[2023-03-18 00:53:42,866] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:53:42,866] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:53:42,866] [INFO] DQC Reference Directory: /var/lib/cwl/stgfcd7cfc2-1856-45ab-87fa-7931dace3435/dqc_reference
[2023-03-18 00:53:44,411] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:53:44,411] [INFO] Task started: Prodigal
[2023-03-18 00:53:44,411] [INFO] Running command: cat /var/lib/cwl/stg462f8829-fd1b-4874-9224-5d0102987a2b/OceanDNA-b38586.fa | prodigal -d OceanDNA-b38586/cds.fna -a OceanDNA-b38586/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:53:57,204] [INFO] Task succeeded: Prodigal
[2023-03-18 00:53:57,205] [INFO] Task started: HMMsearch
[2023-03-18 00:53:57,205] [INFO] Running command: hmmsearch --tblout OceanDNA-b38586/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfcd7cfc2-1856-45ab-87fa-7931dace3435/dqc_reference/reference_markers.hmm OceanDNA-b38586/protein.faa > /dev/null
[2023-03-18 00:53:57,383] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:53:57,384] [INFO] Found 6/6 markers.
[2023-03-18 00:53:57,398] [INFO] Query marker FASTA was written to OceanDNA-b38586/markers.fasta
[2023-03-18 00:53:57,399] [INFO] Task started: Blastn
[2023-03-18 00:53:57,399] [INFO] Running command: blastn -query OceanDNA-b38586/markers.fasta -db /var/lib/cwl/stgfcd7cfc2-1856-45ab-87fa-7931dace3435/dqc_reference/reference_markers.fasta -out OceanDNA-b38586/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:53:58,030] [INFO] Task succeeded: Blastn
[2023-03-18 00:53:58,031] [INFO] Selected 29 target genomes.
[2023-03-18 00:53:58,031] [INFO] Target genome list was writen to OceanDNA-b38586/target_genomes.txt
[2023-03-18 00:53:58,049] [INFO] Task started: fastANI
[2023-03-18 00:53:58,049] [INFO] Running command: fastANI --query /var/lib/cwl/stg462f8829-fd1b-4874-9224-5d0102987a2b/OceanDNA-b38586.fa --refList OceanDNA-b38586/target_genomes.txt --output OceanDNA-b38586/fastani_result.tsv --threads 1
[2023-03-18 00:54:13,579] [INFO] Task succeeded: fastANI
[2023-03-18 00:54:13,579] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfcd7cfc2-1856-45ab-87fa-7931dace3435/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:54:13,580] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfcd7cfc2-1856-45ab-87fa-7931dace3435/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:54:13,594] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:54:13,594] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 00:54:13,594] [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 ursingii	strain=CIP 107286	GCA_000368825.1	108980	108980	type	True	78.9087	164	708	95	below_threshold
Acinetobacter ursingii	strain=FDAARGOS_1095	GCA_016726205.1	108980	108980	type	True	78.7327	169	708	95	below_threshold
Acinetobacter septicus	strain=FDAARGOS_1401	GCA_019355975.1	465797	465797	type	True	78.6	173	708	95	below_threshold
Acinetobacter gerneri	strain=CIP 107464	GCA_000368565.1	202952	202952	type	True	78.5318	163	708	95	below_threshold
Acinetobacter stercoris	strain=KPC-SM-21	GCA_900323515.1	2126983	2126983	type	True	78.4626	117	708	95	below_threshold
Acinetobacter junii	strain=CIP 64.5	GCA_000368765.1	40215	40215	type	True	78.4581	152	708	95	below_threshold
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	78.4055	154	708	95	below_threshold
Acinetobacter gerneri	strain=KCTC 12415	GCA_000747725.1	202952	202952	type	True	78.3968	162	708	95	below_threshold
Acinetobacter gerneri	strain=MTCC 9824	GCA_000430245.1	202952	202952	type	True	78.287	166	708	95	below_threshold
Acinetobacter populi	strain=PBJ7	GCA_002174125.1	1582270	1582270	type	True	78.145	215	708	95	below_threshold
Acinetobacter larvae	strain=BRTC-1	GCA_001704115.1	1789224	1789224	type	True	78.1285	121	708	95	below_threshold
Acinetobacter pollinis	strain=SCC477	GCA_015627175.1	2605270	2605270	type	True	78.1056	83	708	95	below_threshold
Acinetobacter rudis	strain=DSM 24031	GCA_000829675.1	632955	632955	type	True	78.0433	121	708	95	below_threshold
Acinetobacter ihumii	strain=Marseille-P8049	GCA_900625095.1	2483802	2483802	type	True	78.0371	157	708	95	below_threshold
Acinetobacter sichuanensis	strain=WCHAc060041	GCA_003024515.2	2136183	2136183	type	True	78.0132	167	708	95	below_threshold
Acinetobacter seifertii	strain=NIPH 973	GCA_000368065.1	1530123	1530123	type	True	77.9919	141	708	95	below_threshold
Acinetobacter brisouii	strain=CIP 110357	GCA_000488275.1	396323	396323	type	True	77.9736	150	708	95	below_threshold
Acinetobacter rudis	strain=CIP 110305	GCA_000413895.1	632955	632955	type	True	77.8996	123	708	95	below_threshold
Acinetobacter guerrae	strain=AC 1271	GCA_009372255.1	1843371	1843371	type	True	77.8333	158	708	95	below_threshold
