[2023-03-16 18:36:54,193] [INFO] DFAST_QC pipeline started.
[2023-03-16 18:36:54,193] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 18:36:54,193] [INFO] DQC Reference Directory: /var/lib/cwl/stg8847aeba-84f7-48b3-a091-bf78c8cc8d30/dqc_reference
[2023-03-16 18:36:56,433] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 18:36:56,434] [INFO] Task started: Prodigal
[2023-03-16 18:36:56,434] [INFO] Running command: cat /var/lib/cwl/stgecd239c5-4848-4ae7-9345-ebeb9cf53c1a/OceanDNA-b38579.fa | prodigal -d OceanDNA-b38579/cds.fna -a OceanDNA-b38579/protein.faa -g 11 -q > /dev/null
[2023-03-16 18:37:12,610] [INFO] Task succeeded: Prodigal
[2023-03-16 18:37:12,610] [INFO] Task started: HMMsearch
[2023-03-16 18:37:12,610] [INFO] Running command: hmmsearch --tblout OceanDNA-b38579/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8847aeba-84f7-48b3-a091-bf78c8cc8d30/dqc_reference/reference_markers.hmm OceanDNA-b38579/protein.faa > /dev/null
[2023-03-16 18:37:12,815] [INFO] Task succeeded: HMMsearch
[2023-03-16 18:37:12,815] [INFO] Found 6/6 markers.
[2023-03-16 18:37:12,834] [INFO] Query marker FASTA was written to OceanDNA-b38579/markers.fasta
[2023-03-16 18:37:12,834] [INFO] Task started: Blastn
[2023-03-16 18:37:12,835] [INFO] Running command: blastn -query OceanDNA-b38579/markers.fasta -db /var/lib/cwl/stg8847aeba-84f7-48b3-a091-bf78c8cc8d30/dqc_reference/reference_markers.fasta -out OceanDNA-b38579/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:37:13,450] [INFO] Task succeeded: Blastn
[2023-03-16 18:37:13,451] [INFO] Selected 25 target genomes.
[2023-03-16 18:37:13,451] [INFO] Target genome list was writen to OceanDNA-b38579/target_genomes.txt
[2023-03-16 18:37:13,465] [INFO] Task started: fastANI
[2023-03-16 18:37:13,466] [INFO] Running command: fastANI --query /var/lib/cwl/stgecd239c5-4848-4ae7-9345-ebeb9cf53c1a/OceanDNA-b38579.fa --refList OceanDNA-b38579/target_genomes.txt --output OceanDNA-b38579/fastani_result.tsv --threads 1
[2023-03-16 18:37:34,567] [INFO] Task succeeded: fastANI
[2023-03-16 18:37:34,567] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8847aeba-84f7-48b3-a091-bf78c8cc8d30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 18:37:34,567] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8847aeba-84f7-48b3-a091-bf78c8cc8d30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 18:37:34,579] [INFO] Found 23 fastANI hits (2 hits with ANI > threshold)
[2023-03-16 18:37:34,580] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 18:37:34,580] [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 radioresistens	strain=CIP 103788	GCA_000368905.1	40216	40216	type	True	99.1481	936	986	95	conclusive
Acinetobacter radioresistens	strain=NBRC 102413	GCA_006757745.1	40216	40216	type	True	99.1186	936	986	95	conclusive
Acinetobacter variabilis	strain=NIPH 2171	GCA_000369625.1	70346	70346	type	True	79.5462	350	986	95	below_threshold
Acinetobacter pittii	strain=CIP70.29	GCA_024390955.1	48296	48296	type	True	79.2494	307	986	95	below_threshold
Acinetobacter indicus	strain=CIP 110367	GCA_000488255.1	756892	756892	type	True	79.1822	368	986	95	below_threshold
Acinetobacter indicus	strain=DSM 25388	GCA_000830155.1	756892	756892	type	True	79.1446	363	986	95	below_threshold
