[2023-03-15 15:18:22,066] [INFO] DFAST_QC pipeline started.
[2023-03-15 15:18:22,066] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 15:18:22,066] [INFO] DQC Reference Directory: /var/lib/cwl/stg0a0ba8ae-82bb-4ff4-ad9c-2cac9a6e13c3/dqc_reference
[2023-03-15 15:18:23,184] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 15:18:23,184] [INFO] Task started: Prodigal
[2023-03-15 15:18:23,184] [INFO] Running command: cat /var/lib/cwl/stgd95924a4-3c5e-4aeb-9e10-8a08ee1ba393/OceanDNA-b38580.fa | prodigal -d OceanDNA-b38580/cds.fna -a OceanDNA-b38580/protein.faa -g 11 -q > /dev/null
[2023-03-15 15:18:31,491] [INFO] Task succeeded: Prodigal
[2023-03-15 15:18:31,491] [INFO] Task started: HMMsearch
[2023-03-15 15:18:31,491] [INFO] Running command: hmmsearch --tblout OceanDNA-b38580/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0a0ba8ae-82bb-4ff4-ad9c-2cac9a6e13c3/dqc_reference/reference_markers.hmm OceanDNA-b38580/protein.faa > /dev/null
[2023-03-15 15:18:31,707] [INFO] Task succeeded: HMMsearch
[2023-03-15 15:18:31,707] [INFO] Found 6/6 markers.
[2023-03-15 15:18:31,733] [INFO] Query marker FASTA was written to OceanDNA-b38580/markers.fasta
[2023-03-15 15:18:31,734] [INFO] Task started: Blastn
[2023-03-15 15:18:31,735] [INFO] Running command: blastn -query OceanDNA-b38580/markers.fasta -db /var/lib/cwl/stg0a0ba8ae-82bb-4ff4-ad9c-2cac9a6e13c3/dqc_reference/reference_markers.fasta -out OceanDNA-b38580/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:18:32,298] [INFO] Task succeeded: Blastn
[2023-03-15 15:18:32,301] [INFO] Selected 18 target genomes.
[2023-03-15 15:18:32,301] [INFO] Target genome list was writen to OceanDNA-b38580/target_genomes.txt
[2023-03-15 15:18:32,316] [INFO] Task started: fastANI
[2023-03-15 15:18:32,316] [INFO] Running command: fastANI --query /var/lib/cwl/stgd95924a4-3c5e-4aeb-9e10-8a08ee1ba393/OceanDNA-b38580.fa --refList OceanDNA-b38580/target_genomes.txt --output OceanDNA-b38580/fastani_result.tsv --threads 1
[2023-03-15 15:18:42,077] [INFO] Task succeeded: fastANI
[2023-03-15 15:18:42,078] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0a0ba8ae-82bb-4ff4-ad9c-2cac9a6e13c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 15:18:42,078] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0a0ba8ae-82bb-4ff4-ad9c-2cac9a6e13c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 15:18:42,088] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2023-03-15 15:18:42,089] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 15:18:42,089] [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 modestus	strain=CCM 8639	GCA_014636095.1	1776740	1776740	type	True	96.6896	337	394	95	conclusive
Acinetobacter tjernbergiae	strain=DSM 14971	GCA_000759995.1	202955	202955	type	True	87.4813	323	394	95	below_threshold
Acinetobacter tjernbergiae	strain=CIP 107465	GCA_000488175.1	202955	202955	type	True	87.4407	319	394	95	below_threshold
Acinetobacter tjernbergiae	strain=DSM 14971	GCA_000374425.1	202955	202955	type	True	87.4168	321	394	95	below_threshold
Acinetobacter parvus	strain=DSM 16617	GCA_000248155.2	134533	134533	type	True	84.6796	232	394	95	below_threshold
Acinetobacter parvus	strain=CIP 108168	GCA_000368025.1	134533	134533	type	True	84.6478	235	394	95	below_threshold
Acinetobacter colistiniresistens	strain=NIPH 2036	GCA_000413935.1	280145	280145	type	True	84.0433	276	394	95	below_threshold
Acinetobacter gyllenbergii	strain=CIP 110306	GCA_000413855.1	134534	134534	type	True	83.6078	277	394	95	below_threshold
Acinetobacter gyllenbergii	strain=MTCC 11365	GCA_000414075.1	134534	134534	type	True	83.6057	274	394	95	below_threshold
Acinetobacter proteolyticus	strain=NIPH 809	GCA_000367945.1	1776741	1776741	type	True	83.5345	283	394	95	below_threshold
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	83.3717	250	394	95	below_threshold
Acinetobacter junii	strain=CIP 64.5	GCA_000368765.1	40215	40215	type	True	83.3541	252	394	95	below_threshold
Acinetobacter vivianii	strain=CCM 8642	GCA_014635885.1	1776742	1776742	type	True	83.1465	252	394	95	below_threshold
Acinetobacter venetianus	strain=RAG-1	GCA_000271425.1	52133	52133	type	True	82.5876	268	394	95	below_threshold
Acinetobacter haemolyticus	strain=NCTC10305	GCA_900444835.1	29430	29430	type	True	81.7164	238	394	95	below_threshold
Acinetobacter pittii	strain=CIP70.29	GCA_024390955.1	48296	48296	type	True	79.6436	164	394	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	79.0483	156	394	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_020911985.1	470	470	type	True	79.0289	158	394	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 15:18:42,091] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38580/tc_result.tsv