Acinetobacter brisouii	strain=DSM 18516	GCA_000931655.1	396323	396323	type	True	77.8182	153	708	95	below_threshold
Acinetobacter lanii	strain=185	GCA_011578285.1	2715163	2715163	type	True	77.8062	178	708	95	below_threshold
Acinetobacter piscicola	strain=LW15	GCA_002233755.1	2006115	2006115	type	True	77.7157	176	708	95	below_threshold
Acinetobacter baretiae	strain=B10A	GCA_015627105.1	2605383	2605383	type	True	77.713	76	708	95	below_threshold
Acinetobacter baylyi	strain=DSM 14961	GCA_000621045.1	202950	202950	type	True	77.6571	140	708	95	below_threshold
Acinetobacter baylyi	strain=CIP 107474	GCA_000368685.1	202950	202950	type	True	77.6349	137	708	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:54:13,594] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38586/tc_result.tsv
[2023-03-18 00:54:13,594] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:54:13,594] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:54:13,594] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfcd7cfc2-1856-45ab-87fa-7931dace3435/dqc_reference/checkm_data
[2023-03-18 00:54:13,595] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:54:13,598] [INFO] Task started: CheckM
[2023-03-18 00:54:13,598] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38586/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38586/checkm_input OceanDNA-b38586/checkm_result
[2023-03-18 00:54:49,464] [INFO] Task succeeded: CheckM
[2023-03-18 00:54:49,464] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 00:54:49,466] [INFO] ===== Completeness check finished =====
[2023-03-18 00:54:49,466] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:54:49,466] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38586/markers.fasta)
[2023-03-18 00:54:49,467] [INFO] Task started: Blastn
[2023-03-18 00:54:49,468] [INFO] Running command: blastn -query OceanDNA-b38586/markers.fasta -db /var/lib/cwl/stgfcd7cfc2-1856-45ab-87fa-7931dace3435/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38586/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:54:50,483] [INFO] Task succeeded: Blastn
[2023-03-18 00:54:50,484] [INFO] Selected 13 target genomes.
[2023-03-18 00:54:50,484] [INFO] Target genome list was writen to OceanDNA-b38586/target_genomes_gtdb.txt
[2023-03-18 00:54:50,497] [INFO] Task started: fastANI
[2023-03-18 00:54:50,497] [INFO] Running command: fastANI --query /var/lib/cwl/stg462f8829-fd1b-4874-9224-5d0102987a2b/OceanDNA-b38586.fa --refList OceanDNA-b38586/target_genomes_gtdb.txt --output OceanDNA-b38586/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:54:57,781] [INFO] Task succeeded: fastANI
[2023-03-18 00:54:57,789] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 00:54:57,790] [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
GCA_001626925.1	s__Acinetobacter sp001626925	99.8785	664	708	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.78	99.66	0.96	0.94	7	conclusive
GCF_900096915.1	s__Acinetobacter marinus	86.0496	569	708	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000368565.1	s__Acinetobacter gerneri	78.5218	164	708	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.97	99.97	1.00	0.99	3	-
GCF_012371325.1	s__Acinetobacter sp012371325	78.4698	157	708	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.91	97.28	0.89	0.84	6	-
GCF_002174125.1	s__Acinetobacter populi	78.1392	216	708	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003268395.1	s__Acinetobacter sp003268395	78.0918	192	708	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900096995.1	s__Acinetobacter puyangensis	78.0683	206	708	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900766635.1	s__Acinetobacter sp900766635	78.0153	87	708	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003024515.2	s__Acinetobacter sichuanensis	78.0132	167	708	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008693185.1	s__Acinetobacter qingfengensis	77.9279	148	708	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000773685.1	s__Acinetobacter sp000773685	77.9033	117	708	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331075.1	s__Acinetobacter sp004331075	77.9004	147	708	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.07	96.07	0.89	0.89	2	-
GCA_008017315.1	s__Acinetobacter sp008017315	77.7381	191	708	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:54:57,790] [INFO] GTDB search result was written to OceanDNA-b38586/result_gtdb.tsv
[2023-03-18 00:54:57,790] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:54:57,792] [INFO] DFAST_QC result json was written to OceanDNA-b38586/dqc_result.json
[2023-03-18 00:54:57,792] [INFO] DFAST_QC completed!
[2023-03-18 00:54:57,792] [INFO] Total running time: 0h1m15s