Acinetobacter pecorum	strain=Sa1BUA6	GCA_014837015.1	2762215	2762215	type	True	79.0908	353	986	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	79.0855	316	986	95	below_threshold
Acinetobacter towneri	strain=CIP 107472	GCA_000368785.1	202956	202956	type	True	79.0356	309	986	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_020911985.1	470	470	type	True	79.0136	312	986	95	below_threshold
Acinetobacter seohaensis	strain=DSM 16313	GCA_018403785.1	281376	281376	type	True	78.948	291	986	95	below_threshold
Acinetobacter towneri	strain=DSM 14962	GCA_000688495.1	202956	202956	type	True	78.9273	298	986	95	below_threshold
Acinetobacter pseudolwoffii	strain=ANC 5044	GCA_002803605.1	2053287	2053287	type	True	78.8621	337	986	95	below_threshold
Acinetobacter tandoii	strain=CIP 107469	GCA_000400735.1	202954	202954	type	True	78.7789	333	986	95	below_threshold
Acinetobacter portensis	strain=AC 877	GCA_009372215.1	1839785	1839785	type	True	78.6882	263	986	95	below_threshold
Acinetobacter piscicola	strain=LW15	GCA_002233755.1	2006115	2006115	type	True	78.6878	279	986	95	below_threshold
Acinetobacter chinensis	strain=WCHAc010005	GCA_002165375.2	2004650	2004650	type	True	78.6598	345	986	95	below_threshold
Acinetobacter rongchengensis	strain=WCHAc060115	GCA_003611475.1	2419601	2419601	type	True	78.6071	295	986	95	below_threshold
Acinetobacter chengduensis	strain=WCHAc060005	GCA_003664645.1	2420890	2420890	type	True	78.3879	295	986	95	below_threshold
Acinetobacter tjernbergiae	strain=CIP 107465	GCA_000488175.1	202955	202955	type	True	78.3468	248	986	95	below_threshold
Acinetobacter venetianus	strain=RAG-1	GCA_000271425.1	52133	52133	type	True	78.2429	271	986	95	below_threshold
Acinetobacter venetianus	strain=CIP 110063	GCA_000368585.1	52133	52133	type	True	78.2271	272	986	95	below_threshold
Acinetobacter halotolerans	strain=JCM 31009	GCA_004208515.1	1752076	1752076	type	True	78.1613	249	986	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 18:37:34,580] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38579/tc_result.tsv
[2023-03-16 18:37:34,580] [INFO] ===== Taxonomy check completed =====
[2023-03-16 18:37:34,580] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 18:37:34,580] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8847aeba-84f7-48b3-a091-bf78c8cc8d30/dqc_reference/checkm_data
[2023-03-16 18:37:34,581] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 18:37:34,592] [INFO] Task started: CheckM
[2023-03-16 18:37:34,592] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38579/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38579/checkm_input OceanDNA-b38579/checkm_result
[2023-03-16 18:38:30,282] [INFO] Task succeeded: CheckM
[2023-03-16 18:38:30,283] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 18:38:30,285] [INFO] ===== Completeness check finished =====
[2023-03-16 18:38:30,286] [INFO] ===== Start GTDB Search =====
[2023-03-16 18:38:30,286] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38579/markers.fasta)
[2023-03-16 18:38:30,286] [INFO] Task started: Blastn
[2023-03-16 18:38:30,286] [INFO] Running command: blastn -query OceanDNA-b38579/markers.fasta -db /var/lib/cwl/stg8847aeba-84f7-48b3-a091-bf78c8cc8d30/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38579/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:38:31,339] [INFO] Task succeeded: Blastn
[2023-03-16 18:38:31,340] [INFO] Selected 29 target genomes.
