[2023-03-16 08:20:04,390] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:20:04,390] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:20:04,390] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf6ed9a7-efa1-41bb-8237-a8f846cc6150/dqc_reference
[2023-03-16 08:20:05,528] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:20:05,529] [INFO] Task started: Prodigal
[2023-03-16 08:20:05,529] [INFO] Running command: cat /var/lib/cwl/stgf55947e1-422f-4a4b-8593-cc6ce65abf44/OceanDNA-b38548.fa | prodigal -d OceanDNA-b38548/cds.fna -a OceanDNA-b38548/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:20:22,987] [INFO] Task succeeded: Prodigal
[2023-03-16 08:20:22,988] [INFO] Task started: HMMsearch
[2023-03-16 08:20:22,988] [INFO] Running command: hmmsearch --tblout OceanDNA-b38548/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf6ed9a7-efa1-41bb-8237-a8f846cc6150/dqc_reference/reference_markers.hmm OceanDNA-b38548/protein.faa > /dev/null
[2023-03-16 08:20:23,189] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:20:23,189] [INFO] Found 6/6 markers.
[2023-03-16 08:20:23,213] [INFO] Query marker FASTA was written to OceanDNA-b38548/markers.fasta
[2023-03-16 08:20:23,214] [INFO] Task started: Blastn
[2023-03-16 08:20:23,214] [INFO] Running command: blastn -query OceanDNA-b38548/markers.fasta -db /var/lib/cwl/stgdf6ed9a7-efa1-41bb-8237-a8f846cc6150/dqc_reference/reference_markers.fasta -out OceanDNA-b38548/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:20:23,836] [INFO] Task succeeded: Blastn
[2023-03-16 08:20:23,839] [INFO] Selected 16 target genomes.
[2023-03-16 08:20:23,840] [INFO] Target genome list was writen to OceanDNA-b38548/target_genomes.txt
[2023-03-16 08:20:23,850] [INFO] Task started: fastANI
[2023-03-16 08:20:23,850] [INFO] Running command: fastANI --query /var/lib/cwl/stgf55947e1-422f-4a4b-8593-cc6ce65abf44/OceanDNA-b38548.fa --refList OceanDNA-b38548/target_genomes.txt --output OceanDNA-b38548/fastani_result.tsv --threads 1
[2023-03-16 08:20:34,763] [INFO] Task succeeded: fastANI
[2023-03-16 08:20:34,764] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf6ed9a7-efa1-41bb-8237-a8f846cc6150/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:20:34,764] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf6ed9a7-efa1-41bb-8237-a8f846cc6150/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:20:34,774] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2023-03-16 08:20:34,774] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 08:20:34,774] [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
Acinetobacter baylyi	strain=CIP 107474	GCA_000368685.1	202950	202950	type	True	99.9572	1023	1025	95	conclusive
Acinetobacter baylyi	strain=DSM 14961	GCA_000621045.1	202950	202950	type	True	99.9524	1019	1025	95	conclusive
Acinetobacter soli	strain=KCTC 22184	GCA_000760595.1	487316	487316	type	True	83.0465	612	1025	95	below_threshold
Acinetobacter ursingii	strain=CIP 107286	GCA_000368825.1	108980	108980	type	True	80.6049	466	1025	95	below_threshold
Acinetobacter ursingii	strain=FDAARGOS_1095	GCA_016726205.1	108980	108980	type	True	80.5496	493	1025	95	below_threshold
Acinetobacter septicus	strain=FDAARGOS_1401	GCA_019355975.1	465797	465797	type	True	80.468	490	1025	95	below_threshold
Acinetobacter ihumii	strain=Marseille-P8049	GCA_900625095.1	2483802	2483802	type	True	80.3554	499	1025	95	below_threshold
Acinetobacter guerrae	strain=AC 1271	GCA_009372255.1	1843371	1843371	type	True	80.2813	486	1025	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_020911985.1	470	470	type	True	79.3894	387	1025	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	79.3744	381	1025	95	below_threshold
Acinetobacter gerneri	strain=KCTC 12415	GCA_000747725.1	202952	202952	type	True	79.334	281	1025	95	below_threshold
Acinetobacter gerneri	strain=MTCC 9824	GCA_000430245.1	202952	202952	type	True	79.3125	281	1025	95	below_threshold
Acinetobacter stercoris	strain=KPC-SM-21	GCA_900323515.1	2126983	2126983	type	True	78.9824	280	1025	95	below_threshold
Acinetobacter johnsonii	strain=NCTC10308	GCA_900444855.1	40214	40214	suspected-type	True	78.9537	305	1025	95	below_threshold
Acinetobacter haemolyticus	strain=NCTC10305	GCA_900444835.1	29430	29430	type	True	78.9411	320	1025	95	below_threshold
