06:12:36,626] [INFO] Running command: cat /var/lib/cwl/stga0416ac5-1580-40a0-8c06-e3999d73f186/OceanDNA-b35151.fa | prodigal -d OceanDNA-b35151/cds.fna -a OceanDNA-b35151/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:12:45,728] [INFO] Task succeeded: Prodigal
[2023-03-16 06:12:45,728] [INFO] Task started: HMMsearch
[2023-03-16 06:12:45,728] [INFO] Running command: hmmsearch --tblout OceanDNA-b35151/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg57197809-3b93-4879-899b-8fdb653a290b/dqc_reference/reference_markers.hmm OceanDNA-b35151/protein.faa > /dev/null
[2023-03-16 06:12:45,892] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:12:45,893] [WARNING] Found 2/6 markers. [/var/lib/cwl/stga0416ac5-1580-40a0-8c06-e3999d73f186/OceanDNA-b35151.fa]
[2023-03-16 06:12:45,934] [INFO] Query marker FASTA was written to OceanDNA-b35151/markers.fasta
[2023-03-16 06:12:45,935] [INFO] Task started: Blastn
[2023-03-16 06:12:45,935] [INFO] Running command: blastn -query OceanDNA-b35151/markers.fasta -db /var/lib/cwl/stg57197809-3b93-4879-899b-8fdb653a290b/dqc_reference/reference_markers.fasta -out OceanDNA-b35151/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:12:46,401] [INFO] Task succeeded: Blastn
[2023-03-16 06:12:46,407] [INFO] Selected 12 target genomes.
[2023-03-16 06:12:46,407] [INFO] Target genome list was writen to OceanDNA-b35151/target_genomes.txt
[2023-03-16 06:12:46,414] [INFO] Task started: fastANI
[2023-03-16 06:12:46,414] [INFO] Running command: fastANI --query /var/lib/cwl/stga0416ac5-1580-40a0-8c06-e3999d73f186/OceanDNA-b35151.fa --refList OceanDNA-b35151/target_genomes.txt --output OceanDNA-b35151/fastani_result.tsv --threads 1
[2023-03-16 06:12:54,854] [INFO] Task succeeded: fastANI
[2023-03-16 06:12:54,854] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg57197809-3b93-4879-899b-8fdb653a290b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:12:54,855] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg57197809-3b93-4879-899b-8fdb653a290b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:12:54,863] [WARNING] Following organisms are indistinguishable with ANI. [Escherichia coli(562), Shigella boydii(621), Shigella dysenteriae(622), Shigella flexneri(623), Shigella sonnei(624)]
[2023-03-16 06:12:54,863] [INFO] Found 12 fastANI hits (9 hits with ANI > threshold)
[2023-03-16 06:12:54,863] [INFO] The taxonomy check result is classified as 'indistinguishable'.