[2023-03-15 15:18:42,094] [INFO] ===== Taxonomy check completed =====
[2023-03-15 15:18:42,094] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 15:18:42,094] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0a0ba8ae-82bb-4ff4-ad9c-2cac9a6e13c3/dqc_reference/checkm_data
[2023-03-15 15:18:42,095] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 15:18:42,158] [INFO] Task started: CheckM
[2023-03-15 15:18:42,158] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38580/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38580/checkm_input OceanDNA-b38580/checkm_result
[2023-03-15 15:19:09,071] [INFO] Task succeeded: CheckM
[2023-03-15 15:19:09,072] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.84%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 15:19:09,110] [INFO] ===== Completeness check finished =====
[2023-03-15 15:19:09,110] [INFO] ===== Start GTDB Search =====
[2023-03-15 15:19:09,110] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38580/markers.fasta)
[2023-03-15 15:19:09,112] [INFO] Task started: Blastn
[2023-03-15 15:19:09,112] [INFO] Running command: blastn -query OceanDNA-b38580/markers.fasta -db /var/lib/cwl/stg0a0ba8ae-82bb-4ff4-ad9c-2cac9a6e13c3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38580/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:19:09,912] [INFO] Task succeeded: Blastn
[2023-03-15 15:19:09,916] [INFO] Selected 16 target genomes.
[2023-03-15 15:19:09,916] [INFO] Target genome list was writen to OceanDNA-b38580/target_genomes_gtdb.txt
[2023-03-15 15:19:09,930] [INFO] Task started: fastANI
[2023-03-15 15:19:09,930] [INFO] Running command: fastANI --query /var/lib/cwl/stgd95924a4-3c5e-4aeb-9e10-8a08ee1ba393/OceanDNA-b38580.fa --refList OceanDNA-b38580/target_genomes_gtdb.txt --output OceanDNA-b38580/fastani_result_gtdb.tsv --threads 1
[2023-03-15 15:19:19,361] [INFO] Task succeeded: fastANI
[2023-03-15 15:19:19,371] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 15:19:19,371] [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_014636095.1	s__Acinetobacter modestus	96.6896	337	394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.76	96.94	0.90	0.86	5	conclusive
GCF_002165255.2	s__Acinetobacter sp002165255	93.8353	299	394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.92	96.70	0.85	0.83	6	-
GCF_000374425.1	s__Acinetobacter tjernbergiae	87.4168	321	394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.99	97.83	0.97	0.93	5	-
GCA_003987695.1	s__Acinetobacter sp003987695	86.7461	290	394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.01	98.01	0.75	0.75	2	-
GCF_000368025.1	s__Acinetobacter parvus	84.6478	235	394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.44	96.79	0.91	0.83	11	-
GCF_000413935.1	s__Acinetobacter colistiniresistens	84.0433	276	394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.98	96.69	0.90	0.86	10	-
GCF_013072695.1	s__Acinetobacter sp013072695	83.9926	285	394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011753255.1	s__Acinetobacter sp011753255	83.6984	269	394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000369005.1	s__Acinetobacter beijerinckii	83.6983	275	394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.53	96.54	0.91	0.85	5	-
GCF_000413855.1	s__Acinetobacter gyllenbergii	83.6078	277	394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.05	97.97	0.95	0.91	6	-
GCF_000367945.1	s__Acinetobacter proteolyticus	83.535	283	394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.84	97.76	0.89	0.87	5	-
GCF_000369645.1	s__Acinetobacter sp000369645	83.4438	277	394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.86	98.16	0.89	0.84	9	-
GCF_000368765.1	s__Acinetobacter junii	83.3894	251	394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.03	97.21	0.88	0.81	75	-
GCF_009884975.1	s__Acinetobacter dispersus	83.3052	275	394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.44	95.54	0.90	0.89	4	-
GCF_000369805.1	s__Acinetobacter sp000369805	83.2294	275	394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014635885.1	s__Acinetobacter vivianii	83.1465	252	394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.48	96.89	0.92	0.86	8	-
--------------------------------------------------------------------------------
[2023-03-15 15:19:19,373] [INFO] GTDB search result was written to OceanDNA-b38580/result_gtdb.tsv
[2023-03-15 15:19:19,374] [INFO] ===== GTDB Search completed =====
[2023-03-15 15:19:19,378] [INFO] DFAST_QC result json was written to OceanDNA-b38580/dqc_result.json
[2023-03-15 15:19:19,378] [INFO] DFAST_QC completed!
[2023-03-15 15:19:19,378] [INFO] Total running time: 0h0m57s