[2023-03-17 09:41:39,499] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:41:39,499] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:41:39,499] [INFO] DQC Reference Directory: /var/lib/cwl/stgbacb9c19-9531-4b6f-8ba3-00d0a99d1abf/dqc_reference
[2023-03-17 09:41:40,720] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:41:40,720] [INFO] Task started: Prodigal
[2023-03-17 09:41:40,721] [INFO] Running command: cat /var/lib/cwl/stg09c266c0-93a1-4380-beb4-68178c21fcae/OceanDNA-b38590.fa | prodigal -d OceanDNA-b38590/cds.fna -a OceanDNA-b38590/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:41:58,928] [INFO] Task succeeded: Prodigal
[2023-03-17 09:41:58,928] [INFO] Task started: HMMsearch
[2023-03-17 09:41:58,928] [INFO] Running command: hmmsearch --tblout OceanDNA-b38590/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbacb9c19-9531-4b6f-8ba3-00d0a99d1abf/dqc_reference/reference_markers.hmm OceanDNA-b38590/protein.faa > /dev/null
[2023-03-17 09:41:59,131] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:41:59,131] [INFO] Found 6/6 markers.
[2023-03-17 09:41:59,152] [INFO] Query marker FASTA was written to OceanDNA-b38590/markers.fasta
[2023-03-17 09:41:59,154] [INFO] Task started: Blastn
[2023-03-17 09:41:59,154] [INFO] Running command: blastn -query OceanDNA-b38590/markers.fasta -db /var/lib/cwl/stgbacb9c19-9531-4b6f-8ba3-00d0a99d1abf/dqc_reference/reference_markers.fasta -out OceanDNA-b38590/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:41:59,781] [INFO] Task succeeded: Blastn
[2023-03-17 09:41:59,782] [INFO] Selected 15 target genomes.
[2023-03-17 09:41:59,782] [INFO] Target genome list was writen to OceanDNA-b38590/target_genomes.txt
[2023-03-17 09:41:59,855] [INFO] Task started: fastANI
[2023-03-17 09:41:59,855] [INFO] Running command: fastANI --query /var/lib/cwl/stg09c266c0-93a1-4380-beb4-68178c21fcae/OceanDNA-b38590.fa --refList OceanDNA-b38590/target_genomes.txt --output OceanDNA-b38590/fastani_result.tsv --threads 1
[2023-03-17 09:42:11,026] [INFO] Task succeeded: fastANI
[2023-03-17 09:42:11,027] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbacb9c19-9531-4b6f-8ba3-00d0a99d1abf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:42:11,027] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbacb9c19-9531-4b6f-8ba3-00d0a99d1abf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:42:11,036] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2023-03-17 09:42:11,036] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 09:42:11,036] [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 venetianus	strain=RAG-1	GCA_000271425.1	52133	52133	type	True	97.4305	971	1096	95	conclusive
Acinetobacter venetianus	strain=CIP 110063	GCA_000368585.1	52133	52133	type	True	97.4197	1004	1096	95	conclusive
Acinetobacter modestus	strain=CCM 8639	GCA_014636095.1	1776740	1776740	type	True	83.5407	749	1096	95	below_threshold
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	83.3828	751	1096	95	below_threshold
Acinetobacter junii	strain=CIP 64.5	GCA_000368765.1	40215	40215	type	True	83.3744	746	1096	95	below_threshold
Acinetobacter vivianii	strain=CCM 8642	GCA_014635885.1	1776742	1776742	type	True	83.3077	758	1096	95	below_threshold
Acinetobacter proteolyticus	strain=NIPH 809	GCA_000367945.1	1776741	1776741	type	True	83.2119	779	1096	95	below_threshold
Acinetobacter gyllenbergii	strain=MTCC 11365	GCA_000414075.1	134534	134534	type	True	83.1348	777	1096	95	below_threshold
Acinetobacter gyllenbergii	strain=CIP 110306	GCA_000413855.1	134534	134534	type	True	83.0812	791	1096	95	below_threshold
Acinetobacter colistiniresistens	strain=NIPH 2036	GCA_000413935.1	280145	280145	type	True	83.0056	751	1096	95	below_threshold
Acinetobacter haemolyticus	strain=CIP 64.3	GCA_000369065.1	29430	29430	type	True	82.7357	702	1096	95	below_threshold
Acinetobacter haemolyticus	strain=NCTC10305	GCA_900444835.1	29430	29430	type	True	82.6797	711	1096	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_020911985.1	470	470	type	True	80.0218	481	1096	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	79.9738	488	1096	95	below_threshold
Acinetobacter pittii	strain=CIP70.29	GCA_024390955.1	48296	48296	type	True	79.9401	485	1096	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 09:42:11,037] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38590/tc_result.tsv
[2023-03-17 09:42:11,037] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:42:11,037] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:42:11,037] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbacb9c19-9531-4b6f-8ba3-00d0a99d1abf/dqc_reference/checkm_data
[2023-03-17 09:42:11,037] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:42:11,042] [INFO] Task started: CheckM
[2023-03-17 09:42:11,042] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38590/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38590/checkm_input OceanDNA-b38590/checkm_result
[2023-03-17 09:42:58,511] [INFO] Task succeeded: CheckM
[2023-03-17 09:42:58,511] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.35%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 09:42:58,595] [INFO] ===== Completeness check finished =====
[2023-03-17 09:42:58,595] [INFO] ===== Start GTDB Search =====
[2023-03-17 09:42:58,595] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38590/markers.fasta)
[2023-03-17 09:42:58,596] [INFO] Task started: Blastn
[2023-03-17 09:42:58,596] [INFO] Running command: blastn -query OceanDNA-b38590/markers.fasta -db /var/lib/cwl/stgbacb9c19-9531-4b6f-8ba3-00d0a99d1abf/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38590/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:42:59,612] [INFO] Task succeeded: Blastn
[2023-03-17 09:42:59,614] [INFO] Selected 17 target genomes.