[2023-03-16 06:12:54,863] [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
Shigella sonnei	strain=ATCC 29930	GCA_002950395.1	624	624	type	True	97.7989	261	287	95	indistinguishable
Shigella sonnei	strain=NCTC12984	GCA_900457155.1	624	624	type	True	97.7839	262	287	95	indistinguishable
Shigella boydii	strain=NCTC12985	GCA_900457095.1	621	621	type	True	97.7438	245	287	95	indistinguishable
Shigella boydii	strain=FDAARGOS_1139	GCA_016726285.1	621	621	type	True	97.5549	247	287	95	indistinguishable
Shigella flexneri 2a	strain=ATCC 29903	GCA_002950215.1	42897	623	type	True	97.523	254	287	95	indistinguishable
Shigella boydii	strain=DMB SH130	GCA_003572535.1	621	621	type	True	97.4381	239	287	95	indistinguishable
Shigella dysenteriae	strain=NCTC4837	GCA_900457215.1	622	622	suspected-type	True	96.8434	237	287	95	indistinguishable
Shigella dysenteriae	strain=ATCC 13313	GCA_002949675.1	622	622	suspected-type	True	96.8052	239	287	95	indistinguishable
Escherichia coli	strain=DSM 30083	GCA_024519395.1	562	562	neotype	True	96.5764	263	287	95	indistinguishable
Escherichia albertii	strain=NBRC 107761	GCA_000759775.1	208962	208962	type	True	89.6312	229	287	95	below_threshold
Escherichia albertii	strain=DSM 17582	GCA_022833075.1	208962	208962	type	True	89.5719	236	287	95	below_threshold
Salmonella enterica subsp. enterica	strain=PartC-Senterica-RM8376	GCA_022869965.1	59201	28901	suspected-type	True	82.1799	179	287	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 06:12:54,864] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35151/tc_result.tsv
[2023-03-16 06:12:54,867] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:12:54,867] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:12:54,867] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg57197809-3b93-4879-899b-8fdb653a290b/dqc_reference/checkm_data
[2023-03-16 06:12:54,868] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:12:54,874] [INFO] Task started: CheckM
[2023-03-16 06:12:54,874] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35151/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35151/checkm_input OceanDNA-b35151/checkm_result
[2023-03-16 06:13:23,574] [INFO] Task succeeded: CheckM
[2023-03-16 06:13:23,574] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.90%
Contamintation: 9.85%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:13:23,667] [INFO] ===== Completeness check finished =====
[2023-03-16 06:13:23,667] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:13:23,667] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35151/markers.fasta)
[2023-03-16 06:13:23,668] [INFO] Task started: Blastn
[2023-03-16 06:13:23,669] [INFO] Running command: blastn -query OceanDNA-b35151/markers.fasta -db /var/lib/cwl/stg57197809-3b93-4879-899b-8fdb653a290b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35151/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:13:24,183] [INFO] Task succeeded: Blastn
[2023-03-16 06:13:24,192] [INFO] Selected 8 target genomes.
[2023-03-16 06:13:24,192] [INFO] Target genome list was writen to OceanDNA-b35151/target_genomes_gtdb.txt
[2023-03-16 06:13:24,199] [INFO] Task started: fastANI
[2023-03-16 06:13:24,199] [INFO] Running command: fastANI --query /var/lib/cwl/stga0416ac5-1580-40a0-8c06-e3999d73f186/OceanDNA-b35151.fa --refList OceanDNA-b35151/target_genomes_gtdb.txt --output OceanDNA-b35151/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:13:29,763] [INFO] Task succeeded: fastANI
[2023-03-16 06:13:29,770] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 06:13:29,770] [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_003697165.2	s__Escherichia coli	96.5899	262	287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	97.07	95.57	0.85	0.72	26859	conclusive
GCF_002965065.1	s__Escherichia sp002965065	94.0923	234	287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902498915.1	s__Escherichia ruysiae	92.9099	242	287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	97.82	96.45	0.94	0.86	36	-
GCF_004211955.1	s__Escherichia sp004211955	92.711	248	287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005843885.1	s__Escherichia sp005843885	92.5474	251	287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	96.83	95.39	0.87	0.80	37	-
GCF_011881725.1	s__Escherichia coli_E	92.2514	241	287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002900365.1	s__Escherichia marmotae	91.1104	245	287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	99.02	98.77	0.90	0.85	82	-
GCF_000026225.1	s__Escherichia fergusonii	91.1093	219	287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	98.80	98.39	0.93	0.89	77	-
--------------------------------------------------------------------------------
[2023-03-16 06:13:29,773] [INFO] GTDB search result was written to OceanDNA-b35151/result_gtdb.tsv
[2023-03-16 06:13:29,776] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:13:29,780] [INFO] DFAST_QC result json was written to OceanDNA-b35151/dqc_result.json
[2023-03-16 06:13:29,780] [INFO] DFAST_QC completed!
[2023-03-16 06:13:29,780] [INFO] Total running time: 0h0m55s