Acinetobacter sichuanensis	strain=WCHAc060041	GCA_003024515.2	2136183	2136183	type	True	78.7914	323	1025	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 08:20:34,775] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38548/tc_result.tsv
[2023-03-16 08:20:34,776] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:20:34,776] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:20:34,776] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf6ed9a7-efa1-41bb-8237-a8f846cc6150/dqc_reference/checkm_data
[2023-03-16 08:20:34,777] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:20:34,783] [INFO] Task started: CheckM
[2023-03-16 08:20:34,784] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38548/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38548/checkm_input OceanDNA-b38548/checkm_result
[2023-03-16 08:21:20,727] [INFO] Task succeeded: CheckM
[2023-03-16 08:21:20,727] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 08:21:20,757] [INFO] ===== Completeness check finished =====
[2023-03-16 08:21:20,757] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:21:20,757] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38548/markers.fasta)
[2023-03-16 08:21:20,758] [INFO] Task started: Blastn
[2023-03-16 08:21:20,759] [INFO] Running command: blastn -query OceanDNA-b38548/markers.fasta -db /var/lib/cwl/stgdf6ed9a7-efa1-41bb-8237-a8f846cc6150/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38548/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:21:21,777] [INFO] Task succeeded: Blastn
[2023-03-16 08:21:21,783] [INFO] Selected 13 target genomes.
[2023-03-16 08:21:21,783] [INFO] Target genome list was writen to OceanDNA-b38548/target_genomes_gtdb.txt
[2023-03-16 08:21:21,795] [INFO] Task started: fastANI
[2023-03-16 08:21:21,795] [INFO] Running command: fastANI --query /var/lib/cwl/stgf55947e1-422f-4a4b-8593-cc6ce65abf44/OceanDNA-b38548.fa --refList OceanDNA-b38548/target_genomes_gtdb.txt --output OceanDNA-b38548/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:21:31,059] [INFO] Task succeeded: fastANI
[2023-03-16 08:21:31,067] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 08:21:31,067] [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_000368685.1	s__Acinetobacter baylyi	99.9572	1023	1025	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.85	98.65	0.98	0.93	13	conclusive
GCF_000760595.1	s__Acinetobacter soli	83.0465	612	1025	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.45	98.17	0.92	0.88	38	-
GCF_000368825.1	s__Acinetobacter ursingii	80.6104	466	1025	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.69	96.95	0.88	0.80	69	-
GCF_900625095.1	s__Acinetobacter sp900625095	80.3788	497	1025	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016624945.1	s__Acinetobacter sp016624945	80.3732	485	1025	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.57	99.14	0.97	0.94	3	-
GCF_009372255.1	s__Acinetobacter guerrae	80.2811	486	1025	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.44	98.41	0.90	0.89	3	-
GCF_000369005.1	s__Acinetobacter beijerinckii	79.4784	315	1025	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.53	96.54	0.91	0.85	5	-
GCF_000368565.1	s__Acinetobacter gerneri	79.2898	289	1025	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.97	99.97	1.00	0.99	3	-
GCF_000369505.1	s__Acinetobacter sp000369505	79.0459	326	1025	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.55	96.55	0.85	0.85	2	-
GCF_900323515.1	s__Acinetobacter stercoris	78.9666	281	1025	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.59	98.59	0.92	0.92	2	-
GCF_003024515.2	s__Acinetobacter sichuanensis	78.7789	324	1025	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002135375.1	s__Acinetobacter sp002135375	78.6922	232	1025	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000368145.1	s__Acinetobacter guillouiae	78.4788	332	1025	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.78	96.36	0.91	0.85	14	-
--------------------------------------------------------------------------------
[2023-03-16 08:21:31,069] [INFO] GTDB search result was written to OceanDNA-b38548/result_gtdb.tsv
[2023-03-16 08:21:31,073] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:21:31,077] [INFO] DFAST_QC result json was written to OceanDNA-b38548/dqc_result.json
[2023-03-16 08:21:31,077] [INFO] DFAST_QC completed!
[2023-03-16 08:21:31,077] [INFO] Total running time: 0h1m27s