[2023-03-16 18:38:31,340] [INFO] Target genome list was writen to OceanDNA-b38579/target_genomes_gtdb.txt
[2023-03-16 18:38:31,439] [INFO] Task started: fastANI
[2023-03-16 18:38:31,439] [INFO] Running command: fastANI --query /var/lib/cwl/stgecd239c5-4848-4ae7-9345-ebeb9cf53c1a/OceanDNA-b38579.fa --refList OceanDNA-b38579/target_genomes_gtdb.txt --output OceanDNA-b38579/fastani_result_gtdb.tsv --threads 1
[2023-03-16 18:38:49,383] [INFO] Task succeeded: fastANI
[2023-03-16 18:38:49,399] [INFO] Found 29 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 18:38:49,399] [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_006757745.1	s__Acinetobacter radioresistens	99.1186	936	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.57	97.95	0.93	0.87	74	conclusive
GCF_000369625.1	s__Acinetobacter variabilis	79.5702	347	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.87	95.07	0.88	0.83	48	-
GCF_000488255.1	s__Acinetobacter indicus	79.165	368	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.50	96.50	0.90	0.82	131	-
GCF_000773685.1	s__Acinetobacter sp000773685	79.1452	285	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902753875.1	s__Acinetobacter bouvetii_A	79.1405	336	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000368785.1	s__Acinetobacter towneri	79.0266	309	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.88	97.09	0.88	0.84	48	-
GCF_015218165.1	s__Acinetobacter piscicola_A	79.0175	285	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.43	98.21	0.96	0.90	7	-
GCF_002165255.2	s__Acinetobacter sp002165255	78.9874	250	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.92	96.70	0.85	0.83	6	-
GCF_000369405.1	s__Acinetobacter sp000369405	78.9593	275	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000196795.1	s__Acinetobacter oleivorans	78.9481	316	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.22	95.12	0.90	0.85	40	-
GCF_013344765.1	s__Acinetobacter lactucae_A	78.9287	282	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.51	97.14	0.90	0.87	4	-
GCF_016599715.1	s__Acinetobacter sp002135245	78.8979	371	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.80	96.56	0.83	0.80	8	-
GCF_002803605.1	s__Acinetobacter pseudolwoffii	78.8857	335	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.62	97.19	0.89	0.84	25	-
GCF_016508255.1	s__Acinetobacter calcoaceticus_E	78.8803	302	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003105055.1	s__Acinetobacter sp003105055	78.8587	316	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001647545.1	s__Acinetobacter sp001647545	78.8493	336	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.85	96.85	0.89	0.89	2	-
GCF_000399685.1	s__Acinetobacter pittii_E	78.8065	311	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000214135.1	s__Acinetobacter sp000214135	78.7821	274	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000400735.1	s__Acinetobacter tandoii	78.7789	333	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.61	97.12	0.93	0.84	5	-
GCF_004331255.1	s__Acinetobacter sp004331255	78.7496	315	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002018365.1	s__Acinetobacter sp002018365	78.7238	285	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.65	95.34	0.86	0.83	71	-
GCF_002233755.1	s__Acinetobacter piscicola	78.6859	279	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002165375.2	s__Acinetobacter chinensis	78.6369	345	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.92	96.92	0.89	0.89	2	-
GCF_003611475.1	s__Acinetobacter rongchengensis	78.6074	295	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009939195.1	s__Acinetobacter kanungonis	78.5973	324	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.15	96.11	0.90	0.89	4	-
GCF_000369805.1	s__Acinetobacter sp000369805	78.3288	272	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000368265.1	s__Acinetobacter sp000368265	78.258	262	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.84	96.49	0.89	0.85	3	-
GCF_000368585.1	s__Acinetobacter venetianus	78.2486	271	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.49	96.30	0.89	0.81	21	-
GCF_004208515.1	s__Acinetobacter halotolerans	78.1467	250	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.44	95.44	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-03-16 18:38:49,399] [INFO] GTDB search result was written to OceanDNA-b38579/result_gtdb.tsv
[2023-03-16 18:38:49,400] [INFO] ===== GTDB Search completed =====
[2023-03-16 18:38:49,402] [INFO] DFAST_QC result json was written to OceanDNA-b38579/dqc_result.json
[2023-03-16 18:38:49,402] [INFO] DFAST_QC completed!
[2023-03-16 18:38:49,403] [INFO] Total running time: 0h1m55s