[2023-03-17 09:42:59,614] [INFO] Target genome list was writen to OceanDNA-b38590/target_genomes_gtdb.txt
[2023-03-17 09:43:00,026] [INFO] Task started: fastANI
[2023-03-17 09:43:00,026] [INFO] Running command: fastANI --query /var/lib/cwl/stg09c266c0-93a1-4380-beb4-68178c21fcae/OceanDNA-b38590.fa --refList OceanDNA-b38590/target_genomes_gtdb.txt --output OceanDNA-b38590/fastani_result_gtdb.tsv --threads 1
[2023-03-17 09:43:13,277] [INFO] Task succeeded: fastANI
[2023-03-17 09:43:13,286] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 09:43:13,287] [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_000368585.1	s__Acinetobacter venetianus	97.4197	1004	1096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.49	96.30	0.89	0.81	21	conclusive
GCF_014636095.1	s__Acinetobacter modestus	83.5407	749	1096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.76	96.94	0.90	0.86	5	-
GCF_002165255.2	s__Acinetobacter sp002165255	83.4975	664	1096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.92	96.70	0.85	0.83	6	-
GCF_011753255.1	s__Acinetobacter sp011753255	83.4928	781	1096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009884975.1	s__Acinetobacter dispersus	83.4015	788	1096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.44	95.54	0.90	0.89	4	-
GCF_000400715.1	s__Acinetobacter sp000400715	83.3787	773	1096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000368765.1	s__Acinetobacter junii	83.3747	746	1096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.03	97.21	0.88	0.81	75	-
GCF_014635885.1	s__Acinetobacter vivianii	83.3163	757	1096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.48	96.89	0.92	0.86	8	-
GCF_000369525.1	s__Acinetobacter sp000369525	83.2896	786	1096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.13	96.00	0.90	0.87	7	-
GCA_003987695.1	s__Acinetobacter sp003987695	83.2467	666	1096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.01	98.01	0.75	0.75	2	-
GCF_000369005.1	s__Acinetobacter beijerinckii	83.2341	804	1096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.53	96.54	0.91	0.85	5	-
GCF_000367945.1	s__Acinetobacter proteolyticus	83.2201	778	1096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.84	97.76	0.89	0.87	5	-
GCF_013072695.1	s__Acinetobacter sp013072695	83.123	782	1096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000413855.1	s__Acinetobacter gyllenbergii	83.0812	791	1096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.05	97.97	0.95	0.91	6	-
GCF_000413935.1	s__Acinetobacter colistiniresistens	83.0141	750	1096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.98	96.69	0.90	0.86	10	-
GCF_000369065.1	s__Acinetobacter haemolyticus	82.7406	701	1096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.85	97.09	0.87	0.81	55	-
GCF_900406815.1	s__Acinetobacter haemolyticus_A	82.5998	712	1096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 09:43:13,291] [INFO] GTDB search result was written to OceanDNA-b38590/result_gtdb.tsv
[2023-03-17 09:43:13,298] [INFO] ===== GTDB Search completed =====
[2023-03-17 09:43:13,306] [INFO] DFAST_QC result json was written to OceanDNA-b38590/dqc_result.json
[2023-03-17 09:43:13,306] [INFO] DFAST_QC completed!
[2023-03-17 09:43:13,306] [INFO] Total running time: 0h1m34s